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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
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