Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India
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http://chickpealab.ucdavis.edu
United States, Ethiopia, India, Pakistan, Turkey, Australia, Canada, Morocco
Domestication Modern breeding
Regi
onal
div
ersi
ficati
on
Wild
Rel
ative
s
Abiotic stress, Biotic stress, Nitrogen fixation, Nutrition, Agronomic traits
Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India
Chickpea is the world’s 2nd most important grain legume and critical to food security in
much of the developing world
•Stagnant yields•Susceptible to pathogens, pests and abiotic stress
• Drought• Heat• Pests and Disease• Nitrogen fixation• Nutrition• Soil adaptation• Domestication
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Domestication Modern breeding
Regi
onal
div
ersi
ficati
on
Wild
Rel
ative
s
6.7M variants 0.172 M variants
Wild species Modern elite varieties
~95% loss of variation
26 representative wilds 29 modern elite varieties
Crop improvement requires a source of variation
Nitrogen fixation and domestication
Migrating adaptive alleles from wild to cultivated
Drought tolerance
Sponsor and Partner Institutions
Our target countries
• Regularly impacted by climatic extremes
Ethiopia• 40% of Africa’s chickpea production
• Historical focus of domestication
India• Major consumer and producer of chickpea.
• Among the lowest yielding countries.
Abiotic and biotic stress drive cultivation practices
Accessing, characterizing and utilizing genetic variation
Breeding needs variation
Wild systems: Starting in south-eastern Turkey
Turkey
Syria Iraq
Iran
C. a
rietin
um
C. r
etic
ulat
umC
. ech
inos
perm
umUsing all 19 variables for Bioclim on DIVA-GIS
Post-domestication diversification: landraces
Nik
olay
Vav
ilov
Time-series analyses: how effects of G changed over ~100 years of climate / environment change
19111914
19171920
19231926
19291932
19351938
19411944
19471950
19531956
19591962
19651968
19711974
19771980
19831986
19891992
19951998
20012004
0
500
1000
1500
2000
2500
3000
# of
Acc
essio
ns
# Date of acquisition
Perc
ent o
f col
lecti
on
Ethiopia*(87) India (261) Turkey (75)
39
We explored chickpea’s center of origin over 56 days in 2013 and 100 days in 2014/15 at ~50 sites
Egil
1 2
3
4
5
6
C. a
rietin
um
C. r
etic
ulat
umC
. ech
inos
perm
umIn the wild: 1002 Km
How do you survey variation for climate resilience?
Altitude: 600m – 2,000mRainfall gradients
SeasonalityTemperature
HumiditySoil types
Microbial communitiesCo-occurring species
Understand environmental heterogeneitysoilsco-occurring speciesabiotic factorsspatial and temporal variation
DNA from thousandsGBS and WGSpopulation genomicsin situ association genetics
C. reticulatum
C. echinospermum
Egil
1 2
3
4
5
6Predominant focus of historical germplasm
1,100 accessions 2013~1,000 accessions 2014/2015
Cicer reticulatumCicer echinospermum
Kara
bace
S2DR
Guna
s
Cerm
ic
Dest
ek
Guve
n
Deric
i
Kesa
ntas
Oya
li
Sarik
aya
Kaya
tape
Kalk
anEgil
Bese
vler
Savu
r
Bari2
Bari3
Bari1
Cudi
1Cu
di2
Sirn
ak
Ort
anca
How will we make the wild alleles useful for breeding?
Evaluation Strategies
In situ association genetics for candidate gene nomination
Association genetics with phenology-normalized NAMs
Advanced backcross introgression lines
Breeding
Ecology and population genomics
Phenotyping
Trait discovery
Genomics-drivenIntrogression
Domestication:10-12,000 years ago
Secondary diversification:~6,000 years ago
Secondary diversification:~3-4,000 years ago
6.7M variants
0.172 M variants
•3 High quality reference genomes: BioNano OM, PacBio, Illumina, dense SNP maps
•26 deep representative wilds (30X)
•250 moderate wilds (10X)
•750 shallow wilds with imputation
•29 cultivated from international project
Developing genomic platforms
Wild species Modern elite varieties
~95% loss of variation
Cicer reticulatumCicer echinospermum
Kara
bace
S2DR
Guna
s
Cerm
ic
Dest
ek
Guve
n
Deric
i
Kesa
ntas
Oya
li
Sarik
aya
Kaya
tape
Kalk
anEgil
Bese
vler
Savu
r
Bari2
Bari3
Bari1
Cudi
1Cu
di2
Sirn
ak
Ort
anca
270 accessions in the multi-lateral system.
Hundreds of additional accessions in partner institutions in Turkey
>26 wild accessions x 5 elite cultivars in pre-breeding pipeline (NAMs and ABIs).
~5,000 Segregating F3
Developing genetic resources: pre-breeding, trait and gene discovery
Microbes impart functional properties (i.e., “health”) to their plant hosts.
… but we lack a solid understanding of these phenomena
Micronutrient uptake
Drought Tolerance
Phosphate solubilization
Disease Tolerance
Nitrogen Fixation
Micronutrient uptake
Drought Tolerance
Phosphate solubilization
Disease Tolerance
Nitrogen Fixation
?
? ?
?
?
??
?
?
? ??
Systematically collect and characterize chickpea’s microbiome
Ethiopia
India
Turkey(Cicer reticulatum)
USA
Canada
Australia
Turkey(Cicer echinospermum)
Global collection of Nitrogen-fixing Mesorhizobium
X
X
X
X
X1
2 4
3 5
6
7
Chickpea’s microbiome
PathogensSymbiontsCommensals
Host
Environment
Genetic resiliency to extreme and variable climates requires a holistic approach
Abiotic stress: Drought, heat, cold
Biotic stress: Fusarium, Pod borer, (Ascochyta)
Nitrogen: Symbiosis and nitrogen “metabolism”.
Nutrition: Inorganic and organic composition.
Agronomic traits: Architecture, flowering time.
Phenotyping and trait targets
UC DavisDoug CookVarma PenmetsaNoelia CarrasquillaAlex GreenspanBetsy AlfordSusan MoengaLisa VancePeter ChangBullo MamoBrendan RielyGul AbbasDagnachew BekeleZahra Samiezade-YazdLei FengPing SongShraddha Suman
Florida International UnivEric von Wettberg
ICRISATVincent VadezHari Sharma
Assam Agric UnivBidyut Sarmah
Punjab Agric UnivSarvjeet Singh
Harran UniversityAdbullah Kahraman
Dicle UniversityBekir BukunFatma Basdemin
AARIAli PeksusluLerzan AykasAbdullah Inan
Turkish Ministry of AgAbdulkadir AydoganHusseyin OzcelikMahmut Gayberi
CSIRO WAJens BergerJohn ThompsonWendy VanceJudith LichtenzveigGraham O’Hara
Banaras Hindu UniversityBirinchi Sarma
UAS-DharwadBhuvaneshwara Patil
EIARAsnake FikreLijalem BalchaKassaye DinegdeZehara DamtewDagnachew BekeleTsegaye GetahunGashaw BedadaSultan Yimer
Addis Aababa Univ Kassahun TesfayeFassil AssefaMasresha Fetene
USCSergey NuzhdinPeter ChangVasantika SinghMatilde CordeiroMin-Gyoung Shin
ICARDAMichel GhanemSripada Udupa
Ege UniversityBhattin Tanyolac
U SaskatchewanBunyamin Taran
Research Partners and Institutions
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