Cotton genomics @sid

COTTON GENOMICS COTTON GENOMICS

Siddhartha Swarup JenaRAD/10-30

Ph.D. Mol. Bio & Biotech

Siddhartha Swarup JenaRAD/10-30

Ph.D. Mol. Bio & BiotechS S Jena

Phylum: Magnoliophyta

Class: Magnoliopsida

Order: Malvales

Family: Malvaceae

Tribe: Gossypieae

Cotton- King of Fibres

Diploid: 2n = 26, tetraploid: 2n = 52

2.7 billion nucleotides.

GossypiumGossypium

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Annual, biennial or perennial

Herbaceous, short shrub or small tree

Primary axis, alternateLeaves have varying

texture, shape, hairiness

Showy cream, yellow, red or purple flowers axilary, terminal or solitary with typically 5 petals

DiversityDiversity

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African-Asian diploids:G. herbaceumG. arboreum

New World tetraploids:G. barbadenseG. hirsutum

Four Independently Domesticated Species!!

Four Independently Domesticated Species!!

G. barbadense

G. hirssutum

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Gossypium hirsutum, also known as Upland cotton, Long Staple Cotton, or Mexican Cotton, produces over 90% of the world’s cotton;

G. barbadense, also known as Sea Island Cotton, Extra Long Staple Cotton, American Pima, or Egyptian Cotton, contributes 8% of the world’s cotton;

G. herbaceum, also known as Levant Cotton, and G. arboreum, also known as Tree Cotton, together provide 2% of the world’s cotton.

Four Independently Domesticated Species!!

Four Independently Domesticated Species!!

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Concerning diploid parentageConcerning diploid parentage

Cytogenetic studies indicate G. raimondii as the closest living relative of D genome parental donor

Hutchinson et al., 1947

– used 5 D-genome species in crosses with G. hirsutum or G. barbadense.

– Indicated G. raimondii as closer to the D-genome than other species tested.

– Innovative approach involving comparative analysis of diverse synthetic allohexaploids.

Liu et al., 2001

– G. raimondii is the sister group to clade of all 5 allopolyploid species

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A-genome perspectivesA-genome perspectives

A-genome of allopolyploid cotton is more similar to the A-genome diploids than the D-genome of the allopolyploid is to that of the D-genome diploids!

G. arboreum and G. herbaceum better models of the progenitor A-genome diploid than G. raimondii is of the D-genome diploid

G. herbaceum more likely the A-genome donor than G. arboreum.

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Biogeographical TheoriesBiogeographical Theories

Theories, based on cytogenetic data, suggested that polyploidization occurred after a Trans-Atlantic dispersal of a species similar to G. herbaceum.

Wendel and Albert, 1992:

Suggest pre-Pleistocene A-genome radiation into Asia, followed by trans-Pacific dispersal to the Americas

Supported by biogeography of D-genome species

Recent arrival of G. raimondii in Peru.

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Allopolyploidization of Cotton Occurred Only Once

Allopolyploidization of Cotton Occurred Only Once

All New World tetraploid cottons contain Old World Cytoplasm.

Must have been one single seed plant in the initial hybridization event.

Long distance dispersals occurred by Transoceanic Voyages.

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Phylogeny and evolution of Gossypium species

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CottonDBCottonDB

CottonDB is a product of the Agricultural Research Service of the US Department of Agriculture and is maintained as a public resource to serve the cotton research community.

CottonDB is a database that contains genomic, genetic and taxonomic information for cotton (Gossypium spp.).

It serves both as an archival database and as a dynamic database which incorporates new data and user resources.

In 1995, CottonDB was initiated. It is the first and most extensively used database for cotton worldwide.

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CottonDBCottonDB

CottonDB is a database that contains genomic, genetic and taxonomic information for cotton (Gossypium spp.).

It serves both as an archival database and as a dynamic database which incorporates new data and user resources.

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CottonDBCottonDB

CottonDB.org contains:

– Genomic markers and nucleotide sequences – Genes, alleles and gene products – BAC clones and clone libraries – TM-1 fingerprint contigs developed by USDA-

ARS/Texas A&M University – Taxonomy of the Gossypium genus – Genetic maps – Contact information and research interests of

colleagues – Relevant bibliographic citations

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Linkage map Linkage map

The first molecular linkage map of the Gossypium species was constructed from an interspecific G. hirsutum × G. barbadense F2 population based on RFLPs.

The map comprised of 2,584 loci at 1.74 cM intervals and covered all 13 homeologous chromosomes of the allotetraploid cottons, representing the most complete genetic map of the Gossypium.

At least six BAC and BIBAC libraries have been developed and made available to the public

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ESTsESTs

281,233 ESTs have been available for the Gossypium species in GenBank.

Of these ESTs,

178,177 were from the polyploid cultivated cottons with 177,154 (63.0%) from G. hirsutum and 1,023 (<1.0%) from G. barbadense.

while 103,056 were from the related diploid species with 39,232 (13.9%) from G. arboreum (A2), 63,577 (22.6%) from G. raimondii (D5), and 247 (<1.0%) from G. herbaceum (A1).

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ESTs cont.ESTs cont.

These ESTs were collectively generated from 32 cDNA libraries constructed from mRNA isolated from 18 genotypes of three species, G. hirsutum, G. arboretum, and G. raimondii, by one-pass sequencing of cDNA clones from one (3′ or 5′ end) or both ends.

Generated from 12 different organs- developing fibers, seedlings, buds, bolls, ovules, roots, hypocotyls, immature embryos, leaves, stems, and cotyledons.

Some of the ESTs were generated from plants growing under biotic or abiotic stress conditions such as drought, chilling, and pathogens.

A predominant feature of the cotton EST set is the significant preference of their tissue sources for fiber or fiber-bearing ovules than other organs.

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Physical mapping Physical mapping

To date the database is limited to information concerning our ongoing physical mapping effort in three species of cotton, including the two cultivated 'AADD' tetraploid species Gossypium barbadense and G. hirsutum, and the wild DD genome species G. raimondii.

BAC libraries for all three species are currently being assayed using genomic and cDNA clones derived from linkage maps, and also dispersed repetitive DNA clones.

The physical mapping database has been constructed using the BACMan data management application

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QTLsQTLs

QTLs for fiber quality properties in two Upland cottons, compared with those of ELS (extra long staple) cotton, with regard to their locations and gene effects.

A total of thirteen QTLs have been identified, four for fiber strength, three for fiber length, and six for fiber fineness

They are located on different chromosomes or linkage groups of our molecular maps comprised of 355 DNA markers covering 4,766 cM (Haldane function) of the cotton genome in 50 linkage groups

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Cotton Vs ArabidopsisCotton Vs Arabidopsis

Although cotton genome is large and complex, its physical size of a cM is only 50% larger than that of Arabidopsis

A high level of homology between Arabidopsis and Gossypium genomes and abundant polymorphism among Gossypium germplasm were detected using conserved cDNAs from Arabidopsis genome.

The upland cotton genome consists of approximately 61% unique sequences and low copy number DNA

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Chloroplast genomeChloroplast genome

The chloroplast genome of cotton is 160,317 base pairs (bp) in length, and is composed of a large single copy (LSC) of 88,841 bp, a small single copy (SSC) of 20,294 bp, and two identical inverted repeat (IR) regions of 25,591 bp each.

The genome contains 114 unique genes, of which 17 genes are duplicated in the IRs. In addition, many open reading frames (ORFs) and hypothetical chloroplast reading frames (ycfs) with unknown functions were deduced.

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Chloroplast genome cont.Chloroplast genome cont.

Compared to the chloroplast genomes from 8 other dicot plants, the cotton chloroplast genome showed a high degree of similarity of the overall structure, gene organization, and gene content.

The cotton chloroplast genome was somewhat longer than the chloroplast genomes of most of the other dicot plants compared here.

However, this elongation of the cotton chloroplast genome was found to be due mainly to expansions of the intergenic regions and introns (non-coding DNA).

Moreover, these expansions occurred predominantly in the LSC and SSC regions.

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Cotton sequencing will greatly help molecular breeding

Cotton sequencing will greatly help molecular breeding

Increases our understanding of cotton physiology and evolution.

Model of polyploid and comparative genome evolution

Maintains the competitive advantage of cotton fiber relative to other fibers

Creates new values for cotton on the farm and beyond the farm gate

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Factors slowing down the cottonsequence progress

Factors slowing down the cottonsequence progress

Its large genome, a relatively large physical size of 2246 Mbp and small chromosomes

Allotetraploid AD genome property,

n=2x=AD=26

A large fraction of genome comprised of repetitive DNA seq.

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THANK YOUTHANK YOU

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