building the base: widening the genetic & adaptive …...sites acc. sites acc. sites acc. sites...

Building the base: Widening the genetic & adaptive

diversity of chickpea

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An alternative Middle East:

centre of plant and animal domestication

Carlos A. Driscoll et al. PNAS 2009;106:9971-9978

Abbo, S, Berger, J & Turner, N. FPB 2003; 30: 1081-1087

Chickpea

12,500

Pea & lentil

11,500-12,500

Domestication: a bottleneck that reduces diversity Domestication syndrome

• Loss of toxicity

• Loss of shattering

• Loss of dormancy etc.

• Increase in grain size etc.

The challenge: improve on ancient domestication by harnessing the remaining (diminishing) bio diversity

We need genetic diversity to adapt our crops to big challenges:

• Pests & disease

• Changing climate

• ↑ production from a ↓base (arable land, peak oil, P etc.)

Narrow base of chickpea-an old story

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•...to widen the genetic base ...it is imperative to reintroduce traits from across the primary gene pool...

•Moreover, a comparative physiological approach ... may reveal adaptive strategies within the genus currently obscured

Base-broadening of chickpea: new wild Cicer genetic resources| Jens Berger CSIRO

Wild relatives, a potential goldmine for chickpea improvement...

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K. B. Singh, L. Robertson, D., & B. Ocampo, 1998. Diversity for abiotic and biotic stress resistance in the wild annual Cicer species. Genetic Resources & Crop Evolution 45: 9-17.

Trait Asco Blight Fusarium Wilt Leaf miner Bruchids Cyst nematode Vegetative cold

C. arietinum HS Range S HS >HS HS

C. reticulatum HS R T S R-T R

C. echinospermum MS-S R R-T HR T MR

C. judaicum HS R R S MR-T >HS

C. pinnatifidum T-MS Range T HS T Range

C. bijugum T-MS RR T-MS HR-R R HR

C. chorassanicum >HS - HR HS MR-T >HS

C. yamashitae >HS - Range HS R HS

C. cuneatum HS R HR Range T >HS

Base-broadening of chickpea: new wild Cicer genetic resources| Jens Berger CSIRO

Constrained by extremely limited collection:

6 | Base-broadening of chickpea: new wild Cicer genetic resources| Jens Berger CSIRO

Partially explained by political instability:


Extant wild collection

GRDC CSP00185: Collection, phenotyping and exploitation of wild Cicer genetic resources for chickpea improvement. 2014-19

1. Targeted collection to widen the habitat range and genetic diversity of existing collections (2013-15)

2. Extensive phenotyping of traits prioritized as limiting Mediterranean adaptation

3. Coordinate wild Cicer-based phenotyping and population development projects in Australia and Turkey, linking these with international collaborations involving the USA, Canada, Ethiopia and India.

Collection engine room

• Entirely contingent on Turkish collaboration (thanks Abdullah, Abdulkadir, Bekir, Bilal & Cengiz. Also Petr Smykal & Josie Piggin)

• Survey while plants are flowering/podding

• Collect GPS-tagged individual leaf samples for population genomics/population discovery (UC Davis)

• Site description/soil samples (Dicle Uni, Cukurova Uni)

• Mature seed collection & multiplication

• Climate & soil characterization (WorldClim & site-based data)

-widen the habitat range - increase genetic diversity

Base-broadening of chickpea: new wild Cicer genetic resources| Jens Berger CSIRO 10 |

Our target


2013-16 Survey & collections

A B C D

F G

Year C. arietinum C. bijugum C. echinospermum C. pinnatifidum C. reticulatum Sites Acc. Sites Acc. Sites Acc. Sites Acc. Sites Acc.

2013 4 68 6 96 1 4 15 294 2014 1 1 1 8 2 76 20 221 2015 8 100 23 239 6 72 2016 1 9 1 10 1 10 1 2 Total 1 1 6 85 17 282 25 253 42 589

E

H


Discrete distributions

• Almost no overlap among Cicer spp • When found at the same site, then in different soil • Except on the C. ret/ech boundary

Wide ranging habitats bijugum echinospermum pinnatifidum reticulatum

Seasonal rainfall (mm) Average 707 566 568 729

Min 525 510 457 525

Max 843 723 691 879

Altitude (m) Average 989 832 910 1079

Min 761 612 540 607

Max 1311 1269 1364 1694

Min seasonal temp (oC) Average -0.7 -0.8 -2.0 -2.1

Min -2.2 -3.1 -8.3 -5.5

Max 0.4 0.2 1.0 0.0

Max seasonal temp (oC) Average 32.5 31.1 26.5 30.6

Min 30.2 25.5 23.6 26.0

Max 33.8 33.5 31.1 33.7



Climate range within all species

--C. ech —C. ret —C. pin --C. bij

• C. echinospermum: more fragmented than C. reticulatum • C. reticulatum: interesting mix.

• Some populations span widely across sites, some are extremely discrete • Some homogenous & distant • Some heterogenous &overlapping


Complex genetic populations in both C. ech & C. ret

• Some variable across v. small scales

• 5 km from Baristepe to Yolagazi = 3 discrete pops (4, 7, 8)

2013-16 Survey & collection outcome


1. Huge increase in world wild Cicer genetic resources 2. Systematic within & between pop sampling 3. Well characterized collection (genotype, RAD Seq;

environment, bioclimate, soils, in situ climate). 4. Collection site habitat range greatly extended 5. Habitat & genetic stratification feasible within & between

species/sites 6. 2013 collection delivered to AGG, 330 accessions of 14 & 15

collection to AARI in Oct 16. Should be accessible with SMTA 7. Turkish & Australian phenotyping underway already

Unprecedented opportunity to test our earlier contention: Is chickpea limited by genetic & adaptive diversity bottlenecks?


Holster up & lets get cracking together…

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