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
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
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
Hinweis der Redaktion
{"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"}