New genetic tools to improve
dryland crop adaptation to abiotic
stress and improve crop resistance
to pests and diseases
C.T. Hash et al.
Presented at the symposium:
DRYLAND CROP PRODUCTION AND CLIMATE VARIABILITY:
40 YEARS OF RESEARCH PARTNERSHIPS WITH ICRISAT IN WCA
during CORAF Science Week, 14-18 May 2012, in Ndjamena, Tchad
Co-workers
• ICRISAT colleagues: S.P. Deshpande, S. Chandra, S. de Villiers,
R.T. Folkertsma, F. Hamidou, M. Kolesnikova-Allen, J. Ndjeunga,
T. Nepolean, P. Ramu, O. Riera-Lizarazu, H.F.W. Rattunde,
F. Sagnard, S. Senthilvel, T. Shah, S.D. Singh, R.K. Srivastava,
Supriya, M. Thudi, V. Vadez, R.K. Varshney, & E. Weltzien;
• Other CGIAR colleagues: M. Blümmel (ILRI), & H. Leung (IRRI);
• WCA NARS partners: I. Angarawai, I.D.K. Atokple, F. Padi,
M.D. Sanogo, O. Sy, & R. Zangré;
• American ARI partners: J. Bennetzen, E.S. Buckler, K.M. Devos,
S. Kresovich, S.E. Mitchell, A.H. Paterson, & J.P. Wilson;
• Australian ARI partners: A. Borrell & D.R. Jordan
• British ARI partners: W.A. Breese, C.J. Howarth, E.S. Jones,
J. Scholes, D.S. Shaw, J.R. Witcombe, & R.S. Yadav;
• French ARI partners: G. Bezançon, C. Billot, M. Deu,
J-C. Glaszmann, J-F. Rami, D. This, & Y. Vigouroux; and
• German ARI partners: A. Buerkert, H.H. Geiger,
B.I.G. Haussmann, & H.K. Parzies
Presentation outline
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ICRISAT-mandate crops
Molecular marker development
Genetic diversity assessment
Molecular marker-based linkage maps &
aligned genome sequences
• QTL mapping
– Conventional bi-parental populations
– Association mapping with inbred germplasm panels
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QTL validation
Marker-assisted selection
Farm-level impact to date
Opportunities
ICRISAT-mandate crops in WCA
Sorghum
Groundnut
Pearl millet
1980s
2012
Molecular marker development
Restriction Fragment Length
Genotyping-by-Sequencing SinglePolymorphisms (RFLPs)
Nucleotide Polymorphism Haplotypes
• 1980s technology
• Current technology
• Slow, laborious, expensive &
• Quicker, cheaper & more
incomplete genome coverage
complete genome coverage
• US$2.50 per data point
• US$40 for 80,000+ data points
• DNA isolation
• DNA isolation
• DNA digestion
• DNA digestion
• Electrophoretic separation
• DNA fragment ligation
• Probe with labels clones
• 95X or 383X pooling
• Develop image
• Skim sequencing 0.1X to 0.3X
• Score polymorphism
• Automated SNP allele scoring
• 300+ polymorphic RFLP loci
• ca. 275,000 polymorphic
for pearl millet
GBS-SNP loci for pearl millet
Genetic diversity assessment
Full data set
by origin
East Asia,
India,
Middle East,
Western Africa,
Central Africa,
Eastern Africa,
Southern
Africa, North
America,
Latin America,
& Australia
New tools
for sorghum
3365entry GCP
Sorghum
Composite
Germplasm
Collection
Genetic diversity assessment
wild
bicolor
caudatum
durra
guinea
margaritiferum
kafir
intermediate
Molecular marker-based linkage
maps & aligned genome sequences
Sorghum genome sequence
• Kresovich et al. (2005) Plant
Physiology 138:1898–1902
• Paterson et al. (2009)
Nature 457:551–556
Physical map of sorghum SSRs
• Ramu, Deshpande et al. (2010)
Molecular Breeding 26:409–
418
Groundnut genome sequence
• Peanut-CRISP led
consortium w/ ICRISAT as
partner
Pearl millet genome sequence
• ICRISAT led consortium
building on rice, sorghum,
& Setaria italica aligned
genome sequences
Millets: genetic & genomic
resources
• Dwivedi et al. (2011) Plant
Breeding Reviews 35:247–375
Physical map of
sorghum SSRs
Ramu, Deshpande
et al. (2010)
Molecular
Breeding 26:
409–418
QTL mapping
Conventional bi-parental populations
• Downy mildew resistance
mapping in pearl millet
– Jones et al. (1995)
Theoretical & Applied
Genetics 91:448–456
• Striga hermonthica
resistance mapping in
sorghum
– Haussmann et aI. (2004)
Theoretical & Applied
Genetics 109: 1005–1016
Association mapping w/ germplasm panels
• Identification of PhyC as a
major gene controlling
flowering in pearl millet,
with major shifts in allele
frequency in Niger
between 1976 and 2003
– Vigouroux et al. (2011) PLoS
ONE 6(5):e19563
• Candidate-gene approach
to mapping flowering
genes in West African
sorghum
– Bhosale et al. (2012) BMC
Plant Biology 12:32
QTL validation by
MABC & phenotyping
Sorghum stay-green
• Trait mapped independently in
Australia & USA (Purdue & TAMU)
• MABC to assess utility of 6 QTLs from
donor B35 = BTx642 in different
genetic backgrounds
– Hash et al. (2003) Field Crops Research
84:79–88
– SARI-led project (Water for Food Challenge
Programme), & ICRISAT-led project
(Generation Challenge Programme )
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ICSV 111 & S 35
ISIAP Dorado
IRAT 204
R 16
Subsequently tested in Ethiopia
(release pending for 4 introgression
lines), Ghana (again), India, & Sudan
QTL validation by
MABC & phenotyping
Sorghum Striga resistance
• QTLs mapped based on
phenotyping in Kenya & Mali
• Marker-assisted backcrossing
to introgress resistance from
donor N13 into locallypreferred varieties from
– Eritrea: ???
– Kenya: Failed as breeding
program got too far ahead of
marker-data generation
– Mali: Successful
– Sudan: Successful
 advancing towards
cultivar release
Marker-assisted
selection
Backcrossing
Genome-wide selection (GWS)
Marker-assisted back-crossing
(MABC)
• Pearl millet
Testing GWS for
downy mildew
resistance, Striga
resistance, &
grain yield in
pearl millet w/
support from
the McKnight
Foundation
– Downy mildew resistance
– Terminal drought tolerance
– Stover nutritional quality (foliar
disease resistance)
• Sorghum
– Shoot fly resistance
– Stay-green component of drought
tolerance & ruminant nutritional
value
Backcross nested association
mapping (BCNAM)
– Jordan et al. (2011) Crop Science
51:1444–1457
Testing GWS for sorghum in
improvement in Mali w/ support
from the Generation Challenge
Programme
Farm-level impact
to date
Nothing in WCA to date, but earlygeneration MABC products in farmerpreferred backgrounds are in pipeline
An excellent example from India:
• 15 years of ARI/ICRISAT/
NARS collaboration led to
release of pearl millet hybrid
“HHB 67 Improved” in 2005
• By 2011 this maintenance
breeding product was grown
on >950,000 ha in Rajasthan
& Haryana states, with annual
net benefits to farmers
estimated at US$20 million,
with US$13.5 m to growers
there and US$6 m to seed
producers in Andhra Pradesh
Emerging
opportunities
GbS-SNPs as a tool for orphan crops Aligned crop genome sequences
White fonio accessions from Mali
Pearl millet
Groundnut
Mapping pearl millet
Striga resistance
• Recently remade cross of
wild & inbred parents as
mapping population received
from US-based partner was
mixed up
• Produced new plant x plant
F1s & advanced these to F3
progenies with DNA sampling
of 300 F2 plants
– New population segregates for
a single recessive gene for
male-sterility
– Also likely to segregate for root
traits, including P-acquisition
ability
Mapping pearl millet
tolerance to low soil P
• Assessing performance of
150+ diverse inbreds, & their
testcross hybrids, under low
and high soil P conditions
• Genotyping with SSR, DArT,
& GbS-SNP markers
• Merge data sets for
Association Mapping
Similar approach taken in India to
identify new QTLs for terminal
drought tolerance using a newly
developed Pearl Millet inbred
Germplasm Association Panel
(PMiGAP)
Value-chain participatory
genome-wide selection
• GbS-SNP markers saturate
genome enough to permit
effective marker-assisted
selection for any heritable
trait in any species
• Need greater than ever for
prioritization of breeding
targets, use of appropriate
experimental designs,
generation of high quality
phenotype data, and
thorough statistical analysis
of the resulting data sets
• Thank you!
• Nagodé!
• Fofo!
• Merci de
votre
attention!