The document discusses innovative approaches for gene discovery and breeding in rice, focusing on the utilization of wild rice species to introduce valuable alleles into cultivated rice, notably through the development of chromosome segment substitution lines (CSSLs). It highlights the challenges posed by reproductive barriers between different rice species, specifically the s1 locus affecting fertility. Additionally, the document outlines the progress in developing interspecific bridges and nested association mapping to enhance drought tolerance and other traits in rice varieties.

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