GRM2013: Establishing a molecular breeding program based on the aluminum tolerance gene AltSB and the P efficiency QTL Pup-1, for increasing sorghum production in Sub-Saharan Africa -- F Rattunde
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GRM2013: Establishing a molecular breeding program based on the aluminum tolerance gene AltSB and the P efficiency QTL Pup-1, for increasing sorghum production in Sub-Saharan Africa -- F Rattunde
1. Establishing a molecular breeding program
based on the aluminum tolerance gene AltSB
and the P efficiency QTL Pup-1, for
increasing sorghum production in Sub-
Saharan Africa
GCP GRM 27-30 September, 2013
Fred Rattunde with
Willmar Leiser, Bob Schaffert, Jurandhir
Magalhaes, Sam Gudu, Soumana
Souley, Tom Hash, Eva Weltzien
2. Goal and Objectives
• Goal: Enhance sorghum resilience and
productivity in low-P and high Al
saturation environments in Africa
• Objectives:
– Create random-mating (ms3) source
populations with diversity for low-P
adaptation and Al tolerance combined with
required grain, glume, and plant traits
– Apply molecular marker selection tools for
Low-P and Al tolerance to effectively derive
superior lines from the random-mated
populations for the predominant low-input
production systems in Sub-Saharan Africa
4. Mali Low-P Population Donors
Donor Parent Type Origin
< Delay
Maturity in -P
> Grain Yield
in –P
1 CMDT45 LR Mali x
2 Seguetana LR Mali x
3 IS15401 LR Cameroon x
4 B2-3 LR Burkina x
5 B2-5 LR Burkina x x
6 DouaG LR Mali x
7 CSM660 LR Mali x
8 Lina3 Bred Population x
9 NafalenP6 Bred Population x
10 Dagnali Kossurou LR Mali x
• Ten donor parents: selected based on yield in Sko’06 and ’07
–P envs. (standardized) or < delay flowering in –P vs +P in
2009 Sko
• Source of Male-sterility: 19 Progenies originating from
farmers’ selections from Diversified Guinea populations
6. Low-P/Al-tol Population advancement
Rainy season 2012: Final random-mating of 23 bulks,
representing different donor combinations (8 reps,
randomized)
Harvested 444 preferred and 251 acceptable panicles
from sterile plants, created Population bulk
Offseason 2012/2013: 1500 S0 plants produced 571
S1 lines (50% sterile, some plants did not reach
flowering)
Rainy season 2013: 571 S1-lines
grown for selfing, preliminary
assessment of critical traits
for adaptation, and sampling
for GBS
8. Low-P and Al-Tolerance in Niger
Donor Parent OS 2009/10 RS 2010 OS 2010/11
RS 2011 -
drought RS 2012 -flood
1. Lonkosaw X ms3 pop F2 RM RM - failed RM - failed
2. Macia X ms3 pop F2 RM RM - failed RM - failed
3. ST9007-5-3-4 X ms3 pop F2 RM RM - failed RM - failed
4. Mota Maradi* X ms3 pop F2 RM RM - failed RM - failed
5. Bagoba X ms3 pop F2 RM RM - failed RM - failed
6. Jenjari V328 X ms3 pop F2 RM RM - failed RM - failed
7. Serena X ms3 pop F2 RM RM - failed RM - failed
8. Male V332 X ms3 pop F2 RM RM - failed RM - failed
9. Kaoura X ms3 pop F2 RM RM - failed RM - failed
10. ST9007-5-4-3 X ms3 pop F2 RM RM - failed RM - failed
11. Balankoma X ms3 pop F2 RM RM - failed RM - failed
12. 90SN-2 X ms3 pop F2 RM RM - failed RM - failed
13. Socomba 162 X ms3 pop F2 RM RM - failed RM - failed
14. SSD35 X ms3 pop F2 RM RM - failed RM - failed
15. L28 X ms3 pop F2 RM RM - failed RM - failed
16. MDK X ms3 pop F2 RM RM - failed RM - failed
17. SC 566 --- --- --- RM - failed RM - failed
* might have AltSB
9. Field testing of EMBRAPA BC lines
in Niger 2013
• Evaluation of BC –lines with IRAT 204 and local parent
with ALTSB allele introduced, received from EMBRAPA at
Sadore and Kollo
Sadore 2013
SC 566CSM-63E
11. Al-Tolerance Lab Testing
Phenotyping
• Al- seedling screening facility
installed at Samanko, Mali
• Set of selected diverse lines
from ICRISAT panel tested in
2012
• Good correspondence with
results obtained in Brazil
Genotyping for AltSB with
KASPar
• 188 sorghum genotypes from
WCA screened for AltSB
• 9% found to have AltSB alleles
• High frequency of Guinea-
race
Name Race
SAKOYKA-BA Guinea
CSM 485 Guinea
DIO-A Guinea
DOUA-G Guinea
IS 15401 Guinea
SL22 Guinea
MDK Durra
EL KURUMBASSAU Guinea-Caudatum
MOTA Caudatum-Guinea
EL RURUKA Caudatum-Guinea
EL DELE Guinea
(IS 15401*98-SB-F2-78)-3-1 Guinea-Caudatum
(IS 15401*98-SB-F2-78)-7-3 Guinea-Caudatum
(IS 15401*98-SB-F2-78)-7-5 Guinea-Caudatum
TOROBA Guinea
SL22-1 Guinea
IS 30804 Guinea
12. GWAS for low P adaptation
21% 40% 50%
188 genotypes
200k SNPs
Phenotyped in 14 –P environments
13. SNPs for GY in low P
similar to Sucrose-
phosphate synthaseAltSB
specific low P SNP
non-specific low P SNP
LD between these SNPs and AltSB markers: R²<0.1
14. AltSB effect on low-P grain yield
Grain yield in low P
Grain yield ratio –P/+P
Al-tolerant allele
16. Proposed Population Progeny Testing
• 571 S1s derived from lowP and Al-Tol Mali
Population to be genotyped by GBS and
allele specific markers (AltSB and Pup-1)
to:
– Determine Allele freq Altsb and Pup-1
– Conduct genomic selection (best and worst
genotypes) using marker effects from
previous prediction set to validate utility in
independent population
– Conduct selection using AltSB, Pup-1 and the
SNPs identified with GWAS
– Compare effectiveness of different approaches
based on 2014 field phenotyping
17. Conclusions: Implementing molecular
breeding for LowP/Al_tol
(from Genetic Resource to Farmers’ Field)
• Sorghum RM Populations with diversity for
lowP and AltSB and key traits for varietal
adoption available in Mali and Kenya
• Field phenotyping for LowP established,
successful, but # of sites limited
• EMBRAPA Lab Al_tol screening method
established in Mali
• Molecular approaches for selecting LowP
adaptation showing potential
• Phenotyping and genotyping LowP
Population derived progenies: test molecular
methods (GS & MAS) for applied breeding
for Low-P production conditions
18. Publications and Acknowledgements
• Leiser W, Rattunde F, Piepho HP,
Parzies H. 2011 Getting the
most out of sorghum low-
input field trials in West-
Africa using spatial
adjustment.
• Leiser, W.L., H.F.W. Rattunde, H.-
P. Piepho, E. Weltzien, A. Diallo,
A.E. Melchinger, H.K. Parzies, and
B.I.G. Haussmann. 2012.
Selection Strategy for
Sorghum Targeting
Phosphorus-limited
Environments in West Africa:
Analysis of Multi-environment
Experiments. Crop Science
52(6): 2517.
• IER: Abdoulaye Diallo,
• IPR: Chiaka Diallo
• INRAN: Soumana Souley
• Moi University: Sam Gudu
• University Hohenheim:
Willmar Leiser, H.-P. Piepho,
• Embrapa: Jurandhir
Magalhaes, R. Schaffert, soil
science
• ICRISAT: F.Rattunde,
E.Weltzien
• Cornell University: Sharon
Mitchell
Funding:
GCP – ALTFIELD, CG CI
McKnight Foundation: WA CoP
BMZ: Abiotic Stress Project