New genetic tools to improve dryland crop adaptation to abiotic

Report
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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•
•
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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!

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