Markers-Assisted Selection for Plant Breeding

P. K. Gupta
Molecular Biology Laboratory Department of Agricultural Botany Ch.Charan Singh University, Meerut

MAS vs Transgenics
MAS should be preferred over transgenic, if genetic variation is available in gene pool MAS is also desirable, if visual selection is difficult & cost/time ineffective Sometimes, both approaches are used (e.g. insect/disease resistance in rice)

Marker-Assisted Selection for Conventional 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

Steps Involved in MAS

Development of trait-associated markers Selection of markers (relative contributn) Validation of markers (breeding material) Utilization of markers (several methods) Simultaneous marker developt & utilizatn (e.g. AB-QTL; mapping-as-you-go)

Marker Polymorphism for MAS

Marker-Assisted Backcrossing
Transfer of genes from DG to RG
- Foreground selection (for donors trait) - Background selection (for host genome) (i) 2 step selection (chromosome, genome) (ii) 3-4 step selection (gene region arm chromosome genome)

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)

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

Introgrn Lines (ILs) for gene pyramidg

Zamir (2001) Nat Rev Gen; Ashikari &Matsuoka (2006) Trends Pl Sci

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

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; Improved Sambha Mahsuri; 2. Pearl-millet (HHB-67-2); 3. Maize (Vivek-QPM9) Submergence tolerance: Sub1A

60 Genes/QTL for MAS in Wheat

(Gupta et al. 2009, Mol Breeding)
1
QGw.ccsu-1A.1
(1AS-5 0.20)

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

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

6
Sr26

7
GBSS Null Lr47(7AS-6 0.21)

(1AL1-0.17-0.61)

Glu-A1

Lr46
(1AL3-0.61-1.00)

Bx7, Cre493 PPO (2AL0.77-0.85) QPhs.ccsu-3A.1

(3AL5-0.78-1.00)

PHS, GBSS Null Yr34 (5AL23-0.87-1.00)

Flour Color Sr22 (7AL 0.83-1.00)

QGw.ccsu-1A.3

Yr10,Yr15,Glu-3
(1BS.sat18-0.50-1.00)

Sr2,Fhb1(3BS-0.78-1) Lr13/23

Rht1(4BS8-0.57-0.81)

BGGP GPC-B1,Yr36
(6BS-5 0.49-0.68)

B
1B/1R (1BL1-0.47-0.69) Glu-B1 Lr46(1BL 0.84-0.89)

Sr36, Sr32, Sr39/Lr35, Lr46/Yr29 Cre1(2BL 0.50-0.89) Qss.msub-3BL

(3BL-0.81-1.00)

Cr

Yls

Cre8 Lr9 (6BL-0.79-1.00)

Yfc, Rlnn1, Bo1, LMA

Rht8
(C-2DS 0.47-1.00)

Rht2 (4DS3-0.67-0.82)

PinA (5DS7-0.67-0.78)

Lr34/Yr18 (7DS-4 0.61-1.00) Stb4

Sr33

D
Sr30, Lr1 Glu-D1
(1DL2-0.41-1.00)

Cre3, PPO

(2DL9-0.76-1.00)

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

Almt-1
(4DL 0.710.86)

Pch1, Lr19/Sr25, GBSS Null Bdv2 (7DS-8 0.77-1.00)

Figure 1

MAS in Cereals
Maize, Wheat, Barley (CIMMYT, USA, Australia, Canada) Markers for genes for all major traits (>20 in each case) except yield and abiotic stresses being used for MAS: -insect -pest resistance, protein quality, & other agronomic traits

GeneGene -Assisted selection (GAS) for Bread Making Quality

Objective provide an integrated manipulation of bread Objective: making characteristics using molecular markers
Molecular markers for gluten strength
STS for Glu-1

Molecular markers for hardness New varieties

SNPs for Pinb-D1

Molecular markers for grain protein content

CAPS for Gpc-B1

MAS for Blight and Blast of Rice

Bacterial Blight

Blast Disease

Pyramiding Xa Genes for Bacterial Blight 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+xa13+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 IARI

Joseph et al. 2004. Mol Breed 13:377

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

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

Bacterial Blight in Rice

Pyramiding of Genes for Blast Resistance in Rice

Pi-2(t)+Pi-9(t) in Kalinga III &Vandana (CRRI)* *C101A51Pi-2(t) & O. minutaPi-9(t); Pi-1(Pi1)+Pi-2(Piz-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 100:11211128); *alleles indicated in parenthesis

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

Resistance for Rice Blast Disease

Submergence Tolerance in Rice Swarna- Sub1A (Nature, Aug 06)

BC3F2, BC2F3 Sub1 donor IR49830

Swarna

six varieties* close to release at national & state levels in Bangladesh & India
*Swarna, IR64,CR1009, BR11, TDK1, Samba Mahsuri

Marker Assisted Resistance Breeding

Some Often Cited Examples Soybean Cyst Nematode Cregan et al. 2000; Meksem et al., 2001 Resistance against Gall Midge in Rice Madan Mohan (ICGEB; Now at UDSC)
Two Hybrids Released in India

Pearl-millet (HHB-67-2 from HHB-67 (HAU) (downy mildew resistant): ICRISAT Maize (Vivek-QPM9): VPKAS, Almora

Hybrid Rice Cultivars in China (e.g., Shanyou 63; Restorer Line Minghui 63 Improved)

Gene Pyramiding for Biotic & Abiotic Stresses in Barley

South Aust. Barley Impr. Program (SABIP)
- CCN (Ha2/Ha4), BYDV (Yd2), SFNB (Rpt4) & Mn effi.(Mel1) -Sloop Sloop SA;Sloop Vic
Source: Chebec(Ha2), Franklin (Yd2) & Keel (Ha4, Rpt4 & Mel1)

- CCN, SFNB, leaf rust, leaf scald, boron tol. & thermostable -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 -amylase

SFNB, Spot Form Net Blotch

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

Limited success: 20 QTLs in maize, 2 QTLs in rice 9311* & 3 QTLs in tomato**;
Edwards, Monsanto, St. Louis, USA *O. rufipogon RGC105491 to O. sativa 9311 (Liang et al. 2004, Euphytica); ** Crossing ILs (S. pennellii S. lycopersicum M82), Gur & Zamir (2004) PLoS Biol 2:e245
M.

No benefit (epistasis & env.): QTL from Steptoe (high yield) & Morex (malting) in Barley 10 Morex NILs & 1 Steptoe NIL
(Kandemir et al., 2000 Mol Breed 6:157)

Pyramiding Additional Genes Over Transgenes

Rice: CO39NILPiz-5 IR50Piz-5 transform Xa21 = IR50Piz-5+Xa21 (Crop Sci 42:p2072, 2002) Rice: IRBB21Xa21 Minghui 63Xa21(MAS) Minghui 63cry1Ab+cry1Ac (GM) = Minghui 63cry1Ab+ cry1Ac+Xa21
(Minghui 63 is a widely used cms restorer line for hybrid rice in China)

(Jiang et al. 2004 Plant Breed 123:112-116) Soybean: QTL for insect resistance from PI 229358 to GM Jack-Btcry1Ac (Walker et al. 2002; Mol Breed 9:43)

Reasons for Low Impact & Future Needs for MAS

Non-availability of robust markers Epistasis, background and g e Still cost-ineffective: high throughput & low cost genoytpic centres needed Plant breeder-molecular biologist gap Association mapping needed MARS & GWS for complex/multiple traits

Further Reading on MAS

Gupta et al. (2009). MAS for conventional plant breeding. Plant Breed Rev 33:145-217 Gupta et al. (2009). MAS in Wheat: Mol Breeding (Special Issue): 24: (published online, 11 December, 2009) Gupta et al. (2009). MAS for complex and multiple traits in crops. (under preparation) Several Other Reviews on this Active Area