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GENETICS AND PLANT BREEDING

Elements of Genetics

Dr. B. M. Prasanna

National Fellow Division of Genetics

Indian Agricultural Research Institute New Delhi-110012

(12-06- 2007)

CONTENTS IntroductionHistoryCellCell DivisionSpecial ChromosomesDominance RelationshipsGene InteractionsMultiple AllelesSex DeterminationSex LinkageLinkage and Crossing OverGenetic MappingStructural Changes in ChromosomesNumerical Changes in ChromosomesNature of the Genetic MaterialGene Regulation Operon ConceptGene ConceptMutationPolygenic and Quantitative InheritanceExtrachromosomal InheritancePlant Tissue Culture

Keywords Mitosis, Meiosis

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Introduction In biology, heredity is the passing on of characteristics from one generation to the next. It is the reason why offspring look like their parents. It also explains why cats always give birth to kittens and never puppies. The process of heredity occurs among all living organisms, including animals, plants, bacteria, protists and fungi. Genetic variation refers to the variation in a population or species. Genetics is the study of heredity and variation in living organisms. Two research approaches were historically important in helping investigators understand the biological basis of heredity. The first of these approaches, ‘transmission genetics’, involved crossing organisms and studying the offsprings' traits to develop hypotheses about the mechanisms of inheritance. The second approach involved using cytological techniques to study the machinery and processes of cellular reproduction. This approach laid a solid foundation for the more conceptual understanding of inheritance that developed as a result of transmission genetics. Ever since 1970s, with the advent of molecular tools and techniques, geneticists are able to intensively analyze genetic basis of trait variation in various organisms, including plants, animals and humans.

History Pre-Mendelian and Post-Mendelian Concepts of Heredity It was apparent to ancient humans that offspring resembled their parents. The Greek philosophers had a variety of ideas about heredity: Theophrastus proposed that male flowers caused female flowers to ripen; Hippocrates speculated that "seeds" were produced by various body parts and transmitted to offspring at the time of conception, and Aristotle thought that male and female semen mixed at conception. Aeschylus, in 458 BC, proposed the male as the parent, with the female as a "nurse for the young life sown within her". Various hereditary mechanisms were envisaged without being properly tested or quantified. These included “blending inheritance” and the “inheritance of acquired traits”. Nevertheless, people were able to develop domestic breeds of animals as well as crops through artificial selection. During the 1700s, Dutch microscopist Anton van Leeuwenhoek (1632-1723) discovered "animalcules" in the sperm of humans and other animals. Some scientists speculated they saw a "little man" (homunculus) inside each sperm. These scientists formed a school of thought known as the "spermists". They contended the only contributions of the female to the next generation were the womb in which the homunculus grew, and prenatal influences of the womb. An opposing school of thought, the “ovists”, believed that the future human was in the egg, and that sperm merely stimulated the growth of the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring was determined well before conception. “Pangenesis” was an idea that males and females formed "pangenes" in every organ. These pangenes subsequently moved through their blood to the genitals and then to the children. The concept originated with the ancient Greeks and influenced biology until little over 100 years ago. The terms "blood relative", "full-blooded", and "royal blood" are relics of pangenesis. Francis Galton, Charles Darwin's cousin, experimentally tested and disproved pangenesis during the 1870s.

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Charles Darwin proposed a theory of evolution in 1859 and one of its major problems was the lack of an underlying mechanism for heredity. Darwin believed in a mix of blending inheritance and the inheritance of acquired traits (pangenesis). Blending inheritance would lead to uniformity across populations in only a few generations and thus would remove variation from a population on which natural selection could act. Darwin's initial model of heredity was adopted by, and then heavily modified by Francis Galton, who laid the framework for the biometric school of heredity. Galton rejected the aspects of Darwin's pangenesis model which relied on acquired traits. The inheritance of acquired traits was shown to have little basis in the 1880s when August Weismann cut the tails off many generations of mice to find that their offspring did continue to develop tails. The idea of particulate inheritance of genes can be attributed to Gregor Mendel who presented his work on pea plants in 1865. The year 1900 gave birth to a new discipline that soon came to be called ‘genetics’. During that year, three botanists, Hugo de Vries, Carl Correns, and Erich Tschermak, reported on their breeding experiments of the late 1890s and claimed to have confirmed the regularities in the transmission of characters from parents to offspring that Mendel had already presented in his seminal paper of 1865. The additional observation that sometimes several elements behaved as if they were linked, contributed to the assumption soon promoted by Walter Sutton and Theodor Boveri that these elements were located in groups on the different chromosomes of the nucleus. Thus, the ‘chromosome theory of inheritance’ was proposed. Toward the end of the first decade of the 20th century, after Bateson had coined the term genetics for the emerging new field of transmission studies in 1906, Wilhelm Johannsen codified this distinction by introducing the notions of genotype and phenotype, respectively. In addition, for the elements of the genotype, he proposed the notion of gene. This terminology was gradually taken up by the genetics community. By the early 1900s, cytologists had demonstrated that heredity is the consequence of the genetic continuity of cells by cell division, had identified the gametes as the vehicles that transmit genetic information from one generation to another, and had collected strong evidence for the central role of the nucleus and the chromosomes in heredity. It was initially assumed the Mendelian inheritance only accounted for large (qualitative) differences, such as those seen by Mendel in his pea plants — and the idea of additive effect of (quantitative) genes was not realized until R.A. Fisher's (1918) classic paper on The Correlation Between Relatives on the Supposition of Mendelian Inheritance. In the 1930s, work by Fisher and others resulted in a combination of Mendelian and biometric schools into the modern synthesis of evolution. From the early 1910s right into the 1930s, the growing community of researchers around Thomas Hunt Morgan used mutants of the fruit fly Drosophila, constructed in ever more sophisticated ways, in order to produce a map of the fruit fly’s genotype in which genes, and alleles thereof, figured as genetic markers occupying a particular locus on one of the four homologous chromosome pairs of the fly. Meanwhile, cytological work added credence to the materiality of genes-on-chromosomes.

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In 1941, George Beadle and Edward Tatum showed that mutations in genes caused errors in certain steps in metabolic pathways. This showed that specific genes code for specific proteins, leading to the "one gene-one enzyme" hypothesis. Oswald Avery, Collin Macleod, and Maclyn McCarty showed in 1944 that DNA holds the gene's information. In 1953, James D. Watson and Francis Crick demonstrated the molecular structure of DNA, the genetic material in all organisms, except some viruses. Mendelian Principles of Heredity The principles of inheritance were derived by a 19th century monk, Gregor Johann Mendel (born in Moravia, which was then a part of Austria, and now in Czeck Republic), who conducted plant hybridization experiments in his monastery. Between 1856 and 1863, he cultivated and tested some 28,000 garden pea (Pisum sativum) plants. His experiments brought forth two generalizations which later were known as Mendel’s principles of heredity or Mendelian inheritance. These were described in his essay "Experiments on Plant Hybridization" that was read to the Natural History Society of Brunn on February 8 and March 8, 1865, and was published in 1866. Gregor Mendel is now regarded as the ‘Father of Genetics’, as he introduced a new formal tool for the analysis of heredity and variation in organisms, initiated the hybridization experiments that were based on a new experimental regime: the selection of discrete character pairs. His findings allowed other scientists to simplify the emergence of traits to mathematical probability. A large portion of Mendel's findings can be traced to his choice to start his experiments only with true breeding

plants. He measured only absolute characteristics such as colour, shape, and position of the offspring. His data was expressed numerically and subjected to statislarge sampling size he used gave credibility several successive generations of his pea plaattention to procedure and detail, Mendel's world of genetics. While Mendel's researchheredity that he discovered also apply to peheredity are essentially the same for all comp

Gregor Mendel and the first page of his classical

Through the selective cross-breeding of gdiscovered that certain traits show up characteristics. For instance, the pea flowersnot appear in the offspring of pea plants. Meand apparently only occur in one of two for(ii) flower position (axillary or terminal); (yellow or green); (v) seed shape (round orand (vii) pod colour (yellow or green).

tical analysis. This method of data reporting and the to his data. He also had the foresight to look through nts and record their variations. Without his careful

work could not have had the impact it made on the was with plants, the basic underlying principles of ople and other animals because the mechanisms of lex life forms.

paper

arden pea plants over many generations, Mendel in offspring without any blending of parent are either purple or white--intermediate colours do ndel analyzed seven traits that are easily recognized

ms. These are: (i) flower colour (purple and white); (iii) stem length (long or short); (iv) seed colour wrinkled); (vi) pod shape (inflated or constricted);

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Before we consider Mendel’s principles of heredity, it is important to understand the genetic terminology of ‘genotype’ and ‘phenotype’. The genetic makeup of an organism is its ‘genotype’. The genotype consists of the alleles that the organism inherits from its parents. For example, the pea plant flower colour could be PP, Pp or pp. The P allele is the dominant allele and represents purple flowers (PP or Pp). The p allele is the recessive allele. A plant with both recessive alleles (pp) gives white flowers. When both alleles of a gene are same, the organism is said to be homozygous for that characteristic. An organism may be homozyous dominant (genotype PP) or homozygous recessive (genotype pp). When the two alleles in the pair are different, the organism is heterozygous (genotype Pp) for that characteristic. The physical manifestation or appearance of an organism as a result of its genotype is called ‘phenotype’. In the above example, the phenotype of a PP or Pp pea plant is ‘purple flowers’. The phenotype of a pp pea plant is ‘white flowers’. Mendel's observations from his experiments on the garden pea plants can be summarized in two principles: (i) principle of segregation; and (ii) principle of independent assortment.

(i)Principle of Segregation: In the pea plants that either produces yellow or green pea seeds exclusively, Mendel found that the first offspring generation (F1) always had yellow seeds. However, the following generation (F2) consistently had a 3:1 ratio of yellow to green seed colour. Also, the observation that these traits do not show up in offspring plants with intermediate forms was critically important because the leading theory in biology at the time was that inherited traits blend from generation to generation.

It is important to realize that, in Mendel’s experiment, the starting parent plants were homozygous for seed colour. That is to say, they each had two identical forms (or alleles) of the gene for this trait.

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The plants in the F1 generation were all heterozygous. In other words, they each had inherited two different alleles--one from each parent plant. It becomes clearer when we look at the actual genetic makeup, or genotype, of the pea plants instead of only the phenotype, or observable physical characteristics. Note that each of the F1 generation plants (shown above) inherited a Y allele (for yellow seed colour) from one parent and a y allele (for green seed colour) from the other. When the F1 plants breed, each has an equal chance of passing on either Y or y alleles to each offspring. With all of the seven pea plant traits that Mendel examined, one form appeared dominant over the other, which is to say, it masked the presence of the other allele. For example, when the genotype for seed colour is Yy (heterozygous), the phenotype is yellow. However, the dominant yellow allele does not alter the recessive allele for green seed colour physically in any way. Thus, both alleles can be passed on to the next generation unchanged; in other words, the ‘purity of the alleles and the gametes’ is maintained. The principle of segregation essentially has four parts.

1. Alternative versions of genes (alleles) account for variations in inherited characteristics. Alleles are different versions of genes that influence a specific character. For example, each human has a gene that controls eye colour, but there are variations among these genes in accordance with the specific colour the gene "codes" for.

2. For each characteristic, an organism inherits two alleles, one from each parent. This means that when the zygote and somatic cells are produced, for each gene there shall be two alleles, one allele comes from the mother and one from the father. These alleles may be the same (true-breeding organisms/homozygous; e.g. YY and yy), or different (hybrid/heterozygous; e.g. Yy).

3. If the two alleles of a gene influencing a specific trait differ, then the allele that encodes the dominant trait is fully expressed in the organism's appearance; the other allele encoding the recessive trait has no noticeable effect on the organism's appearance. In other words, only the dominant trait is seen in the phenotype of the heterozygote (e.g., Yy). This allows the recessive allele to be passed on to the offspring even if it is not expressed.

4. The two alleles for each characteristic segregate during gamete production. This means that each gamete will contain only one allele for each gene. This allows the maternal and paternal alleles to be combined in the offspring, ensuring genetic variation.

It is often misconstrued that the gene itself is dominant, recessive, codominant, or incompletely dominant. It is, however, the trait, or gene product that the allele encodes that is dominant, etc. (ii)Principle of Independent Assortment: Using the same basic procedure as for a monohybrid cross (considering inheritance of one trait at a time), Mendel next studied the simultaneous inheritance of two traits—a dihybrid cross. A dihybrid cross is a cross between individuals that involves two pairs of contrasting traits. He wanted to see if the factors for two different traits segregated independently of each other during gamete formation. When he crossed pure strains displaying round, yellow seeds (RRYY) with strains that had wrinkled, green seeds (rryy), in the

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F1 generation (all plants RrYy), he observed only yellow, smooth seeds, since yellow seed colour is dominant over green colour, and round seed character is dominant over the wrinkled seed, respectively. However, in the F2 generation, the phenotype was determined by a random combination of the four segregated traits as shown in the figure below.

The segregation in the F2 generation for the dihybrid cross, presented above, will result in pea plants with the following four phenotypes: 9/16 with round, yellow seeds (with genotypes RR YY, RR Yy, Rr YY, and Rr Yy)

3/16 with round green seeds (with genotypes RR yy, Rr yy)

3/16 with wrinkled, yellow seeds (with genotypes rr YY and rr Yy)

1/16 with wrinkled, green seeds (with genotype rr yy)

Therefore, a phenotypic ratio of 9:3:3:1 is expected when heterozygotes for two traits are crossed, provided there is no interaction between these two genes (R and Y) and the alleles at each of these two genes are segregating independently. Thus, according to the principle of independent assortment, different pairs of alleles influencing different characters are passed on to the offsprings independently of each other. The result is that new combinations of genes present in neither parent are possible. Thus, a pea plant’s inheritance of the ability to produce yellow or green seed colour is independent of the inheritance of the round or wrinkled seed character. Likewise, the inheritance of a particular eye colour in humans (black versus brown or blue) does not increase or decrease the likelihood of having five fingers or six fingers on each hand. Mendel's work did not receive as much attention as it deserved, although it was not completely unknown to the biologists of the time. This was attributed to various reasons, including the limited circulation of the scientific journal in which Mendel published his work, and the enormous influence of Charles Darwin’s theories. Due to his responsibilities at the Monastery,

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Mendel himself did not strongly pursue his scientific research. In 1900, however, Mendel’s work was ‘rediscovered’ independently by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak. The most vigorous promoter of Mendelism in Europe was William Bateson, who coined the term "genetics", "gene", and "allele" to describe many of its tenets. The model of heredity was highly contested by other biologists because it implied that heredity was discontinuous, in opposition to the apparently continuous variation observable. Many biologists also dismissed the theory because they were not sure it would apply to all species, and there seemed to be very few true Mendelian characters in nature. However, later work by biologists and statisticians such as R.A. Fisher showed that if multiple Mendelian factors were involved for individual traits, they could produce the diverse amount of results observed in nature. Thomas Hunt Morgan and his colleagues would later integrate the theoretical model of Mendel with the chromosome theory of inheritance, in which the chromosomes of cells were thought to hold the actual hereditary particles. Mendel’s principles of inheritance, along with the understanding of unit inheritance and dominance, were the beginnings of modern science of genetics. In the time since Mendel's original experiments, we have come to learn that there are some extensions to Mendelian principles, including the fact that some alleles are incompletely dominant, that some genes are sex-linked, and that some pairs of genes do not assort independently because they are physically linked on a chromosome. Probability and Chi-square Test Probability is a branch of mathematics that deals with calculating the likelihood of a given event's occurrence, which is expressed as a number between 1 and 0. An event with a probability of 1 can be considered a certainty: for example, the probability of a coin toss resulting in either "heads" or "tails" is 1, because there are no other options, assuming the coin lands flat. An event with a probability of 0.5 can be considered to have equal odds of occurring or not occurring: for example, the probability of a coin toss resulting in "heads" is 0.5, because the toss is equally as likely to result in "tails." An event with a probability of 0 can be considered impossibility: for example, the probability that the coin will land (flat) without either side facing up is 0, because either "heads" or "tails" must be facing up. A probability may be expressed as a decimal (0.75), a percentage (75%), or a fraction (3/4). The probability concept has great utility in genetics. For instance, the chance of inheriting one of two alleles from a parent is 50%. Genetic ratios are most properly expressed as probabilities – for example, ¾ round seed: ¼ wrinkled seed. These values predict the outcome of each fertilization event, such that the probability of each zygote having the round seed is ¾, whereas the probability for having the wrinkled seed is ¼. Probabilities range from 0, when the event is certain not to occur, to 1.0 when the event is certain to occur. Being able to predict ratios of genotypes and phenotypes of a cross from known parental genotypes is but a first step in understanding Mendelian genetics. Predicting results of a monohybrid cross A cross between individuals that involves one pair of contrasting traits is called a monohybrid cross. For example, a cross between a pea plant that is homozygous for producing purple

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flowers (genotype PP) and one that is homozygous for producing white flowers (genotype pp). The application of the probability concept provides a simple method to calculate probable results of a genetic cross. Example 1: Homozygous x Homozygous P = Dominant Purple; p = Recessive White

The progeny that result from a cross between genotype PP and genotype pp will all have Pp, and therefore, show purple flowers. Thus, there is a 100% probability that the offspring will have the Genotype Pp (Heterozygous Dominant) and the phenotype purple flower colour. Example 2: Homozygous x Heterozygous B = Dominant Black; b = Recessive Brown

Consider the results of a cross between Genotype BB and Genotype Bb. The gametes from the genotype BB will all be B, since the genotype is homozygous. However, from the genotype Bb, half the gametes will be B and half will be b. By considering the combination of these alleles from the male and female parents, the possible genotypes that can result from this cross will be BB and Bb. The predicted genotype BB is 2/4 or 50% and the genotype Bb is 2/4 or 50%. That means, there is a 50% probability that the offspring will have the genotype BB (Homozygous Dominant) and the phenotype Black. There is a 50% probability that the offspring will have the genotype Bb (heterozygous dominant) and the phenotype Black. The probability of the phenotype of Black coat in every case is 4/4 or 100%. Example 3: Heterozygous x Heterozygous B = Dominant Black; b = Recessive Brown

Consider the results of a cross between genotype Bb and genotype Bb. Half of the gametes from the genotype Bb will be B and the other half will be b. By considering the combination of these alleles from the male and female parents, the possible genotypes that can result from this cross will be BB (¼); Bb (½) and bb (¼). The probability of the phenotype of black coat in this case is 3/4 (BB + Bb) or 75%, and the probability of the phenotype of brown coat is ¼ (bb). The ratio of the genotypes that appear in offspring is called the genotypic ratio (1:2:1 in this case), and the ratio of the phenotypes that appear in offspring is called the phenotypic ratio (3:1 in this case). Example 4: Test Cross Test cross is used to determine the genotype of an individual. You perform a test cross in which an individual of unknown genotype is crossed with a Homozygous Recessive (bb) individual. A testcross can determine the genotype of any individual whose phenotype is dominant. For example, if we do not know whether the genotype of a plant is BB or Bb, we may conduct a test cross with homozygous recessive (bb) for that trait. If the unknown genotype is BB

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(homozygous dominant) all the offspring from the test cross will be black (Bb). If the genotype is heterozygous (Bb), about 1/2 the offspring will be black. Predicting results of a dihybrid cross Predicting the results of a dihybrid cross is more complicated than predicting the results of a monohybrid cross because there are more possible combinations. Consider the following example in the pea plants.

R = Dominant Round; r = Recessive Wrinkled

Y = Dominant Yellow; y = Recessive Green

Suppose you want to predict the results of a cross between a pea plant that is homozygous for genes responsible for round seed shape and yellow seed colour (RRYY) with another pea plant homozygous for genes responsible for wrinkled seed shape and green seed colour (rryy). The independently assorted alleles in the gametes from one parent will all be RY, and the independently assorted alleles in the gametes from another parent will all be ry. Therefore, genotype of all the offspring resulting from this cross will be heterozygous for both genes, that is, RrYy, and the phenotype of all the F1 offspring will be round and yellow-coloured seeds. Consider next a cross between two pea plants heterozygous for round and yellow seeds, with genotype Rr Yy. The gametes for both parents will be RY, Ry, rY, ry. If the segregation of the alleles of the gene responsible for round seed shape (R and r) is independent of the segregation of the alleles of the gene responsible for the seed colour (Y and y), and there is no interaction between the two genes (R and Y), the offspring of this dihybrid cross will show the following phenotypic segregation pattern: ¾ round (with genotype RR or Rr) x ¾ yellow (with genotype YY or Yy) = 9/16 round, yellow (R- Y-)

¾ round (with genotype RR or Rr) x ¼ green (with genotype yy) = 3/16 round, green (R- yy)

¼ wrinkled (with genotype rr) x ¾ yellow (with genotype YY or Yy) = 3/16 wrinkled, yellow (rr Y-)

¼ wrinkled (with genotype rr) x ¼ green (with genotype yy) = 1/16 wrinkled, green (rryy) In the above case, we simply used the combination of genetic knowledge with the probability rules to predict the results. This is based on the logic that for a single gene with two alleles showing dominance-recessive relationship, the F2 phenotypic segregation will be 3:1 (in the above case, ¾ round: ¼ wrinkled, and ¾ yellow: ¼ green). Therefore, for predicting the probability of occurrence of a pea plant in the F2 generation, from this dihybrid cross, with both round seed shape and yellow seed colour, we need to multiply the individual probability for getting round seed shape with that of the yellow seed colour. Chi-square Test An important question to answer in any genetic experiment is how we can decide if our data fits any of the Mendelian ratios that we discussed earlier. A statistical test that can test out ratios is the Chi-Square or Goodness of Fit test. The chi-square formula is as follows:

Degrees of freedom (d.f.) = n-1 where n is the number of classes

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Let us test the following hypothetical data to determine if it fits a 9:3:3:1 ratio.

Observed Values Expected Values

315 Round, Yellow seeds 9/16 x 556 = 312.75 Round, Yellow seeds

108 Round, Green seeds 3/16 x 556 = 104.25 Round, Green seeds

101 Wrinkled, Yellow seeds 3/16 x 556 = 104.25 Wrinkled, Yellow seeds

32 Wrinkled, Green seeds 1/16 x 556 = 34.75 Wrinkled, Green seeds

556 Total number of seeds 556.00 Total number of seeds

Number of classes (n) = 4

Degrees of freedom (d.f.) = n - 1 = 4 - 1 = 3

Chi-square value = 0.47

By statistical convention, we use the 0.05 probability level as our critical value. If the calculated chi-square value is less than the table chi-square value at the applicable degree of freedom (in this case, 3), we accept the hypothesis. If the value is greater than the table value, we reject the hypothesis. In this case, the table Chi-square value at d.f. = 3 is 7.82. Therefore, the calculated chi-square value (0.47) is less than the table value, and hence, we accept the hypothesis that the data fits a 9:3:3:1 ratio. Cell A cell is a dynamic, living little ‘factory’. It is the smallest living unit that can carry out the basic functions of life: growth, metabolism and reproduction. Some simple organisms are made up of only one cell (unicellular), while most plants and animals are made up of huge numbers of cells (multicellular). Each cell has its own role to play in the life of the plant or animal and is adapted to perform those particular functions. For example, the skin, the bones, the muscles and the brain are all made of cells. There are over 200 different types of cells in a human body. The plant cells are quite different from the cells of the other organisms in the eukaryotic kingdom. Their distinctive features are:

• A large central vacuole (enclosed by a membrane, the tonoplast), which maintains the cell's turgor and controls movement of molecules between the cytosol and sap. Without enough water, there is less pressure in the vacuoles and the plant wilts.

• A cell wall made up of cellulose and protein, and in many cases lignin, and deposited on the outside of the cell membrane. This contrasts with the cell walls of fungi, which are made of chitin, and prokaryotes, which are made of peptidoglycan.

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• The plasmodesmata, linking pores in the cell wall that allow each plant cell to communicate with other adjacent cells. This is different from the network of hyphae used by fungi.

• Plant cells also contain chloroplasts, which are tiny disks full of a green substance called chlorophyll. They trap the light energy that plants need for making food by photosynthesis.

• Plant groups without flagella (including conifers and flowering plants) also lack centrioles that are present in animal cells

Three distinct types of plant cells (parenchyma, collenchyma and sclerenchyma) are classified according to the structure of their cell walls and features of their protoplast. These three major classes of cells can then differentiate to form the tissue structures of roots, stems, and leaves. Plants have different types of tissues. While they have similar locations within all species of plants, the amount of these tissues varies for different plant species. Prominent types of tissues in plants are: • Dermal tissue - The outermost covering of a plant • Vascular tissue - Responsible for transport of materials throughout the plant • Ground tissue - Performs photosynthesis, starch storage and structural support; ground

tissues may be composed of one of three cell types

The animal cell is distinct from other eukaryotes, most notably plant cells, as they lack cell walls and chloroplasts, and they have smaller vacuoles. Due to the lack of a rigid cell wall, animal cells appear to be circular (though are often deformed by surrounding cells) under microscopes - in three dimensions the cells are normally spherical. Human cells are biologically categorized as animal cells. Most plant and animal cells contain an important inner part, called the nucleus, which can be seen under a microscope. It controls what the cell does and how it develops. The nucleus is a membrane-enclosed organelle, and contains most of the cell's genetic material, organized as multiple long linear DNA (Deoxyribonucleic acid) molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes make up

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the cell's nuclear genome. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression. The main structural elements of the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and keeps its contents separated from the cellular cytoplasm, and the nuclear lamina, a meshwork within the nucleus that adds mechanical support much like the cytoskeleton supports the cell as a whole. Because the nuclear membrane is impermeable to most molecules, nuclear pores are required to allow movement of molecules across the envelope. These pores cross both membranes of the envelope, providing a channel that allows movement of small molecules and ions. The movement of larger molecules such as proteins is carefully controlled, and requires active transport facilitated by carrier proteins. Nuclear transport is of paramount importance to cell function, as movement through the pores is required for both gene expression and chromosomal maintenance. Although the interior of the nucleus does not contain any membrane-delineated bodies, its contents are not uniform, and a number of subnuclear bodies exist, made up of unique proteins, RNA (Ribonucleic Acid) molecules, and DNA conglomerates. The best known of these is the nucleolus, which is mainly involved in assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate messenger RNA (mRNA). Chromosome Structure In the nucleus of each cell, the DNA molecule is packaged into thread-like structures called chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. Chromosomes are not visible in the cell’s nucleus—not even under a microscope—when the cell is not dividing. However, the DNA that makes up chromosomes becomes more tightly packed during cell division and is then visible under a microscope. Most of what researchers know about chromosomes was learned by observing chromosomes during cell division. Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm of the chromosome is labeled the “p arm.” The long arm of the chromosome is labeled the “q arm.” The location of the centromere on each chromosome gives the chromosome its characteristic shape, and can be used to help describe the location of specific genes. Metaphase chromosomes differ from one another in size and shape, and the absolute length of any one chromosome varies depending on the stage of mitosis in which it was fixed. However, the relative position of the centromere is constant, which means that that the ratio of the lengths of the two arms is constant for each chromosome. This ratio is an important parameter for chromosome identification, and also, the ratio of lengths of the two arms

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allows classification of chromosomes into several basic morphological types as shown in the figure. Centromere position and arm ratios can assist in identifying specific pairs of chromosomes, but inevitably several or many pairs of chromosomes appear identical by these criteria. The ability to identify specific chromosomes with certainty was revolutionized by discovery that certain dyes would produce reproducible patterns of bands when used to stain chromosomes. Chromosome banding has since become a standard and indispensible tool for cytogenetic analysis, and several banding techniques have been developed.

• Q banding: chromosomes are stained with a fluorescent dye such as quinacrine

• G banding: produced by staining with Giemsa after digesting the chromosomes with trypsin

• C banding: chromosomes are treated with acid and base, then stained with Giesma stain

Each of these techniques produces a pattern of dark and light (or fluorescent versus non-fluorescent) bands along the length of the chromosomes. Importantly, each chromosome displays a unique banding pattern, analagous to a "bar code", which allows it to be reliably differentiated from other chromosomes of the same size and centromeric position. Each species has a normal diploid number of chromosomes. Cytogenetically normal humans, for example, have 46 chromosomes (44 autosomes and two sex chromosomes). Cattle have 60 chromosomes. Mosquitos have 6 chromosomes, earthworms have 36 chromosomes, chimps have 48 chromosomes, and horses have 64 chromosomes. Plants also vary widely in chromosome number; for example, rice has 12 chromosomes, maize has 20 cof chromosomes is found in the Adders tongue fern, which has more than 1,000 chromosomes. Most species have, on average, 10–50 chromosomes.

hromosomes. The largest number

sually, the chromosomes are graded and numbered

e by

organisms.

Uaccording to their decreasing length. Such a characterization of a species' chromosomes is called a karyotype. In humans, chromosome 1 is normally the longest. X- and Y-chromosomes are depicted last. Cell Division Cells have the extraordinary ability to make nearly identical copies of themselves by the process of cell division. Sincexisting cells, cell division is essential for the continuation of life.

Karyotype of human chromosomes

new cells are only produced

There are a variety of reasons that might cause a cell to divide: • Multicellular organisms grow in size and complexity by making more cells. • Old and damaged cells are continuously replaced by the division of cells. • Single-celled organisms such as bacteria divide to make new, independent

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Tw v at

he Cell Cycle rowing and dividing go through a

itosis s the process of cell division of either a diploid (2n) or haploid (n) eukaryotic cell

he beginning of mitosis is called prophase. In early prophase, the centrosomes move toward

naphase begins when the pairs of sister chromatids separate. The separated chromatids are

he chromosomes arrive at the poles in telophase, and new nuclear membranes form around

ivision of the cytoplasmic components is called cytokinesis. In animal cells, cytokinesis occurs

plant cells, a number of small vesicles fuse at the metaphase plate to form the cell plate. Over

o e ents are required for successful cell reproduction. First, the ‘parent’ cell must ensure theach new ‘daughter’ cell receives a complete copy of its hereditary information. This information is transmitted in the form of complex molecules called DNA, and directs the various activities of the cell throughout its lifetime. The second requirement is the partitioning of cytoplasm between the two daughter cells. TCells that are grepeating series of events called the cell division cycle (or cell cycle). One cell cycle describes the period between a cell's creation by mitosis, and its subsequent division into two daughter cells. During the first phase (G1), the cell grows and prepares for DNA replication, which occurs in the subsequent S phase. Further growth takes place in the G2 phase, and finally mitosis occurs in the M phase.G1, S, and G2 are collectively called interphase. G1 stands for gap 1, or presynthesis; S for synM is the mitotic division phase.

thesis; G2 for gap 2, or post-synthesis.

MMitosis iwhereby the two daughter cells are produced that are genetically identical to the parent cell. Topposite poles of the cell, organizing the spindle microtubules between them. The sister chromatids become visible in the nucleus as they condense. In late prophase, the nuclear membrane breaks down and some of the spindle microtubules attach to the sister chromatids. The microtubules pull the chromatid pairs to the midline of the cell, or metaphase plate.

he chromatids remain lined up between the poles of the cell during metaphase. T Anow called chromosomes, and move toward the poles of the cell. Tthem. Dwhen a ring of actin and myosin filaments constricts the plasma membrane at the equator. Eventually, the parent cell is divided into two cells. Intime, the cell plate reaches across the cell and joins with the plasma membrane. The process of mitosis and cytokinesis creates two separate cells, each with an identical set of chromosomes. After cytokinesis, the daughter cells will enter interphase.

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Mitosis maintains a constant amount of genetic material from cell generation to cell generation. Consider a hypothetical diploid cell with one pair of homologous chromosomes. Consider also that this cell is Aa; that is, it is heterozygous for a pair of alleles with A coming from one parent and a from the other parent. In the figure below, notice how we start and end with cells having the same genotype.

Meiosis Meiosis is the process by which one diploid eukaryotic cell divides to generate haploid cells often called gametes. The word "meiosis" comes from the Greek meioun, meaning "to make smaller," since it results in a reduction in chromosome number in the gamete cell.

• Meiosis occurs in diploid cells. Through two successive divisions, four haploid cells are produced, each with half the chromosome number of the parental cell.

• Meiosis occurs only in sexually reproducing organisms. Depending on the organism, it may produce haploid gametes, which do not divide further but instead fuse to produce a diploid zygote; or it may produce haploid spores, which divide by mitotic cell cycles and produce unicellular or multicellular organisms.

• In animals, where the somatic (body) cells are diploid, the products of meiosis are the gametes.

• In many fungi and some algae, meiosis occurs immediately after two haploid cells fuse, and mitosis then produces a haploid multicellular "adult" organism (e.g., filamentous fungi, algae) or haploid unicellular organisms (e.g., yeast, unicellular algae).

• Plants and some algae have both haploid and diploid multicellular stages. The multicellular diploid stage is the sporophyte. Meiosis in a sporophyte produces haploid spores. These spores alone are capable of generating a haploid multicellular stage called a gametophyte. The gametophyte produces gametes by mitotic cell cycles.

There are several features unique to meiosis, most importantly the pairing and genetic recombination between homologous chromosomes. However, the preparatory steps that lead up to meiosis are identical in pattern and name to the interphase of the mitotic cell cycle. Interphase is immediately followed by meiosis I and meiosis II. Meiosis I consists of segregating the homologous chromosomes from each other, and forming two haploid cells each containing one of the segregates. Meiosis II consists of separation of each chromosome's sister chromatids, and producing four haploid cells out of the two haploid cells. Meiosis I and II are both divided into prophase, metaphase, anaphase, and telophase subphases, similar in purpose to their analogous subphases in the mitotic cell cycle. Therefore, meiosis encompasses the interphase (G1, S, G2), meiosis I (prophase I, metaphase I, anaphase I, telophase I), and meiosis II (prophase II,

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metaphase II, anaphase II, telophase II). Meiosis I is also called as ‘reductional division’ while meiosis II is called as ‘equational division’ (as it is similar to mitosis). Meiosis I

Prophase I: The first stage of Prophase I is the leptotene stage, also known as leptonema, from Greek words meaning "thin threads." During this stage, individual chromosomes begin to condense into long strands within the nucleus. However the two sister chromatids are still so tightly bound that they are indistinguishable from one another. The zygotene stage, also known as zygonema, from Greek words meaning "paired threads," occurs as the chromosomes approximately line up with each other into homologous chromosomes. The combined homologous chromosomes are said to be bivalent. They may also be referred to as a tetrad, a reference to the four sister chromatids. The two chromatids become "zipped" together, forming the synaptonemal complex, in a process known as synapsis. The pachytene stage, also known as pachynema, from Greek words meaning "thick threads," heralds crossing over. Nonsister chromatids of homologous chromosomes randomly exchange segments of genetic information over regions of homology (Sex chromosomes, however, are not identical, and only exchange information over a small region of homology.) Exchange takes place at sites where recombination nodules (chiasma) have formed. The exchange of chromosomal segments between the non-sister chromatids results in a recombination of genetic information; each chromosome has the complete set of genetic information it had before, and there are no gaps formed as a result of the process. Because the chromosomes cannot be distinguished in the synaptonemal complex, the actual act of crossing over is not perceivable through the microscope. During the diplotene stage, also known as diplonema, from Greek words meaning "two threads," the synaptonemal complex degrades and homologous chromosomes separate from one another a little. However, the homologous chromosomes of each bivalent remain tightly bound at chiasmata, the regions where crossing over occurred. Chromosomes condense further during the diakinesis stage, from Greek words meaning "moving through." This is the first point in meiosis where the four parts of the tetrads are actually visible. Sites of crossing over entangle together, effectively overlapping, making chiasmata clearly visible. Other than this observation, the rest of the stage closely resembles prometaphase of mitosis; the nucleolus disappears, the nuclear membrane disintegrates into vesicles, and the mitotic spindle begins to form. During these stages, centrioles are migrating to the two poles of the cell. These centrioles, which were duplicated during interphase, function as microtubule coordinating centers. Centrioles sprout microtubules, essentially cellular ropes and poles, during crossing over. They invade the nuclear membrane after it disintegrates, attaching to the chromosomes at the kinetochore. The kinetochore functions as a motor, pulling the chromosome along the attached microtubule toward the originating centriole, like a train on a track. There are two kinetochores on each tetrad, one for each centrosome. Prophase I is the longest phase in meiosis. Microtubules that attach to the

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kinetochores are known as kinetochore microtubules. Other microtubules will interact with microtubules from the opposite centriole. These are called nonkinetochore microtubules. Metaphase I: Homologous pairs move together along the phase plate: as kinetochore microtubules from both centrioles attach to their respective kinetochores, the homologous chromosomes align along an equatorial plane that bisects the spindle, due to continuous counterbalancing forces exerted on the bivalents by the microtubules emanating from the two kinetochores. The physical basis of the independent assortment of chromosomes is the random orientation of each bivalent along the metaphase plate. Anaphase I: Kinetochore microtubules shorten, severing the recombination nodules and pulling homologous chromosomes apart. Since each chromosome only has one kinetochore, whole chromosomes are pulled toward opposing poles, forming two diploid sets. Each chromosome still contains a pair of sister chromatids. Nonkinetochore microtubules lengthen, pushing the centrioles further apart. The cell elongates in preparation for division down the middle. Telophase I: The first meiotic division effectively ends when the centromeres arrive at the poles. Each daughter cell now has half the number of chromosomes but each chromosome consists of a pair of chromatids. The microtubules that make up the spindle network disappear, and a new nuclear membrane surrounds each haploid set. The chromosomes uncoil back into chromatin. Cytokinesis, the pinching of the cell membrane in animal cells or the formation of the cell wall in plant cells, occurs, completing the creation of two daughter cells. Cells enter a period of rest known as interkinesis or interphase II. No DNA replication occurs during this stage. Note that many plants skip telophase I and interphase II, going immediately into prophase II. Meiosis II

Prophase II takes an inversely proportional time compared to telophase I. In this prophase we see the disappearance of the nucleoli and the nuclear envelope again as well as the shortening and thickening of the chromatids. Centrioles move to the polar regions and are arranged by spindle fibres. The new equatorial plane is rotated by 90 degrees when compared to meiosis I, perpendicular to the previous plane. In metaphase II, the chromosomes with two sister chromatids (sharing a centromere) organize themselves at the equatorial plate. This is followed by anaphase II, where the centromeres are cleaved, allowing the kinetochores to pull the sister chromatids apart. The sister chromatids by convention are now called sister chromosomes, and they are pulled toward opposite poles. The process ends with telophase II, which is similar to telophase I, marked by uncoiling and lengthening of the chromosomes, and disappearance of the microtubules. Nuclear envelopes reform; cleavage or cell wall formation eventually produces a total of four daughter cells, each with a haploid set of chromosomes. Meiosis is now complete. The process of meiosis and gamete formation is fundamentally the same in males and females. However, whereas gametogenesis (formations of gametes) results in four functional sperm cells

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for each meiotic division in males, the same process in females gives rise to only a single functional egg capable of being fertilized and developing into an embryo. Special Chromosomes

(i)Polytene Chromosomes Polytene chromosomes form when multiple rounds of replication produce chromatids that remain synapsed together in a haploid number of chromosomes. They have characteristic light and dark banding patterns which can be used to identify chromosomal rearragements and deletions. Polytene chromosomes were originally observed in the larval salivary glands of Chironomus midges by Balbiani in 1881, but the hereditary nature of these structures was not confirmed until they were studied in Drosophila melanogaster in the early 1930s. They are known to occur in secretory tissues of other dipteran insects such as Sciara and also in protists, plants, mammals. These chromosomes have primarily been used to (i) to locate genes; and (ii) to analyze structural c (ii)Lampbrush Chromosomes The lampbrush type of chromosome is characteristic of growing oocytanimals with the exception of mammals and certain insects. The celongated diplotene bivalents, sometimes reaching lengths of a michromosomes were first seen in sections of salamander (AmbystomaFlemming in 1882. Ten years later they were described in the oocytes(1892). The name ‘lampbrush’ was given by Ruckert, who likened thelampbrush, equivalent to the 20th Century test-tube brush. A lampbrush chromosome is a meiotic half bivalent. This means thachromatids. The entire lampbrush bivalent will therefore have a totchromosome strands are dotted with about 5000 chromomeres (dark stalso seen in interphase chromosomes). Twin loops (length 400-800 nm) emerge from chromomeres. An identical pattern of twinned loops occurs on both pairs of sister chromatids. Lampbrush chromosomes are ideally suited for analysis of selective gene activity. Why do lampbrush chromosomes exist at all? They are characteristic of eggs that develop rather quickly into compleindependently of the parent. A frog's egg, for example is fertilized, depthen develops into a complex tadpole within a few days. Lampbtherefore be regarded mainly as an adaptive feature that has evolved tfor rapid early development. The fact that they are not developed in mregarded as an advanced feature that is consistent with the relatively development.

Polytene chromosomes in Drosophila

hanges in chromosomes.

es in the ovaries of most hromosomes are greatly llimeter or more. These mexicanum) oocytes by of a dogfish by Ruckert objects to a 19th Century

t it must consist of two al of 4 chromatids. The aining irregular structures

x multicellular organisms osited by the mother and rush chromosomes may

o pre-programme the egg ammalian eggs could be

slow pace of mammalian

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(iii)B Chromosomes B chromosomes are small supernumerary chromosomes found in many eukaryotic nuclei, and are believed to be largely non-coding and probably parasitic on the host genome. These were discovered about 100 years ago in an insect, and shortly after in plants, and since then they have remained one of the most enigmatic parts of the genome. The essential properties which distinguish the B chromosomes (Bs) from the normal A chromosomes (As) is that the Bs are dispensable, they pair (or sometimes not) only amongst themselves and they have irregular modes of inheritance – including mitotic or meiotic drive in some cases. B chromosomes have tendency to accumulate in meiotic cell products resulting in an increase of their number over generations. However, this effect is counterbalanced for selection against infertility. Detailed studies on B chromosomes have been carried out on Bs in only a few species, like maize, rye and Brachycome dichromosomatica. Notwithstanding the fact that these particular B systems are species-specific, and have their own distinctive properties, some useful new information is emerging about their selfish nature (host-parasite interactions) and possible modes of origin from the A chromosome complement. Dominance Relationships In genetics, ‘dominance relationship’ refers to how the alleles for a single locus interact to produce a phenotype. For example, flower colour in sweet peas (Lathyrus odoratus) is controlled by a single gene with two alleles. The three genotypes are PP, Pp, and pp. The flower colour for PP (purple) and pp (white) do not depend on the dominance relationship. However, the heterozygote Pp could theoretically have many different colours, e.g., purple, white, or a light purple. The colour of flowers produced by the heterozygous plants depends on the dominance relationship between the two alleles in question. There are three main kinds of dominance relationships:

• Simple dominance (simple Mendelian inheritance) • Incomplete (partial) dominance • Codominance

The dominant/recessive relationship is made possible by the fact that most higher organisms are diploid: that is, most of their cells have two copies of each chromosome -- one copy from each parent. Polyploid organisms have more than two copies of each chromosome, and follow similar rules of dominance but, for simplicity, will not be discussed here. Similarly, organisms that are normally haploid do not show dominance relationships. (i)Simple Dominance Consider the simple example in peas of flower colour, first studied by Gregor Mendel. The dominant allele (say, P) confers red colour, and the recessive allele (p) confers white colour. In a given individual, the two corresponding alleles of the chromosome pair fall into one of three patterns: PP, pp or Pp. If the two alleles are the same (homozygous), the trait they represent will be expressed. But if the individual carries one of each allele (heterozygous), only the dominant one will be expressed. The recessive allele will simply be suppressed. Dominant traits are recognizable by the fact that they do not skip generations, as recessive traits do. It is therefore quite possible for two parents with red flowers to have a white flowers among

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their progeny, but two such white offspring could not have purple offspring (although very rarely, one might be produced by mutation). In this situation, the red-flowered individuals in the first generation must have both been heterozygous (carrying one copy of each allele). In the PP and Pp cases, the offspring shall show red flower due to the dominant P. Only in the pp case is there expression of the recessive white flower phenotype. (ii)Incomplete Dominance In incomplete dominance (sometimes called partial dominance), a heterozygous genotype creates an intermediate phenotype. In this case, only one allele (usually the wild type) at the single locus is expressed, creating an intermediate phenotype. A cross of two intermediate phenotypes (= monohybrid heterozygotes) will result in the reappearance of both parent phenotypes and the intermediate phenotype. The classic example of this is the flower colour of snapdragon. Cross a true-breeding red strain with a true-breeding white strain and the F1 are all pink (heterozygotes) (see Figure). Self-fertilize the F1 and you get an F2 ratio of 1 red: 2 pink: 1 white. (iii)Codominance In codominance, neither phenotype is completely dominant. Instead, the heterozygous individual expresses both phenotypes. A common example is the ABO blood group system. A and B alleles are codominant, but both are dominant over O. The only possible genotype for a type O person is OO. Type A people have either AA or AO genotypes. Type B people have either BB or BO genotypes. Type AB has only the AB (heterozygous) genotype. Homozygous A individuals have only the A antigen, homozygous B individuals have only the B antigen, homozygous O individuals produce neither antigen, while a fourth phenotype (AB) produces both A and B antigens. Gene Interactions After Mendel's work was rediscovered, it became clear that simple Mendelian model is not sufficient to predict experimental observations in all situations. Two or more genes govern the expression of many characters in almost all organisms. These genes affect the development of the concerned characters in various ways. The phenomenon of two or more genes governing the development of a single character in such a way that they affect the expressions of each other in various ways is known as gene interaction. The classical Mendelian phenotypic ratio in the F2 generation expected from a dihybrid AaBb is 9:3:3:1. This phenotypic ratio resulted from assuming: (i) only two alleles of two different genes, A and B, affecting two different traits and (ii) complete dominance of one allele over another allele (recessive) located on corresponding position on the homologous chromosome. Neither of these conditions need apply and this sets the stage for manifold modifications of the classical F2 ratio. Nevertheless, the Mendelian basis for modified ratios is secure; indeed, we can only interpret deviations by employing the classical ratio as a scaffold for the creative construction of new F2 ratios.

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Epistasis: The term ‘epistasis’ is derived from a Greek word that means ‘standing upon’. In a generic sense, it refers to any situation in which the action of one locus masks the allelic effects at another locus. The locus whose expression is masked is described as hypostatic, and the locus whose alleles cause the masking is described as epistatic. To keep the descriptions of genotype as simple as possible, we will follow the standard convention of using a capital letter followed by a hyphen (A–) to describe any genotype that contains at least one copy of the dominant allele (AA, Aa). Thus, the designation A– B– will describe any genetic combination that includes at least one dominant allele at each locus (AA BB, AA Bb, Aa BB, or Aa Bb). Different modified F2 ratios can be obtained in dihybrid crosses with various types of interaction at two different genetic loci, as outlined in the following table.

F2 Genotypic Classes Interaction type

A– B– A– bb aa B– aa bb Classical ratio 9 3 3 1

Complementary gene action 9 7

Dominant epistasis 12 3 1

Recessive epistasis 9 3 4

Duplicate dominant gene action 15 1

Dominant suppression 13 3

Duplicate genes with cumulative effect 9 6 1

A– B– refers to genotypes AA BB, AA Bb, Aa BB and Aa Bb; A– bb refers to genotypes AA bb and Aa bb; aa B– refers to genotypes aa BB and aa Bb. Complementary gene action (F2 ratio = 9:7): Blocking any step in a sequential enzymatic process can prevent synthesis of the final product of the pathway. Anthocyanin pigment synthesis in sweet peas is an example where blocking of either of two steps will prevent pigment formation. Only the double dominant genotype produces both of the needed enzymes and is able to synthesize the pigment. The F2 progeny ratio is 9/16 pigmented (A– B–) to 7/16 unpigmented (A– bb, aa B–, or aa bb). Similar results can also be obtained if the products of two independently coded enzymes must interact to yield the final product. Crossing two strains of sweet peas that are white because of different mutations in the anthocyanin biosynthetic pathway can result in F1 progeny with purple flowers. Dominant epistasis (F2 ratio = 12:3:1): When the dominant phenotype of one gene conceals or masks the phenotype of another gene, the situation is referred to as dominant epistasis. An example of dominant epistasis is the fruit colour in squash. Two unlinked genes, W and G influence fruit colour. At the first gene, white coloured squash phenotype is dominant to coloured squash phenotype, and the gene symbols are W = white, and w = coloured. At the second gene, yellow is dominant to green, and the symbols used are G = yellow, and g = green. If the dihybrid is selfed, three phenotypes are produced in a 12 (white) :3 (yellow):1 (green) ratio. When the dominant W allele negates the effect of either G or g allele, the white coloured fruit phenotype is obtained (9/16 W– G- + 3/16 W– gg); when the recessive w allele allows the expression of the G allele, the result is a yellow coloured fruit phenotype (ww G–); and when the

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recessive w allele allows the expression of the g allele, the phenotype of the fruit shall be green (ww gg). Recessive epistasis (F2 ratio = 9:3:4): In recessive epistasis, expression of the homozygous recessive state at one locus totally blocks expression of traits controlled by a second locus. A case of recessive epistasis well known to most people is the yellow coat colour of Labrador retriever dogs. Two alleles, B and b, stand for black and brown coats, respectively, but the allele e of another gene is epistatic on these alleles, giving a yellow coat. Therefore the genotypes B– ee and bb ee are both of yellow phenotype, whereas B– E– and bb E– are black and brown, respectively. Yellow dogs can make black or brown pigment, as can be seen in their noses and lips. The action of the allele e is to prevent deposition of the pigment in hairs. Duplicate dominant gene action (F2 ratio = 15:1): If either of two genes can achieve the same phenotype, it can lead to duplicate dominant gene action. In this case, only the double recessive genotype (1/16 aa bb) in the F2 generation of a dihybrid cross will exhibit the recessive phenotype. For example, in Winter wheat, a dominant allele at either of two loci causes the wheat to have a Spring growth pattern (A– B–; A– bb or aa B–) that includes lack of ability to survive over the Winter. Only the double recessive (aa bb) exhibits the Winter wheat growth characteristics, which permit it to be planted and germinated in the Fall and then to survive in a dormant state through the Winter and mature during the following Spring and early Summer. Dominant suppression or Inhibitory gene action (F2 ratio = 13:3): A prominent example of dominant suppression or inhibitory gene action involves the anthocyanin pigmentation in maize kernels. A locus R determines whether the kernels are red coloured (R–) or white (rr), in combination with another gene, C (as explained in case of complementary gene action). However, another allele at the same locus, C, called C-I (inhibitor of C) can block the expression of anthocyanin pigmentation even in heterozygous genotypes (C-I/C). So, the C-I allele is dominant over the C allele. Thus, in the F2, we get segregation for 13/16 white (C-I– R–; C-I– rr; CC rr) and 3/16 coloured (CC R–). Duplicate genes with cumulative effect (F2 ratio = 9:6:1): An interesting example is the genetic control of the shape of the fruit in summer squash. Elongated fruits are homozygous recessive (aa bb) at two separate loci that influence shape. At the other extreme, fruits that have at least one dominant allele at each of the two loci (A– B–) are flattened to a disc shape. Fruits that are recessive at one of the loci but have at least one dominant allele at the other exhibit an intermediate spherical shape, with no obvious phenotypic difference based on which locus carries the dominant allele (A– bb or aa B–). These results in an F2 phenotypic ratio of 9/16 disc-shaped, 6/16 spherical, and 1/16 elongated. Penetrance: For some genotypes, the expected phenotype is not always expressed. This phenomenon is referred to as penetrance, which is defined as the fraction of individuals with a particular genotype that express at least some degree of the expected phenotype. For example, a gene responsible for polydactyly in humans (presence of additional finger instead of five or an additional toe in the foot) is not expressed in everyone with the genotype. Thus, for genotypes known to have less than 100% penetrance, it is not safe to assume that absence of the phenotype means absence of the genotype. Some cases of lack of penetrance may reflect epistasis. However, there are other cases in which the cause for non-penetrance is not known.

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Expressivity: Among those individuals that express a phenotype to some extent, the intensity of the expression is referred to as expressivity. For example, in type D brachydactyly, this affects only one thumb in some individuals and both thumbs in others, as well as sometimes being non-penetrant. Yet another good example is the expression of genes that cause white spotting in mice and various other animals, such as cats, in which the area of pigmentation loss can vary greatly from one individual to another. Expressivity is also very much influenced by environmental factors, such as temperature of various body parts. Multiple Alleles Multiple alleles are more than two forms of the same gene in the population. For the sake of simplicity, we usually use examples of genes with only two possible alleles (A and a). But, a single gene can actually have many possible alleles (A, a, A1, A2, A', etc.). For example, hair colour in mice is determined by a single gene with a series of alleles, each resulting in different colouration. There are alleles for black, brown, agouti, gray, albino, and others. The twist here is that the same allele can be dominant or recessive depending on context. For instance the allelic series for coat colour in mice may be written as agouti > black > albino. This means that agouti is dominant to black, and black is dominant to albino; agouti is necessarily also dominant to albino. If the black allele is in the presence of an agouti allele, the mouse will be agouti because black is recessive to agouti. If that same black allele is paired with an albino allele, the mouse will be black since black is dominant to albino. There may be multiple alleles within the population, but individuals have only two of those alleles. This is because individuals have only two biological parents, and only one allele is contributed by each parent. An excellent example of multiple allele inheritance is human blood type. Blood type exists as four possible phenotypes: A, B, AB and O. There are three alleles for the gene that determines blood type, IA, IB and i. With three alleles we have several possible combinations of genotypes and resulting phenotypes, as shown in the following table.

Genotype Phenotype Genotype Phenotype

IA IA Type A IB i Type B

IA i Type A IA IB Type AB

IB IB Type B i i Type O

(i)Pseudoalleles Multiple alleles had been supposed to represent changes in a single gene, and there were two criteria for their recognition: (i) they occupied the same locus in a chromosome, and were not separable by crossing over; (ii) if mutations are in different homologous chromosomes (trans condition), they do not complement each other and show a mutant phenotype, since neither of the homologous chromosomes has a wild-type allele. Researchers discovered some examples of multiple alleles which do not exactly follow the above rules. In such cases, which were called as ‘pseudoalleles’, the trans situation shows a mutant phenotype, but both the wild type and the double mutant can be reconstituted by crossing over. Evidently, each mutant carries the wild-type composition that the other has lost, but the section of the chromosome that includes them is a functional unit that must be intact in at least one chromosome to produce the wild-type

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phenotype. Examples where pseudoallelic series were reported include lozenge locus in Drosophila that causes changes in the pigmentation of the eyes and also certain other morphological changes. The discovery of pseudoalleles in Drosophila by geneticists like Oliver, Green, and Lewis, has made it evident that the event leading to recombination can occur probably anywhere along the length of the chromosome or genetic string inside or outside of genes. Later studies, particularly fine-structure analysis of the gene, clearly showed that there is no strong basis for recombination-based distinction of ‘multiple alleles’ and ‘pseudoalleles’; thus, the term ‘pseudoalleles’ became obsolete. (ii)Pleiotropy Pleiotropy is the phenomenon whereby a single gene has multiple consequences in the same organism. Pleiotropic effects stem from both normal and mutated genes, but those caused by mutations are often more noticeable and easier to study. Pleiotropy is actually more common than the opposite, since in a complex organism, a protein from a single gene is likely to be expressed in more than one tissue, and the cascade of problems caused by a mutation is likely to lead to numerous complications throughout the organism. Single-gene defects with effects in only one tissue are more common for nonessential features such as hair texture or eye colour. Sickle cell disease is a classic example of pleiotropy. This disease develops in persons carrying two defective alleles for a blood protein, beta-hemoglobin. Mutant beta-hemoglobins are misaligned inside a blood cell and cause misshaped red blood cells at low oxygen concentrations. Deformed blood cells impair circulation. Impaired circulation damages kidneys and bone. In this case, the gene defect itself only affects one tissue, the blood. The consequences of that defect are found in other tissues and organs. Pleiotropic outcomes are common with hormones. Hormones are signals that create multiple responses in tissues that carry receptors for them. The receptor binds to the hormone and triggers a cascade of reactions inside the cell. A defective receptor loses or misinterprets the signal. When the hormone insulin meets defective insulin receptors on an individual's cells, the person is more likely to develop type II diabetes. Cells do not open their gateways to let sugar in from the bloodstream, and the cells almost starve to death in the midst of plenty. Meanwhile, sugar accumulates in the blood and causes all sorts of ramifications for blood circulation, and it damages capillaries in all areas, from kidneys, to eyes, to feet. Sex Determination Sex determination in a biological system refers to the development of sexual characteristics in an organism. Most sexual organisms have two sexes. In many cases, sex determination is genetic: males and females have different alleles or even different genes that specify their sexual morphology. In animals, this is often accompanied by chromosomal differences. In other cases, sex is determined by environmental variables (such as temperature) or social variables (the size of an organism relative to other members of its population). The details of some sex-determination systems are not yet fully understood. The XX/XY sex-determination system is one of the most familiar sex-determination systems and is found in human beings and most other mammals. In the XY sex-determination system,

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females have two of the same kind of sex chromosome (XX), while males have two distinct sex chromosomes (XY). Some species (including humans) have a gene SRY on the Y chromosome that determines maleness; others (such as the fruit fly) use the presence of two X chromosomes to determine femaleness. In the XX/X0 sex determination, which is a variant of the XY system, females have two copies of the sex chromosome (XX) but males have only one (X0). The 0 denotes the absence of a second sex chromosome. This system is observed in a number of insects, including the grasshoppers and crickets of order Orthoptera and in cockroaches (order Blattodea). The nematode C. elegans is male with one sex chromosome (X0); with a pair of chromosomes (XX) it is a hermaphrodite. The ZW sex-determination system is found in birds and some insects and other organisms. The ZW sex-determination system is reversed compared to the XY system: females have two different kinds of chromosomes (ZW), and males have two of the same kind of chromosomes (ZZ). It is unknown whether the presence of the W chromosome induces female features or the duplication of the Z chromosome induces male ones; unlike mammals, no birds with a double W chromosome (ZWW) or a single Z (Z0) have been discovered. Probably either condition causes embryonic death or both chromosomes are responsible for gender selection. In Lepidoptera, examples of Z0, ZZW and ZZWW females can be found. This suggests that the W chromosome is essential in female determination in some species (ZZW), but not in others (Z0). In Bombyx mori (the commercial silkworm), the W chromosome carries the female-determining genes. Haplodiploidy is found in insects belonging to Hymenoptera, such as ants and bees. Haploid individuals are male. Diploid individuals are generally female but may be sterile males. Thus, if a queen bee mates with one drone her daughters share ¾ of their genes with each other, not ½ as in the XY and ZW systems. This is believed to be significant for the development of eusociality, as it increases the significance of kin selection. Non-genetic sex-determination systems also exist in nature. In some species of reptiles, including alligators and the tuatara, sex is determined by the temperature at which the egg is incubated. Other species, such as some snails, practice sex change: adults start out male, and then become female. In tropical clown fish, the dominant individual in a group becomes female while the other ones are male. Some species have no sex-determination system. Earthworms and some snails are hermaphrodites; a few species of lizard, fish, and insect are all female and reproduce by parthenogenesis. In some arthropods, sex is determined by infection. Bacteria of the genus Wolbachia alter their sexuality; some species consist entirely of ZZ individuals, with sex determined by the presence of Wolbachia.

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Sex Linkage For most inherited traits, the gender of the bearer of the genes is immaterial. Characteristics like free earlobes, fur colour, etc., generally operate the same in males as they do in females. But, there are exceptions. Sex Linked Traits are traits whose loci are literally on the sex chromosomes, so their transmission from generation to generation is affected by the sex chromosome complement of the individual. Because the gene controlling the trait is located on the sex chromosome, sex linkage is linked to the gender of the individual. In any species with non-homologous sex chromosomes, these traits can be significant. Usually such genes are found on the X chromosome. The Y chromosome is thus missing such genes. The result is that females will have two copies of the sex-linked gene while males will only have one copy of this gene. If the gene is recessive, then males only need one such recessive gene to have a sex-linked trait rather than the customary two recessive genes for traits that are not sex-linked. This is why males exhibit some traits more frequently than females. The first demonstration of sex linkage was the red eye colour gene in Drosophila, the fruit fly. Normal fruit fly eye colour is a dull brick red. Mutations in this gene cause the eyes to be white. The white allele is recessive, but it was quickly determined that the inheritance pattern for this gene was different from those of other genes being studied, which are located on chromosomes other than sex chromosomes (autosomes). In some kinds of matings, reciprocal crosses produced different results, something which had never been observed to happen with other genes. It turned out that this particular eye colour gene was located on the X chromosome. It turned out that this particular eye colour gene was located on the X chromosome. The red eye phenotype is dominant over the white eye phenotype. As females have two chromosomes X (with a locus for eye color), they might be homozygous or heterozygous for either allele. Males, who carry only one X chromosome, are always hemizygous. They carry only the one X chromosome inherited from their mother, and it determines their eye colour. Let us consider the results of mating between homozygous red eyed females (++) mate with hemizygous white eyed males (w-). In the offspring, all the daughters shall be red eyed heterozygotes (+w) and all sons shall be red eyed hemizygotes (+-). In contrast, when the homozygous white eyed females (ww) mate with hemizygous red eyed males (+-), in the offspring, all the daughters shall be red eyed heterozygotes (+w) and all sons shall be white eyed hemizygotes (w-). Thus, X-linked traits have a number of interesting aspects. First, because females possess two X chromosomes and males possess only one, X-linked recessive traits appear far more commonly in males than in females. This is clear from simple statistics. A male will show the X-linked recessive trait due to receiving only a single copy of the allele, because he has no second X chromosome to carry a dominant allele which might hide the recessive. Females must inherit the recessive trait twice to show it, just as they do for any other recessive trait. This is a much more unlikely outcome. This is the source of the misconception that only males can display X-linked traits like colour blindness. Some prominent examples of sex-linked traits in humans are red-green colour blindness, hemophilia and Duchenne muscular dystrophy.

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There are also a very few genes which are Y-linked (or holandric). Y-linked genes are carried on the Y chromosome, and are thus passed directly from father to son. Every son has a copy of his father’s Y chromosome. In any pedigree showing unbroken lines of male descent, all of the connected males have copies of the same Y chromosome, and thus share any Y-linked characteristics. Sex limited traits are generally autosomal, meaning that they are not found on the X or Y chromosomes. The genes for these traits behave exactly the same way that any autosomal gene behaves. The difference here comes in the expression of the genes in the phenotype of the individual. Sex-limited traits are expressed in only one gender. The traits are generally associated with primary or secondary sexual characteristics, and thus are expressed only in the gender which utilizes those characteristics. For example, there are genes which influence how much milk a lactating mother produces when she’s nursing a baby. These genes are carried by both males and females, but only females ever express them. Sex influenced traits are also autosomal, meaning that their genes are not carried on the sex chromosomes. Again, what makes these traits unusual is the way they are expressed phenotypically. In this case, the difference is in the ways the two genders express the genes. One classic example of a sex influenced trait is pattern baldness in humans (sometimes called “male pattern baldness,” though the condition isn’t restricted to males). This gene has two alleles, “bald” and “non-bald.” The behaviors of the products of these genes are highly influenced by the hormones in the individual, particularly by the hormone testosterone. In the presence of high

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levels of testosterone, the baldness allele has a very powerful influence. In the presence of low levels of testosterone, this allele is quite ineffectual. All humans have testosterone, but males have much higher levels of this hormone than females do. The result is that in males, the baldness allele behaves like a dominant allele, while in females it behaves like a recessive allele. As in all cases, dominance only matters in the heterozygote, so this means that heterozygous males will experience hair loss and heterozygous females will not. Even homozygous females may experience no more than a thinning of their hair, but many develop bald spots or have receding hairlines. An interesting note about this gene is that it is often incorrectly identified as X-linked because of an illusion that males inherit it from their mothers. Males can inherit baldness from either parent, but if a son gets it from his father, both father and son will be bald, and nobody really notices, as we expect sons to look reasonably like their fathers. But if a son loses his hair and his father does not, that’s noteworthy, and the conclusion people have drawn (correctly) is that the son inherited baldness from his mother. But recall that with X-linkage sons always inherit traits from their mothers and never from their fathers. In the case of baldness, a son can inherit from either parent. It is just that we notice it more in the case of inheritance from the mother.

Linkage and Crossing Over Linkage refers to a situation where two or more genes are located on the same chromosome. Recall that if genes at two loci are on separate chromosomes, then they segregate independently. These loci are said to be unlinked. Linkage provides a way to map genes on chromosomes. Until modern gene mapping techniques linkage was the only way to do this. Even today linkage is important when used with other techniques to determine where on chromosomes certain genes are, especially for genes which have not been well studied and for understanding the mode of transmission for many genetic disorders. Crossing Over The figure shows a tetrad during prophase 1 of Meiosis before crossing over takes place in a heterozygote with genotype Aa Bb, then shows one of many cross over events that could lead to new recombinants. Maternal chromosomes are shown in blue and paternal in red. The figure shows a cross over event that can lead to new chromosome types. These sorts of crossovers occur with frequency r where r is the frequency of recombination, while the third panel shows the four possible chromosomes after meiosis, and their frequencies. Generally the two chromosomes (1,4) are most common. These are often called the non-recombinant or parental chromsomes because there has been no detectable crossing over between the loci during meiosis. This is because when sister chromatids swap segments, no recombination happens since sister chromatids start out prophase I with identical DNA. Chromosomes 2, 3 are recombinants which happen because of crossing over during meiosis. The frequency of recombination, r between two loc is between 0 and 1/2, depending on how closely linked the loci are to each other on the chromosome. If the locus "A" and locus "B" are

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right next to each other then r will be very small. This is because where the cross over event takes place along the chromatids is random. Thus, when the loci are close together, they tend to segregate together. Genes with recombination frequencies less than 50% are present in the same chromosome (linked). Two genes that undergo independent assortment, indicated by a recombination frequency of 50 percent, are either in non-homologous chromosomes or are located far apart in a single chromosome. However, crossing over does not occur between linked genes in every meiotic event, especially when the positions of the genes on the chromosome are very near one another. The frequency with which crossing over occurs between any two linked genes is proportional to the distance between the loci along the chromosome. At very small distances, crossover is very rare, and most gametes are parental. As the distance between two genes increases, crossover frequency increases. The more are the recombinant gametes, fewer shall be parental gametes. When genetic loci are very far apart on the same chromosome, crossing over nearly always occurs, and the frequency of recombinant gametes approaches 50 percent. How do we determine how much crossing-over occurs between linked genes (and, therefore, get an idea of how far apart two loci are)? This information is derived through the construction of a genetic map. Genetic Mapping ‘Genetic mapping’ or ‘Chromosome mapping’ is the assignment of genes to specific locations on a chromosome. A genetic map serves many important functions and is much like understanding the basic human anatomy to allow doctors to diagnose patients with disease. A doctor requires knowledge of where each organ is located as well as the function of this organ to understand disease. Genetic mapping has diverse applications in genetics, breeding and medicine, Scientists use several methods to map genes to the appropriate locations. These methods include family studies, somatic cell genetic methods, cytogenetic techniques, and gene dosage studies. Family studies are used to determine whether two different genes are linked close together on a chromosome. If these genes are linked, it means they are close together on the same chromosome. Additionally, the frequency with which the genes are linked is determined by recombination events (crossing over of the chromosomes during meiosis) between known locations or markers, and determines the linear order or genetic distance. When a genetic locus is first shown to be linked to a particular chromosome, its exact placement on the chromosome will generally not be known. The three point cross (also called as ‘triple test cross’) is a particularly useful technique for identifying the position of a previously unmapped locus relative to two other loci that have already been mapped. In this assay, a heterozygote for three linked genes is crossed with a homozygous recessive for all three. A three point cross makes it possible to determine which of the three loci is located between the other two. Various maps of chromosomes can be developed. These maps are called cytogenetic maps, linkage maps, physical maps, or a DNA sequence map. A cytogenetic map uses bands produced by a dye that stains chromosomes in a karyotpe and assigns genes to these bands. A linkage map, also referred to as a genetic map, orders genes along the DNA strand based on recombination frequency. Linkage mapping involves using two characteristics (and hence their responsible

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genes), both of which are present in one parent, combined with the frequency in which they occur together in the offspring to construct the map. Structural Changes in Chromosomes There are many different types of structural chromosome changes that can occur. These include: duplications, an extra copy of a piece of a chromosome; deletions, the loss of a piece of a chromosome; inversions, a rearrangement of the chromosome material; translocations, an exchange of material between two chromosomes; a ring chromosome, a deletion of the ends of a chromosome followed by the fusion of both ends to form a circular chromosome etc. (i)Duplications A chromosomal duplication is a repetition of a section of a chromosome on the same chromosome. It is sometimes referred to as a 'partial trisomy'. Trisomy refers to three. Therefore, if duplication occurs, that individual would have three copies of that genomic region instead of two. This means there are extra instructions (genes) present that can cause an increased risk for birth defects or developmental problems. In the picture, red arrows point to identical bands on each chromosome. The blue arrow points to a duplication of the band at the red arrow. You can see that the chromosome on the right is longer. One of the prominent examples of the effect of chromosomal duplications is the bar eye phenotype in Drosophila. The eye of the fly is normally an elongated oval shape whereas the bar eye phenotype is much thinner. When the chromosomes of males with bar eye are analyzed, duplication in region 16A of the chromosome is detected. Another mutant of the eye shape is the double bar eye. These individuals have a second duplication of the same 16A region. (ii)Deletions A chromosomal deletion refers to a situation when a part of a chromosome(s) has been deleted. A deletion can occur on any chromosome, at any band, and can be any size (large or small). What a deletion causes depends on how big a piece is missing and what genes are missing in the section (i.e. where the deletion is). In the figure, the area in the blue brackets is not present (deleted) in its pair designated by the red arrow. The presence, and extent of a deletion, can be detected quite readily with polytene chromosomes in Drosophila. A loop will appear on one paired chromosome, and those sequences found in the looped region mark the length of the deletion. These loops are also detectable in other species. (iii)Inversions Inversions result when a segment of a chromosome is excised, inverted 180o, and reintegrated into the same chromosome. Two specific types of inversions are recognized, and they are classified as to whether or not the centromere is a portion of the inverted segment. Paracentric inversion - an inversion of a segment of the chromosome that does not involve the centromeric region

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Pericentric inversion - an inversion of a segment of the chromosome that involves the centromeric region Inversions are not easily detected in homozygotes of species, unless as with humans, distinct chromosomal banding patterns have been established for normal members of that species. Heterozygotes derived from a cross of a normal individual and an individual with an inversion in one chromosome will have specific patterns that occur because of pairing problems. In Drosophila, polytene chromosome will contain loops, evidence that one of the synapsed chromosomes contains an inversion. The appearance of meiotic chromosomes also will be affected if one of the chromosomes has an inversion. Loops appear and define the region in which the inversion has occurred. Furthermore, if recombination occurs in a paracentric inversion region, then one-half of the gametes will be normal and the other half will contain deleted chromosomes. If the recombination involves a pericentric inversion then one-half of the gametes will be normal with respect to the initial chromosomal arrangements and the other gametes will contain chromosomes that contain both additions and deletions. These abnormalities can generate unbalanced gametes and in general, individuals with pericentric inversions are reproductively inferior. (iv)Translocations Translocation refers to a change in position of a chromosomal segment to another region of the same chromosome or to another chromosome. Chromosomal material is maintained here, but in a different arrangement after a translocation. Intrachromosomal translocation involves the movement of a chromosomal segment from one location in the chromosome to another. This is normally non-reciprocal, that is another segment does not exchange places with the first segment. Interchromosomal translocation involves the movement of a chromosomal segment(s) between chromosomes. R ciprocal translocation or balanced translocation occurs when chromosomal segments are exchanged between two non- homologous chromosomes and is the most typical type of translocation. Non-reciprocal translocation or unbalanced translocation is a one-way transfer of a chromosomal segment to another chromosome.

e

Translocations have two genetic consequences:

• If a segment is inserted between two genes then the linkage distance between those two genes will increase.

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• The genes found on the inserted segment will be nearer the genes in the region in which it was inserted, thus defining new linkage relationships among these genes.

Ring Chromosome A ring chromosome can happen in two ways. One is demonstrated in the picture; the end of the p and q arm breaks off and then stick to each other. The blue parts of each are lost thus resulting in loss of information. Second, the ends of the p and q arm stick together (fusion), usually without loss of material. However the ring can cause problems when the cell divides and can cause problems for the individual. It is also possible to have a ring and be apparently healthy with no delays in development. As with all chromosome abnormalities it depends on what is actually found, the size of the ring, how much material was lost, which chromosomes are involved etc. Numerical Changes in Chromosomes Ploidy is the number of homologous sets of chromosomes in a biological cell. The ploidy of cells can vary within an organism. In humans, most cells are diploid (containing one set of chromosomes from each parent), but sex cells (sperm and egg) are haploid. The number of chromosomes in one of the mutually-homologous sets is called the monoploid number (x) or basic chromosome number. (i)Aneuploidy Aneuploidy is the condition of having less than or more than the normal diploid number of chromosomes, and is the most frequently observed type of cytogenetic abnormality. In other words, it is any deviation from euploidy, although many authors restrict use of this term to conditions in which only a small number of chromosomes are missing or added. Generally, aneuploidy is recognized as a small deviation from euploidy for the simple reason that major deviations are rarely compatible with survival, and such individuals usually die prenatally. The two most commonly observed forms of aneuploidy are monosomy and trisomy.

• Monosomy is the presence of only one copy of a chromosome when there are usually two copies (2n-1). An individual having only one chromosome 6 is said to have monosomy 6. A common monosomy seen in many species is X chromosome monosomy, also known as Turner's syndrome. Monosomy is most commonly lethal during prenatal development. In general, loss of chromosome material has a more severe effect on the growth of an organism than does the addition of chromosome material.

• Trisomy is having three chromosomes of a particular type (2n+1). A common autosomal

trisomy in humans in Down syndrome, or trisomy 21, in which a person has three instead of the normal two chromosome 21s. Trisomy is a specific instance of polysomy, a more general term that indicates having more than two of any given chromosome. Changes in the number of sex chromosomes have a less severe effect on development and sometimes individuals with extra sex chromosomes can even be asymptomatic. Examples of the inheritance of an extra sex chromosome include: XXY, XXX or XYY. Klinefelter syndrome is the inheritance of two X chromosomes and one Y chromosome (47, XXY).

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• Nullisomy is a genetic condition involving the lack of one of the normal chromosome pairs for a species (2n-2).

• Tetrasomy refers to the genetic condition where one chromosome is represented four

times (instead of two) while all other chromosomes are present in the normal number (2n+2).

(ii)Polyploidy Diploid species have two homologous chromosome sets. Each type of chromosomes is always represented twice (except the sex chromosomes). Most of the animal species, including all the mammals, are typical diploid species. Polyploid individuals have more than two basic genomes or chromosome sets (3x, 4x, 6x, etc.). They are particularly prominent in the plant kingdom. It is estimated that about 30% to 35% of the plant species are polyploids. Therefore, ‘polyploidy’ is the state where all cells have multiple pairs of chromosomes beyond the basic set. These may be from the same species or from closely related species. Polyploidy occurs commonly in plants, but rarely in animals. Even in diploid organisms many somatic cells are polyploid due to a process called endoreduplication where duplication of the genome occurs without mitosis (cell division). Polyploids can be broadly classified into two groups: autopolyploids and allopolyploids.

Autopolyploids: Autopolyploids have multiple sets of chromosomes or genomes. The genome formula (capital letters represent a group of chromosomes that is generally referred to as the basic genome or chromosome set) is AAA (autotriploidy), or BBBB (autotetraploidy), etc. Autopolyploids are also called polysomic polyploids. For instance, tobacco (Nicotiana tabacum) and cultivated potato (Solanum tuberosum) are both autotetraploid s (AAAA).

Allopolyploids: Allopolyploids can be formed from the hybridisation of two separate species followed by their subsequent chromosome doubling. Typical alloployploids are AABB (allotetraploid), AABBCC (allohexaploid), etc. Allopolyploids are also called as disomic polyploids. A good example is the bread wheat (Triticum aestivum) which is an allohexaploid (AABBDD). Nature of the Genetic Material In contemplating the physical basis for inheritance, the following properties are required of the genetic material: (i) ability to store information; (ii) abiphysical and chemical stability so that information is not lost; (iv) capability for genetic change through generations without major loss of parental information. Since it clearly has a complex function, there must be complexity to its structure. Therefore, during the first half of the 20th century, it was widely felt that proteins held the genetic information due to their complexity. Contemporary hypotheses of deoxyribonucleic acid (DNA) structure proposed a regular, repeating structure with little complexity. Three lines of evidence finally convinced most people that the genetic material was DNA.

lity to transfer info to daughter cells; (iii)

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Transformation experiments were carried out by Frederich Griffith (1928) using the bacterium

the next set of experiments, Oswald Avery, Colin MacLeod, Maclyn McCarty (1944)

lfred Hershey and Martha Chase's experiments (1952)

minutes of blending time,

NA is a nucleic acid that contains the genetic instructions for the development and functioning

tructure of DNA lated by Friedrich Miescher who, in 1869, discovered a microscopic substance

in the pus of discarded surgical bandages. As it resided in the nuclei of cells, he called it

Pneumococcus variants rough (R) and smooth (S), defined by the appearance of a colony as a result of the lack of or presence of a polysaccharide coat, respectively. The studies, depicted in the figure, that heritable factor from the S strain could even transform the R strain into a virulent strain; this was designated as ‘transforming principle’. Inanalyzed what component of the S strain was the transforming principle. They did not use mice to look for pathogenesis but simply looked for a change in appearance of the colonies. They treated samples of the heat killed S strain with different enzymes to degrade specific macromolecular types and then mixed the extracts with the R strain in a test tube and plated culture to see if transformation to the smooth phenotype resulted. While treatment with protease and RNase did not change the ability to transform, treatment with DNase led to lack of transformation. Thus, these researchers concluded that since DNase treatment destroyed both the DNA and the ability to transform, DNA must be the transforming principle. Aconvincingly proved that DNA indeed is the genetic material, using the T2-like bacteriophage, a virus that infects a bacterium. The Head of this bacteriophage is a protein capsule that houses the DNA. The tail and tail fibers are also protein. The virus adheres to the surface of the host cell and injects its genetic material into the cell. The genetic material then directs the host cell to produce more bacteriophages. They grew T2 phage in the presence of 32P (which labels nucleic acids) and 35S (which labels proteins). They allowed the labeled phage to adhere to the bacterial cells and then put the samples in a blender to shear off phage from the surface. After severalmost of the 35S was found outside of the cells while most of the 32P remained with the cells. Furthermore, they showed that new phage progeny had 32P labeling. Since only DNA was labeled with 32P and 32P made its way into cells and was incorporated into new phage, DNA must be the carrier of genetic information. Dof living organisms. All living things contain DNA genomes. A possible exception is a group of viruses that have RNA (Ribonucleic acid) genomes. The genome is often compared to a set of blueprints, since it contains the instructions to synthesize other components of the cell, such as proteins and RNA molecules. In eukaryotes such as animals and plants, DNA is stored inside the cell nucleus, while in prokaryotes such as bacteria, the DNA is in the cell's cytoplasm. Unlike enzymes, DNA does not participate directly in most of the biochemical reactions it controls; rather, various enzymes act on DNA and copy its information into either more DNA, in DNA replication, or transcribe and translate it into protein. In chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins in the nucleus. SDNA was first iso

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"nuclein". In 1929 this discovery was followed by Phoebus Levene's identification of the base, sugar and phosphate in the nucleotide unit. Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups. However, Levene thought the chain was short and the bases repeated in a fixed order. In 1937 William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure. Based on X-ray diffraction images taken by Rosalind Franklin, and the information that the bases were paired, James D. Watson and Francis Crick first suggested an accurate mode of DNA structure, published in 1953 in the scientific journal Nature. In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-ssociated pair of molecules. These two long strands entwine like vines, in the shape of a double

ng. Although these repeating units are very small, DNA polymers

in both the backbone of the molecule, hich holds the chain together, and a base, which interacts with the

the DNA strand is made from alternating phosphate nd sugar residues. The sugar in DNA is the pentose (five carbons)

ent of DNA bases are referred

ched to the two trands. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G)

ahelix. Each DNA strand is a long polymer of simple units called nucleotides, which are held together by a backbone made of sugars and phosphate groups. This backbone carries four types of molecules called bases, and it is the sequence of these four bases that encodes information. The DNA chain is 22 to 24Å wide, and one nucleotide unit is 3.3 Å

locan be enormous molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is 220 million base pairs long. The nucleotide repeats contawother DNA strand in the helix. In general, a base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in DNA, this polymer is referred to as a polynucleotide. The backbone of asugar 2-deoxyribose. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the otheof DNA strands is called antiparallel. The asymmetric ends of a strandto as the

r strand. This arrangem

5' (five prime) and 3' (three prime) ends. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA, besides the presence of the nitrogenous base uracil in place of thymine. The DNA double helix is stabilized by hydrogen bonds between the bases attasand thymine (T). These four bases are shown below and are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.

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These bases are classified into two types; adenine and guanine are fused five- and six-membered

he double helix is a right-handed spiral. As the DNA strands wind around each other, they

ach type of base on one strand forms a bond with just one type of base on the other strand. This

he two types of base pairs form different

NA Replication ential for an organism to grow, but when a cell divides it must replicate the

heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines. A fifth pyrimidine base, called uracil (U), usually replaces thymine in RNA and differs from thymine by lacking a methyl group on its ring. Tleave gaps between each set of phosphate backbones, revealing the sides of the bases inside. There are two of these grooves twisting around the surface of the double helix: one groove is 22 Å wide and the other is 12 Å wide. The larger groove is called the major groove, while the smaller, narrower groove is called the minor groove. Eis called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides joined together across the double helix is called a base pair. In a double helix, the two strands are also held together by forces generated by the hydrophobic effect and pi stacking, but these forces are not affected by the sequence of the DNA. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature. As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms. Tnumbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds. The GC base pair is therefore stronger than the AT base pair. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the associathelices with a high GC content have strongly interacting strands, while short helices with high AT content have weakly interacting strands.

ion between the two strands of DNA. Long DNA

DCell division is essDNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. One polymer of a DNA molecule is the opposite of the other, like a photo negative. If you have

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one side, you could recreate the other. It's this duality that makes it surprisingly simple to make a copy of a DNA molecule. Replication begins with the unwinding of the double helix by an enzyme called helicase. The unwinding can start anywhere along the strand, and once begun, enzymes create two "replication forks" that continue to unzip the helix in both directions. Then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5' to 3' direction, different mechanisms are used to copy the antiparallel strands of the double helix. In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of the original DNA. In prokaryotes (bacteria) most or all of an organism's genetic information is stored in one long, circular DNA ring instead of multiple chromosomes of DNA strings with unconnected ends. These rings are replicated in a very similar manner to eukaryotic DNA, the only real difference being that here only two replication forks are used. While eukaryotes had many replication sites in action at once, prokaryotes replicate so quickly that only two, one working in each direction around the ring, are needed. RNA DNA contains all the information needed to maintain a cell's processes, but these precious blueprints never leave the protected nucleus. How, then, is all this data transmitted to the body of the cell itself where it may be put to use? The answer: by way of RNA. The three types of ribonucleic acid – messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) – allow for the communication and translation of genetic information outside of the nucleus. RNA is a long polymer similar to DNA. The differences are as follows:

1. The five carbon sugar in RNA is ribose, while in DNA it is deoxyribose 2. In place of thymine, RNA uses the nitrogenous base uracil (thus the possible pairs

become C-G and A-U) 3. While DNA is a double-helix, RNA is almost always a single stranded molecule 4. RNA is significantly shorter than DNA 5. DNA is more stable than RNA.

Transcription For an RNA molecule to be created, it must be synthesized from a segment of DNA through a process called transcription. To begin this process an enzyme called RNA polymerase binds to a specific area on a DNA molecule called the promoter. The promoter signals the beginning of a genetically coded message, or gene. The RNA polymerase, upon encountering the promoter that it was looking for, begins to unwind the DNA double helix. As the helix unwinds RNA strand is

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created in the exposed area (this is similar to DNA replication, explained earlier). The RNA is then disconnected from the DNA and the helix is reconnected. This system of unzip, encode, and re-zip continues along the gene until the RNA polymerase encounters a termination signal and the new molecule is complete. Usually, this process can occur to a single gene many times simultaneously if it is in demand, the unzipping enzyme associated with one future RNA molecule would follow the re-zipping portion of another, and so on. The genetic code is the set of rules by which a gene is translated into a functional protein. Each gene consists of a specific sequence of nucleotides encoded in a DNA (or sometimes RNA) strand; a correspondence between nucleotides, the basic building blocks of genetic material, and amino acids, the basic building blocks of proteins, must be established for genes to be successfully translated into functional proteins. Sets of three nucleotides, known as codons, each correspond to a specific amino acid or to a signal; three codons are known as "stop codons" and, instead of specifying a new amino acid, alert the translation machinery that the end of the gene has been reached. There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms. Translation The molecules of messenger RNA (mRNA) leave the nucleus, carrying with them the instructions (encoded in the sequence of their nucleotides) that they picked up from the DNA molecule. In the cytoplasm, mRNA molecules are attracted to the ribosomes. Also in the cytoplasm are a second kind of smaller RNA molecules called transfer RNA (tRNA.) One end of a tRNA molecule has a special site to which only one kind of amino acid can be attached. There are many different types of transfer RNA molecules--actually more than one for each of 18 of the 20 different amino acids found in proteins (methionine and tryptophan being the exceptions.) The other end of each RNA molecule carries a unique tag which identifies it. The tag is written in the usual code of a nucleic acid--a sequence of bases. Each amino aid carrying tRNA molecule has its own three letter code, called anti-codon. For example, the valine tRNA is labeled AAC, the alanine-tRNA is labeled GGC, the phenylalanine -tRNA is labeled AAA and so on. With the strand of messenger RNA lined up at the ribosome, the base pairs again are attracted to their partners, this time the attraction is between the complementary bases of the messenger

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RNA and the transfer RNA. A sequence of three nucleotides in mRNA codes for each amino acid. This sequence is called a ‘codon’. The transfer RNAs carrying amino acids attach to the mRNA by means of base-pairing between the messenger RNA codons and the transfer RNA ‘anticodons’. Each transfer RNA then donates its amino acid, in the proper order, to the growing chain of amino acids that will become the new protein. This assembly of amino acids to form a protein, in a sequence specified by the order of nucleotides in a molecule of messenger RNA (determined, in turn, by the sequence specified by a segment of DNA in the nucleus called a gene) is called translation. Gene Regulation in Prokaryotes Bacteria adapt to changes in their surroundings by using regulatory proteins to turn groups of genes on and off in response to various environmental signals. The DNA of Escherichia coli is sufficient to encode about 4000 proteins, but only a fraction of these are made at any one time. E. coli regulates the expression of many of its genes according to the food sources that are available to it. Most of the control of the gene expression in prokaryotes occurs at the level of transcription (i.e., whether to code for mRNA or not) due to two major reasons: (i) the life span of these organisms is very short (sometimes, only minutes); and (ii) transcription and translation are coupled since there is no nucleus. Operon Concept An operon is a cluster of bacterial genes along with an adjacent promoter that controls the transcription of those genes. When the genes in an operon are transcribed, a single mRNA is produced for all the genes in that operon. This mRNA is said to be polycistronic because it carries the information for several proteins which are functionally related. Jacob and Monod were the first scientists to elucidate a transcriptionally regulated system. They worked on the lactose metabolism system in E. coli. The Lac operon is the classic model for activation and repression of transcription. Concepts of analysis based on the Lac operon can be applied to other systems including animals and plants. When the bacterium is in an environment that contains lactose, it should turn on the enzymes that are required for lactose degradation. These enzymes are: beta-galactosidase (coded by the gene lacZ), lactose permease (coded by the gene lacY) and thiogalactoside transacetylase (coded by the gene lacA). The sequences encoding these enzymes are located sequentially on the E. coli genome. They are preceded by the lacI region which regulates expression of the lactose metabolic genes.

The operator is a short region of DNA that lies partially within the promoter and that interacts with a regulatory protein that controls the transcription of the operon. Here's an analogy. A

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promoter is like a doorknob, in that the promoters of many operons are similar. An operator is like the keyhole in a doorknob, in that each door is locked by only a specific key, which in this analogy is a specific regulatory protein. The regulatory gene lacI produces an mRNA that produces a Lac repressor protein, which can bind to the operator of the lac operon. Regulatory genes are not necessarily close to the operons they affect. The general term for the product of a regulatory gene is a regulatory protein. The Lac regulatory protein is called a repressor because it keeps RNA polymerase from transcribing the structural genes. Thus the Lac repressor inhibits transcription of the lac operon.

In the absence of lactose, the Lac repressor binds to the operator and keeps RNA polymerase from transcribing the lac genes. It would be energetically wasteful for E. coli if the lac genes were expressed when lactose was not present. The effect of the Lac repressor on the lac genes is referred to as ‘negative regulation’. When lactose is present, the lac genes are expressed because allolactose binds to the Lac repressor protein and keeps it from binding to the lac operator. Allolactose is an isomer of lactose. Small amounts of allolactose are formed when lactose enters E. coli. Allolactose binds to an allosteric site on the repressor protein causing a conformational change. As a result of this change, the repressor can no longer bind to the operator region and falls off. RNA polymerase can then bind to the promoter and transcribe the lac genes.

The story is more complicated. For instance, the permease gene always needs to be expressed at a low level, in order for any lactose to get into the cell. So a certain low level of expression is constitutive--that is, occurs all the time, even if "repressed." Most bacterial operons are partly or totally constitutive. lacI expression, for example, is totally constitutive; its promoter is always "turned on," for a very low level of expression, just enough to make a few repressor molecules. A bacterium's prime source of food is glucose. If both glucose and lactose are around, the bacterium wants to turn off lactose metabolism in favour of glucose metabolism. There are regulatory sites upstream of the lac genes that respond to glucose concentration.

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Gene Regulation in Eukaryotes Eukaryotes need to regulate their genes for different reasons than prokaryotes. In prokaryotes, gene regulation allowed them to respond to their environment efficiently and economically. While eukaryotes can respond to their environment, the main reason higher eukaryotes need to regulate their genes is cell specialization. Whereas prokaryotes are (relatively speaking) simple, unicellular organisms, multicellular eukaryotes consist of hundreds of different cell types, each differentiated to serve a different specialized function. Each cell type differentiates by activating a different subset of genes. Because of the multitude of cell types, the regulation of gene expression required to bring about such differentiation is necessarily complex. One way this complexity is demonstrated is in multiple levels of regulation of gene expression. It is necessary to understand that "gene expression" covers the entire process from transcription through protein synthesis. The final measure of whether or not a gene is "expressed" is if the protein is produced, because it is protein that will ultimately carry out the function specified by the gene. Eukaryotic cells are more complex than prokaryotic cells. One obvious example of this is the presence of a nucleus in eukaryotic cells, which separates transcription from translation in a way not seen in prokaryotes. Furthermore, eukaryotic transcripts must be processed before they can be translated. Here is a diagram outlining the steps involved in the production of a protein in eukaryotic cells:

Unlike prokaryotes, where gene regulation occurs predominantly at the level of transcription, in eukaryotes, regulation can occur at any point in this pathway; specifically, it occurs at the levels of transcription, RNA processing, mRNA lifetime (longevity), and translation. Gene Concept A gene is a segment of a nucleic acid that contains the information necessary to produce a functional product, usually a protein. Genes correspond to units of inheritance. They contain regulatory regions dictating under what conditions the product is produced, transcribed regions dictating the structure of the product, and/or other functional sequence regions.

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Whatever the definition of a gene may be, it has to take into account four basic criteria: (i) ability to transmit; (ii) ability to mutate; (iii) ability to recombine; and (iv) capacity to function in terms of development of a phenotype. Of course, these criteria are mutually inter-dependent; there cannot be, for instance, transmission without gene function, or recombination without transmission. The current view of the gene is of necessity an abstract, general, and open one, despite the fact that our comprehension of the structure and organization of the genetic material has greatly increased. Due to the openness of the concept of the gene, it takes different meanings depending on the context. Maxime Singer and Paul Berg have pointed out that many different definitions of the gene are possible. If we want to adopt a molecular definition, they suggest the following definition: "A eukaryotic gene is a combination of DNA segments that together constitute an expressible unit, expression leads to the formation of one or more specific functional gene products that may be either RNA molecules or polypeptides. Each gene includes one or more DNA segments that regulate the transcription of the gene and thus its expression." Thus, the segments of a eukaryotic gene include a transcription unit, which includes the coding sequences, the introns, the flanking sequences – the leader and trailer sequences, and the regulatory sequences, which flank the transcription unit and which are necessary for its specific function. Mutation A mutation is a sudden heritable change in genetic information. Since genetic information is encoded by the order of the nucleotide bases of DNA, adenine (A), thymine (T), guanine (G), and cytosine (C), a mutation represents some sort of change in that order. Mutations may occur in both somatic and sex cells. Only mutations that occur in sex cells can be passed from parent to offspring. The changes in nucleic acid sequences by mutations include substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences. Although many of these mutations are lethal, or cause serious disease, some have minor effects, as the changes they cause in the sequence of encoded proteins are not significant. Many mutations cause no visible effects at all, either because they occur in certain gene sequences (introns), or because they do not change the amino-acid sequence. When the amino acid is changed, though, the protein that gene creates may be quite different, causing harm to the organism. For example, if the sixth amino acid in human hemoglobin is changed from glutamic acid to valine through simple base substitution the change will cause sickle-cell anemia, a painful condition that eventually proves fatal. Mutagens A mutagen is any substance or agent that changes the genetic information (usually DNA) of an organism and thus increases the frequency of mutations above the natural background level. Not all mutations are caused by mutagens: "spontaneous mutations" can occur due to errors in DNA replication, repair and recombination of DNA sequences. In the 1920s, Hermann Muller discovered that X-rays caused mutations in fruit flies. He went on to use X-rays to create Drosophila mutants that he used in his studies of genetics. He also discovered that x-rays did not only mutate genes in fruit flies, but also had effects on the genetic makeup of humans.

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(i)Chemical Mutagens There are many hundreds of known chemical mutagens. Some resemble the bases found in normal DNA; others alter the structures of existing bases; others insert themselves in the helix between bases; while others work indirectly, creating reactive compounds that directly damage the DNA structure. Examples of the chemical mutagens include: (i) base analogs (e.g., 5-bromo-deoxyuridine); (ii) base-altering mutagens (e.g., nitrous acid); and (iii) intercalating agents (e.g., acridine orange). (ii)Physical Mutagens Visible light represents a small slice of the electromagnetic spectrum, which includes long-wavelength (low-energy) radio waves and short-wave-length (high-energy) ultraviolet waves, plus X rays and gamma rays. These high-energy forms can directly disrupt DNA by breaking its chemical bonds. In severe cases, this can break apart chromosomes, causing chromosome aberrations. More often, they create mutagenic free radicals in the cell. X rays were first used by Hermann Muller to induce mutations in fruit flies. They continue to be used to create mutations in model organisms to study genes and their effects. Ultraviolet light is less energetic than X rays but causes mutations nonetheless. The higher-energy form, UV-B, is more toxic than UV-A. Polygenic and Quantitative Inheritance Gregor Mendel studied mainly traits that have distinct alternate forms for instance, purple flower colour vs white flower colour. But many traits are more complex than this and basically can take on any number of continuous values. For example in humans there is not just two classes of people - short vs tall- but a whole range of possible heights. In addition many traits are not controlled by a single gene pair but by many genes interacting with each other and also with the environment. The study of such traits controlled by many genes and also by the environment is called Quantitative Genetics. The inheritance of quantitative traits is typically viewed in terms of what is called ‘polygenic inheritance’. It should be clearly understood that quantitative genetics is effectively an extension of simple Mendelian inheritance in that the combined effect of the many underlying genes results in a continuous distribution of phenotypic values. Quantitative genetics is not limited to continuous traits, but to all traits that are determined by many genes. Continuous traits are quantitative traits with a continuous phenotypic range, as shown the figure for human height. Such traits are usually polygenic, and may also have a significant environmental influence. Statistical research suggested that for quantitative traits the offspring of a cross tended to be intermediate in appearance between the two parents. For instance, if one parent is tall and the other short, the offspring tend to be intermediate in height. In other words, the offspring in a cross tend to be a blend of both parents. At the same time,

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height is influenced by the nutrition a person receives as well as environment in which he/she is grown. Thus, the phenotypic value (P) of an individual is the combined effect of the genotypic value (G) and the environmental deviation (E): P = G + E. The genotypic value is the combined effect of all the genetic effects, including nuclear genes, mitochondrial genes and interactions between the genes. The contribution of those components cannot be determined in a single individual, but they can be estimated for whole populations by estimating the variances for those components. The heritability of a trait is the proportion of the total (i.e. phenotypic) variation (VP) that is explained by the genetic variation (VG). The latter gives an indication how a trait will respond to natural or artificial selection. Extrachromosomal Inheritance Not all inherited characters are determined by genes located in the chromosomes present in the nucleus. A small minority are controlled by genes located in cell organelles in the cytoplasm i.e. cytoplasmic genes, and these, of course, are exceptions to the chromosome theory of inheritance. Since they are extrachromosomal (i.e. outside the chromosomes) such genes do not conform to the Mendelian principles of heredity. One of the earliest and best known examples of cytoplasmic inheritance is that discovered by Correns in a variegated variety of the four-o'clock plant Mirabilis jalapa. Variegated plants have some branches which carry normal green leaves, some branches with variegated leaves (mosaic of green and white patches) and some branches which have all white leaves. Correns discovered that seed produced by flowers carried on the green branches gave progeny which were all normal green. It made no difference whether the phenotype of the branch which carried the flower used for pollen was green, white or variegated. Seed taken from white branches likewise gave all white progeny, regardless of the pollen donor phenotype. These of course died in the seedling stage. Seeds from flowers on variegated branches gave three kinds of progeny, green, white and variegated, in varying proportions; again regardless of the pollen donor phenotype. In other words, the phenotype of the progeny always resembled the female parent and the male made no contribution at all to the character. The effect is seen quite clearly in the difference which Correns found between reciprocal crosses:

Variation in flower colours in a Mirabilis jalapa plant

♀ green x ♂ white = green progeny

♀ white x ♂ green = white progeny

The explanation for this unusual pattern of inheritance is that the genes concerned are located in the chloroplasts within the cytoplasm, not in the nucleus, and are therefore transmitted only through the female parent. In eukaryote organisms, the zygote normally receives the bulk of its cytoplasm from the egg cell and the male gamete contributes little more than a nucleus. Any genes contained in the cell organelles of the cytoplasm will therefore show maternal inheritance. The leaf variegation is due to two kinds of chloroplasts: normal green ones and defective ones lacking in chlorophyll pigment. Chloroplasts are genetically autonomous (i.e. self-determining)

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and have their own system of heredity. There are small circular naked DNA molecules which carry genes controlling some aspects of chloroplast structure and function. A mutation in one of these genes, which affects the synthesis of chlorophyll as in Mirabilis, will therefore follow the chloroplast in its transmission and will not be inherited in the same way as a nuclear gene. The other important point to note about the inheritance of chloroplasts is that they have no regular means of distribution, such as chromosomes do at mitosis, where they can be equally shared out to the daughter cells following division. A plant that begins life as a zygote containing a mixture of normal and mutant chloroplasts cannot therefore maintain the same mixture in all of its somatic cells. The two kinds of plastids are shared out randomly during cell division, according to the way they happen to be placed in the cytoplasm when it is partitioned. Some branches of variegated plants may therefore remain mosaic while others, by chance, may turn out to contain all white or all green chloroplasts in all of their cells. In a similar way the flowers on variegated branch may be of three kinds. Some will have egg cells with all green chloroplasts, some egg cells with all white and others will retain a mixture. Many of the other examples of cytoplasmic inheritance, in a variety of species, appear to involve characters which are associated with functions of the mitochondria. They have to do with defects in growth and ATP energy metabolism. Well-known cases include the ‘Poky’ (slow growing) mutants in the fungus Neurospora and ‘Petite’ mutants' in brewer’s yeast. The mitochondria, like the chloroplasts, are self-replicating organelles which contain their own genes and have a limited number of characters which are independent of the nucleus. They are transmitted mainly through the female line and mutations in their genes show the same pattern or maternal inheritance. Mitochondrial ‘chromosomes’ have a similar circular configuration of ‘naked’ DNA as chloroplasts. Plant Tissue Culture Tissue culture is the culture and maintenance of plant cells or organs in sterile, nutritionally and environmentally supportive conditions (in vitro). It has applications in research and commerce. In commercial settings, tissue culture is often referred to as ‘micropropagation’, which refers to the production of whole plants from cell cultures derived from explants (the initial piece of tissue put into culture) of (usually) meristem cells. Plant tissue culture relies on the fact that many plant cells have the ability to regenerate a whole plant (‘totipotency’). Single cells, plant cells without cell wall (protoplasts), pieces of leaves, or (less commonly) roots can often be used to generate a new plant on culture media given the required nutrients and plant hormones. Conditions for Plant Tissue Culture Freedom from competition: Bacteria, fungi, and other organisms which can be resisted to some degree by a whole plant can easily outcompete an isolated fragment of tissue from the plant in the relatively nutrient-rich environment of a culture flask. Therefore, it is necessary to remove competitor organisms from the culture and isolate it in aseptic conditions, most usually in a small flask or test tube. This is usually done by chemical surface sterilization of the explant with an agent such as bleach at a concentration and for a duration that will kill or remove pathogens without injuring the plant cells beyond recovery. The medium and culture flasks

Culture of plant tissues under aseptic conditions (in Laminar Flow)

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used must also be sterile. Nutrients: When a small portion of a plant is isolated, it is no longer able to receive nutrients or hormones from the plant, and these must be provided to allow growth in vitro. This is accomplished by culturing on or in a defined culture medium. The medium must be periodically replenished. Controlled Environment: Tissue cultures, sustained by the nutritive medium and confined in a protective vessel require a stable and suitable climate. Thus, light and temperature must be more carefully regulated than would be the case the whole plant.

Mpe

Utility of Plant Tissue Culture Tissue culture offers numerous significant benefits over traditional propagation methods:

• The production of exact copies of plants (clones) that produce particularly good flowers, fruits, or have oth

• Much faster rates of growth can be induced in vitro than

• It may be possible to multiply in vitro plants that arecuttings or other traditional methods.

• Under certain conditions, plant material can be stored intime with little or no maintenance.

• Tissue culture techniques are used for virus eradicationhybridization and other procedures that benefit propabasic research.

• The regeneration of whole plants from plant cells that ha

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Genetics. Houghton Mifflin. 5. Human Genome Project Information 2005; http://www.doegenomes.org6. Kearsey MJ & Pooni HS (1996). The Genetic Analysis of Quantitative T7. Kyte L & Kleyn J (1996). Plants from Test Tubes: An Introduction to

Press. 8. Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zip

Cell Biology. 5th edition. WH Freeman: New York. 9. Morgan DO (2007). The Cell Cycle: Principles of Control. London: New

Shoot induction from the explants grown in a nutrient medium

aintenance of tissue-cultured lantlets under controlled nvironment

er desirable traits.

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very difficult to propagate by

vitro for considerable periods of

, genetic manipulation, somatic gation, plant improvement, and

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(2000). An Introduction to Genetic

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10. Pearson H (2006). Genetics: what is a gene? Nature 441: 398-401. 11. Portin P (1993). The concept of the gene: short history and present status. Quart. Rev. Biol. 68: 173-222. 12. Ptashne M (1986). Gene regulation by proteins acting nearby and at a distance. Nature 322: 697-701. 13. Sturtevant AH (2001). A History of Genetics. New York: Cold Spring Harbor Laboratory Press and Electronic

Scholarly Publishing Project (http://www.esp.org). 14. Watson JD & Crick FHC (1953). A structure for Deoxyribose Nucleic Acid. Nature 171: 737- 738. 15. Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene. 5th

edition. New York: Cold Spring Harbor Laboratory Press.

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