New approaches, resources and tools for gene discovery and breeding in rice

Alain Ghesquière/M. Lorieux

Using AA genome species of rice

to discover genes of importance

• Domestication allelic bottleneck• Wild species still have the “lost” alleles• Many traits of agronomical interest• Several examples of successful

introgression• Transgressive effects

Objective : to systematically identify the alien variation provided by a donor or a remote species in a set of introgressed lines selected in a common genetic background (O. sativa)

59 BC3DH lines cover the O. glaberrima genome - Caiapo (O. sativa japonica) x O. glaberrima MG12

Populations : • 3 parents récurrents O. sativa

IR64 - Caiapo - Curinga • 2 accessions d’O. glaberrima• 4 espèces sauvagesO. rufipogonO. meridionalisO. barthiiO. glumaepatula

Development of chromosome segment substitution lines (CSSLs)

CSSLs: Mapping of a major resistance gene to Rice stripe necrosis virus from

O. glaberrima

Gutierrez et al, BMC Plant Biol. 2010Caiapo x MG12

But the construction of CSSls is hampered by reproductive barrier between the two cultivated species

O. sativa x O. glaberrima reproductive barrier

• One of the strongest post-zygotic reproductive barrier in Oryza species

• F1 hybrids:

– Totally male sterile

– Partially female sterile

– S1 is the main factor (Sano 1990)

• S1 limits the use of O. glaberrimain breeding

Fine mapping of the S1 locus

RMC6

_216

78

RM19

357

C6_2

1774

C6_2

1778

C6_2

1804

C6_2

1824

C6_2

1683

7

RMC6

_218

51

RMC6

_219

42

RMC6

_219

89

RMC6

_220

28

RMC6

_220

46RM

1935

9E1

920

E050

6

2,1702,170 2,175 2,180 2,185 2,190 2,195 2,000 2,205

NipponbareMb

Male factor (Koide et al., 2008)

Female factor

•The S1 locus is a complex locus involving a female effect identified by a very strong segregation distortion in F1 and a male effect characterised by a remnant pollen sterility in advanced progeny

Efforts to dissect the different components identified :•Female factor in a 27.8 kbp region nested in the male factor region•Both male and female gamete elimination are probably controlled by the

same factor(s)

3 O. sativa accessions

X

F1 Hybrids

Backcross BC1F1

• MAS for S1s allele (5%)

• Selection for fertility restoration (50%)

Diversified Back cross Inbred Lines BIL (BC1F4)

•SSR – SNP Génotyping• Evaluation for trait of interest with partners

25-30 representative accessions of O. glaberrima

Development of interspecific bridges between the cultivated rice species

Efficiency of S1s selection and increasing of the fertile plants frequency in first BC generation (5% to 40%).

• To expand and to facilitate the use of the African rice introgressions in O. sativa

iBridges outcomes

• 75 pools of BILs, compatible to O. sativa and containing 20-25% of O. glaberrima genes are under construction

• Efficiency of MAS S1s selection and increasing of the fertile plants frequency at first BC generation (5% to 40%)

• Friendly-use markers are available around the the S1 sterility gene

A second generation of Ibridges lines is envisageable by :

• Increasing the mapping of the other interspecific sterility genes• Combined selection of S1 and other sterility loci• Improving crossing scheme and more efficient strategies for future selection

of materials

Expanding the iBridges concept for developing additional iBridges between O. sativa and its other AA-genome (wild) relatives

Provide a broad access of the genetic diversity in the AA species complex (O. rufipogon – O. meredionalis etc..)

Nested Association Mapping (NAM)• Initially developed for Maize (Ed Buckler’s lab)

• More recent Initiatives for sorghum, wheat, Arabidopsis…

• It combine the power of Association Mapping and Fine Mapping to obtain an Ultra-High resolution QTL mapping (gene level)

• Aim: to develop rice NAM, with special focus on drought tolerance

• IRD-CIAT (M. Lorieux) & WARDA (M.N. Ndjiondjop)

Principles : • to develop several inbred populations from a common recurrent parent and a

diversified set of selected varieties and donors• The recurrent parent is sequenced (very high coverage)• The varieties and RILs are genotyped by low coverage (GBS – SNP technology)

Then , the resolution allow for the allelic diversity characterization of a majority of genes underlying any important traits of interest.

Example : Heat map for Days-to-Silking QTL effects in Maize

Buckler et al 2009

Rice NAM

x IR64

Founders : O. sativa cultivars popular in

Africa & LA

All crossed to IR64

SSD

F7

123.....

Coefficient0.00 0.25 0.50 0.75 1.00

Nerica5

CG14

Nerica4

ITA150

WAB56-104

Nerica3

WAB181-1

WAB96-3

IAC165

FARO11

Moroberekan

Lac23

IRAT104

Chocoto

Co39

Rock5

Gambiaka

IET3137

ITA306

BG90-2

Cisadane

Nerica19

IR13240

Tox3100

Suakoko

Kogoni91-1

IR64

Foniap2000

BW348-1

Bouake189

Djoukeme

WAB638-1

ITA212

B6144

FARO31

WAB96-1-1

indica

japonica

NAM Parental lines Diversity (SSRs)Variety of traits

Agronomicyield, aroma, N responsivity, grain quality, etc

Abiotic stresses toleranceDrought, iron toxicity, etc

Biotic stresses: weed competitiveness, AfRGM, Blast resistance, etc

• 20 NAM parental lines

• 15 control varieties

• 36 SSRs

Current status & perspectives• CIAT: 2,000 lines, 10 combinations, F7 harvested• AfricaRice: 2,000 lines, 10 combinations, F7 harvested• Seed exchange on going

• Genotyping: • Low resolution WGS / imputation

(IRIGIN project)• Genotyping By Sequencing

(w S. Dellaporta, Yale Uty)• Phenotyping:

• GRiSP Phenotyping Network

• Tools for data analysis: MapDisto

IR64 x WAB638-1

F4 Plants