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Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
Th1_New approaches, resources and tools for gene discovery
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Th1_New approaches, resources and tools for gene discovery

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3rd Africa Rice Congress …

3rd Africa Rice Congress
Theme 1: climate resilient rice
mini symposium: making greater use of Africa's indigenous genetic diversity
author: Alain Ghesquière/M. Lorieux

Published in: Technology
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  • {"8":"Place dans l’expose ?\nSupprimer tableau\nSimplifier encore\n","3":"(Alain)\nAlléger le texte\nreprendre la figure de 13\nEliminer la référence a Kit\n"}
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    • 1. New approaches, resources and tools for gene discovery and breeding in rice Alain Ghesquière/M. Lorieux
    • 2. 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
    • 3. Development of chromosome segment substitution lines (CSSLs) 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) Populations : • 3 parents récurrents O. sativa IR64 - Caiapo - Curinga • 2 accessions d’O. glaberrima • 4 espèces sauvages O. rufipogon O. meridionalis O. barthii O. glumaepatula 59 BC3DH lines cover the O. glaberrima genome - Caiapo (O. sativa japonica) x O. glaberrima MG12
    • 4. CSSLs: Mapping of a major resistance gene to Rice stripe necrosis virus from O. glaberrima Caiapo x MG12 Gutierrez et al, BMC Plant Biol. 2010
    • 5. But the construction of CSSls is hampered by reproductive barrier between the two cultivated species
    • 6. 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. glaberrima in breeding
    • 7. RMC6_22046 RM19359 E1920 RMC6_22028 RMC6_21989 RMC6_21942 RMC6_21851 C6_216837 C6_21824 C6_21804 C6_21778 C6_21774 RM19357 RMC6_21678 E0506 Fine mapping of the S1 locus Nipponbare Mb 2,170 2,170 2,175 2,180 2,185 2,190 2,195 2,000 2,205 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)
    • 8. Development of interspecific bridges between the cultivated rice species • To expand and to facilitate the use of the African rice introgressions in O. sativa X 3 O. sativa accessions 25-30 representative accessions of O. glaberrima 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 Efficiency of S1s selection and increasing of the fertile plants frequency in first BC generation (5% to 40%).
    • 9. 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..)
    • 10. 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 UltraHigh 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.
    • 11. Example : Heat map for Days-to-Silking QTL effects in Maize Buckler et al 2009
    • 12. Rice NAM Founders : O. sativa  cultivars popular in Africa & LA x All crossed to IR64 SSD 1 2 3 . . . . . F7 IR64
    • 13. NAM Parental lines Diversity (SSRs) Nerica5 CG14 Variety of traits Nerica4 ITA150 japonica WAB56-104 Nerica3 WAB181-1 WAB96-3 IAC165 FARO11 Moroberekan Lac23 IRAT104 Chocoto Co39 Rock5 Gambiaka IET3137 ITA306 BG90-2 Cisadane Nerica19 IR13240 Tox3100 indica Suakoko Kogoni91-1 • 20 NAM parental lines • 15 control varieties • 36 SSRs IR64 Foniap2000 BW348-1 Bouake189 Djoukeme WAB638-1 ITA212 B6144 FARO31 WAB96-1-1 0.00 0.25 0.50 Coefficient 0.75 1.00 Agronomic yield, aroma, N responsivity, grain quality, etc Abiotic stresses tolerance Drought, iron toxicity, etc Biotic stresses: weed competitiveness, AfRGM, Blast resistance, etc
    • 14. 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

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