Feed the Future Innovation Laboratory for

Climate Resilient Chickpea

UC Davis

Ethiopian Institute for Agricultural Research

Harran University and Partners

University of Southern California

Florida International University

- Ecology and community genomics to collect and

understand natural variation.

- Development of novel populations for gene

discovery and breeding.

Radically alter the use of adaptive alleles

for climate resilience in chickpea breeding

Rationally de-construct the genetic

potential of wild populations

• Massively parallel ecology, genomics, population

development, phenotyping and breeding.

Developing climate-resilient chickpea

Premises

1.Chickpea improvement is limited by low genetic

diversity within the cultivated gene pool.

2.Wild species hold promise for chickpea improvement,

but …

… existing wild germplasm collections are

inadequate to fully harness natural adaptations.

Factors limiting use of wild material

• No systematic understanding

of natural variation.

• Extreme phenological

differences.

•Magnitude of effort to create a

comprehensive introgression

resource.

Identify, characterize and transfer natural adaptations for

climate resilience from wild species to cultivated chickpea

Cicer reticulatum

Cicer echinospermum

Cicer ariteinum

Migrating adaptive alleles from wild to cultivated

Nitrogen fixation and

domestication

Migrating adaptive alleles from wild to cultivated

N2 nitrogenase

NH3

16 ATP 16 ADP

Atmospheric N Biological N

How would you sample and then dissect genomic (genetic)

potential across a 60,000 square Km of landscape?

Turkey

Syria Iraq

Iran

C.

arietinum

C. re

ticula

tum

C. echin

ospe

rmum

Approach

Survey diverse climatic and edaphic conditions

Phenotypic priorities

• Tolerance to climatic extremes

• Nitrogen fixation resilience

• Disease resistance

• Soil type adaptation

• Nutrient density

• Etc.

Combine

• Ecology

• Population genomics

• Quantitative biology

• Population development – nested association mapping

• Phenotyping

• Introgression Breeding

Multiple partners

• US, Ethiopia, Turkey, India, Australia, Canada

We explored chickpea’s center of origin over 56 days

Egil

1 2

3

4

5

6

C. reticulatum

C. echinospermum

City/Province Site/location Lat Long Elev Loc ID from Seed Pictures

Adiyaman Oyali / Besni / Adiyaman 37.7337 37.8030 931.27 Oyali all 29 ret

Diyarbakir Cermik / Diyarbakir 38.0537 39.4219 774.16 Cermik all 10 echi

Diyarbakir Egil/Diyarbakir 38.2744 40.0647 986.49 Egil 15 ret 01 Cpinna

Diyarbakir Gunasan/Cermik Diyarbakir 38.0113 39.3747 839.56 Gunasan 05 echi-ret

Diyarbakir Kalkan/Egil/Diyarbakir 38.1618 40.0854 855.08 Kalkan all 16 ret

Diyarbakir Kesentas/Ergani/Diyarbakir 38.2039 39.6067 883.41 Kesentas all 23 ret

Mardin Baristepe / Midyat / Mardin 37.4855 41.3732 975.04 Baristepe 1 all 14 ret

Mardin Baristepe / Midyat / Mardin 37.4592 41.3770 958.62 Baristepe 2 (Muhtar) all 10 ret

Mardin Baristepe / Midyat / Mardin 37.4727 41.3925 962.92 Baristepe 3 (Sal) all 29 ret

Mardin Besevler mezra/Savur/Mardin 37.5167 40.8549 900.41 Besevler all 19 ret

Mardin Dargecit/Mardin 37.5337 41.7282 866.00 Dargecit all 22 BIJUGUM

Mardin Dereici/Savur/Mardin 37.5443 41.0161 996.27 Dereici all 17 ret

Mardin Kayatepe/Savur/Mardin 37.5192 40.9382 1085.86 Kayatepe all 16 ret

Mardin Kilavuz/Dargecit/Mardin 37.4628 41.8104 862.41 Kilavuz ALL 29 BIJUGUM

Mardin Sarikaya / Midyat / Mardin 37.5473 41.0203 1004.61 Sarikaya 15ret 02BIJUGUM

Mardin Savur / Mardin 37.5466 40.9077 914.56 Savur all 04 ret

Sirnak Cudi mountain / Sirnak 37.4268 42.5027 1365.43 Cudi 17 ret 02 BIJUGUM

Sirnak Cudi 2 mountain /Sirnak 37.4317 42.4931 1289.24 Cudi 2 all 17 ret

Sirnak Sirnak / Sirnak 37.5436 42.4539 1695.25 Sirnak all 26 ret

Urfa Destek/Siverek/Urfa 37.7802 39.1730 740.06 Destek all 17 echi

Urfa Guvenli/Siverek/Urfa 37.7418 39.2392 509 Guvenli

Urfa Karabahce/Siverek/Urfa 37.8245 39.7630 1264.41 Karabahce all 27 echi

Urfa Ortanca /Siverek/Urfa 37.4734 39.5632 861.04 Ortanca all 11 echi

Urfa Siv-Diyar road 130.Km from Urfa 37.8212 39.6417 1115.82 Siv-Diyar all 16 echi

Sampled 23 sites across the accessible range

• GPS spatial scale

• 839 plants as DNA

• 422 plants as seed

• >150 soil samples

• Climate data: regional, local and

micro-environment

• Corresponding collection of

symbiont strains/genomes

• Root microbiome

Cicer reticulatum Cicer echinospermum Cicer bijugum Cicer pinnatifidum

Surveyed populations 18 7 13

Collected populations 14 6 3 1

Number of accessions 283 88 64 4

C. reticulatum C. echinospermum C. pinnatifidum Pisum Lens

Annual rainfall (mm) 0-280

280-380

380-530

530-800

700 m

1,700 m

1,000 m

900 m

800 -1,000 m

Spatial, Environmental and Altitudinal Gradients

PC1: Temperature and rainfall gradient. 42% of variance. Increase

latitude = decreased temperature rain.

PC2: Rain, RH and sunshine distribution between vegetative vs

reproductive phases. 28% of variance. High elevation = high veg rain,

and rep phase with low rain, high sunshine and low RH

Sampling Environmental Gradients

A typical oak-pistachio rockland

Genome Sequence Data • ~1,200 Genomes by RAD for initial diversity

• ~200 genomes at 10x for most frequent alleles

• ~1,000 genomes at low WGS for allele frequencies and population

genomics studies, as well as imputation.

Population Genomics •Correlate allele frequencies among like environments to identify

candidate genomic intervals and genes.

•Estimate the nature of local selection based on environment, soil and co-

occurring species data.

•Genome scans for evidence of selection: diversity, LD, hard vs soft

sweeps, modeling candidate gene pathways.

Population Development, Phenotyping, Breeding • Develop purpose-driven NAM populations by crossing for Association

Studies; normalize phenology and growth patterns.

• Develop Chromosome Introgression lines for breeding.

• Massive multi-location phenotyping for a diversity of traits.

Sequencing of the chickpea genome An international consortium

RAD sequencing of 1,215 genomes

Opportunity to understand population structure,

genetic diversity, prioritize WGS, and target

genotypes for population development, etc.

Numerous metrics support division of the

progenitor into distinct groups and

populations

Co

ord

. 2

Coord. 1

Principal Coordinates (PCoA)

Baristepe1

Baristepe2

Baristepe3

Bereslever(4)

Dereichi(5)

Egil(6)

Kalkan(7)

Kayatepe(8)

Oyali(9)

Sarikaya(10)

Savur(11)

Sirnk(12)

Kesentas(19)

Yenil(20)

Control(21)

PCoA: Subdivision within Cicer reticulatum, the

immediate wild progenitor of cultivated

Estimates of populations based on STURCTURE

4 within C. reticulatum, 1 echinospermum, arietinum

>4 populations of the

wild progenitor

Predominant focus of

historical germplasm

cu

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Cicer reticulatum Cicer echinospermum Cicer arietinum

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Cicer reticulatum Cicer echinospermum Cicer arietinum

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Cicer reticulatum Cicer echinospermum Cicer arietinum

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Cicer reticulatum Cicer echinospermum Cicer arietinum

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Reverse introgression

20 wilds x 5 elites = 100 pops

Normalize for cultivated

phenology and growth habit

Quasi-domesticated wild

RILs

20 diverse

wilds

5 adapted

elites

5,000

normalized

NAM-RILS

Breeding-ready

wild introgression

lines

Forward introgression

Segmental introgression of

wild genome intervals in

UC Davis

Doug Cook

Varma Penmetsa

Noelia Carrasquilla

Alex Greenspan

Peter Chang

Bullo Mamo

Sintayehu Mekonnen

Mulualem Kassa

Florida International Univ

Eric von Wettberg

Yadira Reynaldo

Vanessa Sanchez

Damian Nesbeth

USC

Sergey Nuzhdin

Hamdi Kitapci

Wendy Vu

Matilde Cordeiro

Joseph Dunham

MSU

Maren Friesen

Jimmy Woodward

Elanor Siler

Harran University

Adbullah Karhaman

Dicle University

Bekir Bukun

Turkish Ministry of Ag

Abdulkadir Aydogan

Huseyin Ozcelik

Mahmut Gayberi

CSIRO WA

Jens Berger

ICRISAT

Rajeev Varshney

Donghyn Kim

Aamir Kahn

EIAR Ethiopia

Asnake Fikre

Lijalem Korbu

Et al.

CSIRO

U Saskatchewan

Bunyamin Taran