Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India

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

11

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

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0

500

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# of

Acc

essio

ns

# Date of acquisition

Perc

ent o

f col

lecti

on

Ethiopia*(87) India (261) Turkey (75)

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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

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? ?

?

?

??

?

?

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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