68871531 Marker Assisted Selection for Crop Improvement by Dr P K Gupta Hon Emeritus

8/13/2019 68871531 Marker Assisted Selection for Crop Improvement by Dr P K Gupta Hon Emeritus

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Markers-Assisted Selectionfor

Plant Breeding

P. K. GuptaMolecular Biology Laboratory

Department of Agricultural BotanyCh.Charan Singh University, Meerut


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MAS vs Transgenics

• MAS should be preferred over transgenic, ifgenetic variation is available in gene pool

• MAS is also desirable, if visual selection isdifficult & cost/time ineffective

• Sometimes, both approaches are used(e.g. insect/disease resistance in rice)


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Marker-Assisted Selection forConventional Breeding: Why?

- Difficult traits (e.g.,abiotic stresses)

- Traits with low heritability

- Pyramiding of resistance genes- Selection at seedling stage

- Distinguish homo- & heterozygotes- No question of biosafety and bioethics


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Steps Involved in MAS

• Development of trait-associated markers

• ’

• Validation of markers (breeding material)

• Utilization of markers (several methods)

• Simultaneous marker develop’t & utilizat’n(e.g. AB-QTL; ‘mapping-as-you-go’)


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Marker Polymorphism for MAS


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Marker-Assisted Backcrossing

Transfer of genes from DG to RG

- Foreground selection (for donor’s trait)

- Background selection (for host genome)

(i) 2 step selection (chromosome, genome)

(ii) 3-4 step selection (gene region armchromosome genome)


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Restricted Backcrossing &Double Haploidy (DH) for MAS

• BC1F1 pollen for haploids

-gene selection at the haploid stage

-background selection of DHs

• gain over phenotypic selection, and cost

reduced by 40%(Molecular Breeding 2005)


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Some Novel Strategies(for complex & multiple traits)

• Marker-assisted recurrent selection (MARS)and genome-wide selection (GWS)

• AB-QTL: transfer of several traits:Tanksley & Nelson (1996) TAG 92:191

• Introgr’n Lines (ILs) for gene pyramid’g

Zamir (2001) Nat Rev Gen; Ashikari &Matsuoka (2006) Trends Pl Sci• Breeding by DesignTM

Peleman & van der Voort (2003) Trends Plant Sci 8:330


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Achievements of MAS

(details not being discussed)

• MAS Programs World-Wide: USA,Canada, Australia, CIMMYT, IRRI -Many Cultivars Released

• MAS in India: Cultivars Released-1. Rice (Improved PB-1; ImprovedSambha Mahsuri; 2. Pearl-millet(HHB-67-2); 3. Maize (Vivek-QPM9)

• Submergence tolerance: Sub1A


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60 Genes/QTL for MAS in Wheat(Gupta et al. 2009, Mol Breeding)

QGw.ccsu-1A.1

QFhs.ndsu-3AS (3AS4-0.45-1.00)

QPhs.ccsu-3A.1(3AL5-0.78-1.00)

Lr47 (7AS-6 0.21)

Glu-A1(1AL1-0.17-0.61)

(1AL3-0.61-1.00)QGw.ccsu-1A.3

(1AS-5 0.20)

A

Lr37/Yr17/Sr38 (2AS5-0.78-1.00)

PPO (2AL0.77-0.85)

Sr2 Fhb1 3BS-0.78-1

1 2 3 4 5 6 7

PHS, GBSS Null

Yr34 (5AL23-0.87-1.00)

Yr10,Yr15,Glu-3

Lr46 Bx7, Cre 493

Sr26 GBSS Null

Flour Color

Sr22 (7AL 0.83-1.00)

Lr46

GPC-B1,Yr36

Cre1

Cre3, PPO

PinA (5DS7-0.67-0.78)

(2BL 0.50-0.89)

(2DL9-0.76-1.00)

Rht2 (4DS3-0.67-0.82)

- . - .

(6BS-5 0.49-0.68)

(1BL 0.84-0.89)

Glu-B1(1BL1-0.47-0.69)

(1DL2-0.41-1.00)Glu-D1

B

D

Rht8 (C-2DS 0.47-1.00)

Lr24 ( 3DL-0.78-1)Sr24 (3DL2-0.27-0.81)

, .

Qss.msub-3BL(3BL-0.81-1.00)

Almt-1(4DL 0.71–0.86)

(1BS.sat18-0.50-1.00)

1B/1R

Lr13/23

Sr36, Sr32,Sr39/Lr35,Lr46/Yr29 Cr Yls

BGGP

Cre8 Yfc, Rlnn1, Bo1, LMA

Sr33

Sr30, Lr1

Stb4

Pch1, Lr19/Sr25,GBSS Null

Lr9 (6BL-0.79-1.00)

Bdv2 (7DS-8 0.77-1.00)

Lr34/Yr18 (7DS-4 0.61-1.00)

Figure 1


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MAS in Cereals

• Maize, Wheat, Barley (CIMMYT,USA, Australia, Canada)

• ar ers or genes or a ma or tra ts(>20 in each case) except yield andabiotic stresses being used for MAS:

-insect -pest resistance, proteinquality, & other agronomic traits


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ObjectiveObjective: provide an integrated manipulation of bread

making characteristics using molecular markers

GeneGene--Assisted selection (GAS) forAssisted selection (GAS) forBread Making QualityBread Making Quality

o ecu ar mar erso ecu ar mar ersfor hardnessfor hardness

Molecular markers forMolecular markers forgrain protein contentgrain protein content

New varieties

o ecu ar mar erso ecu ar mar ersfor gluten strengthfor gluten strength

CAPS for Gpc-B1

SNPs for Pinb-D1STS for Glu-1


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MAS for Blight and Blast of Rice

Blast DiseaseBacterial Blight


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Pyramiding Xa Genes for BacterialBlight Resistance in Rice

• ‘Angke’ & ‘Conde’ (Indonesian cultivars) xa5 in

the background of xa4 Toennissen et al. (2003) Curr Opin Plant Biol 6:191-198

• PR106 PAU & MH2Rxa5 xa5+xa1 +Xa21

(Mahyco Res. Ctr, Jalna)Singh et al. 2001. TAG (PR106 × IRBB62xa5 + xa13 + Xa21); Mahyco(MH2Rxa5 × IRBB60Xa4 +xa5 +xa13+Xa21)

• PB-1(with basmati quality) with BB resistance

(from IRBB55xa13 +Xa21) at IARIJoseph et al. 2004. Mol Breed 13:377

• Improved Sambha Mahshuri: BLB genes xa5 ,xa13 , Xa21; donor PR 106; DRR, Hyderabad


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Improved Samba Mahsuri (IET 19046)A first variety from Marker Assisted Selection (MAS)


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Bacterial Blight in Rice


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Pyramiding of Genes for BlastResistance in Rice

• Pi-2(t)+Pi-9(t) in ‘Kalinga III’ &‘Vandana’(CRRI)* *C101A51Pi-2(t) & O. minuta Pi-9(t);

Pi-1(Pi1)+Pi-2 (Pi z-5 )+Pi-4 (Pita ) in ‘CO39’(UAS, Bangalore)LAC23Pi -1, 5173Pi -2 & Pai-kan-taoPi-4 → CO39 = CO39Pi-1+Pi-2 +Pi-4

(Hittalmani et al. 2000. TAG 100:1121–1128); *alleles indicated in parenthesis

‘IR50’, ‘Jyothi’(Madras Univ), ‘IR36’, IR50, ‘IR64’ & ‘IR72’(UAS; Hittalmani 2005)


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Resistance for Rice Blast Disease


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Submergence Tolerance in Rice

Swarna- Sub1A (Nature, Aug ’06)BC3F2, BC2F3

Sub1 donorIR49830

Swarna

*Swarna, IR64,CR1009,

BR11, TDK1, Samba Mahsuri

six varieties* close torelease at national &

state levels inBangladesh & India


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Marker Assisted Resistance Breeding

Some Often Cited Examples

• Soybean Cyst NematodeCregan et al. 2000; Meksem et al., 2001

• Resistance against Gall Midge in Rice

a an o an ; ow atTwo Hybrids Released in India• Pearl-millet (HHB-67-2 from HHB-67 (HAU)

(downy mildew resistant): ICRISAT

• Maize (Vivek-QPM9): VPKAS, AlmoraHybrid Rice Cultivars in China(e.g., Shanyou 63; Restorer Line Minghui 63 Improved)


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Gene Pyramiding for Biotic &Abiotic Stresses in Barley

• South Aust. Barley Impr. Program (SABIP)- CCN (Ha2/Ha4 ), BYDV (Yd2 ), SFNB (Rpt4 ) &

-‘ ’ ‘ ’ ‘ ’.Source: Chebec(Ha2 ), Franklin (Yd2 ) & Keel (Ha4, Rpt4 & Mel1)

- CCN, SFNB, leaf rust, leaf scald, boron tol. &thermostable β-amylase to ‘Gairdner’Source: 1.‘Keel’– CNN & SFNB resistance, 2. ‘Fanfare’- rust resistance, 3. H. spontaneum- scab resistance, 4. ‘DH115’ – boron tolerance & 5. SD3 - thermostable β-amylase

SFNB, Spot Form Net Blotch


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Problems in MAS for Yield:Maize/Rice/Tomato/Barley

• Limited success: 20 QTLs in maize†, 2QTLs in rice ‘9311’* & 3 QTLs in tomato**;

. war s, onsanto, t. ou s, . ru pogon ‘ to . sat va ‘

(Liang et al. 2004, Euphytica); ** Crossing ILs (S. pennellii→ S. lycopersicum ‘M82’),Gur & Zamir (2004) PLoS Biol 2:e245

• No benefit (epistasis & env.): QTL from

‘Steptoe’ (high yield) & ‘Morex’ (malting) inBarley→ 10 Morex NILs & 1 Steptoe NIL(Kandemir et al., 2000 Mol Breed 6:157)


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Pyramiding Additional GenesOver Transgenes

• Rice: ‘CO39’NILPiz-5 →IR50Piz-5 → transform Xa21 =IR50Piz-5 +Xa21 (Crop Sci 42:p2072, 2002)

• Rice: IRBB21Xa21→ Minghui 63Xa21(MAS) × Minghui

63cry +cry c

(GM) = ng u 63cry + cry c+ a

(Minghui 63 is a widely used cms restorer line for hybrid rice inChina)

(Jiang et al. 2004 Plant Breed 123:112-116)

• Soybean: QTL for insect resistance from ‘PI229358’ to GM ‘Jack-Bt’cry1Ac

(Walker et al. 2002; Mol Breed 9:43)


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Reasons for Low Impact &Future Needs for MAS

• Non-availability of robust markers• Epistasis, background and g × e

-cost genoytpic centres needed

• Plant breeder-molecular biologist gap

• Association mapping needed• MARS & GWS for complex/multiple traits


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Further Reading on MAS

• Gupta et al. (2009). MAS for conventionalplant breeding. Plant Breed Rev 33:145-217

• Gu ta et al. 2009 . MAS in Wheat: Mol

Breeding (Special Issue): 24: (published on-line, 11 December, 2009)

• Gupta et al. (2009). MAS for complex and

multiple traits in crops. (under preparation)• Several Other Reviews on this Active Area

68871531 Marker Assisted Selection for Crop Improvement by Dr P K Gupta Hon Emeritus

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