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United States Department of Agriculture

Agricultural Research Service

Research Project: High Throughput SNP Genotyping in Chickpea Minicore Collection

Location: Plant Germplasm Introduction and Testing

2012 Annual Report


1a.Objectives (from AD-416):
Development of chickpea genomic resources for discovering genes controlling economic traits, via association mapping of germplasm accessions.


1b.Approach (from AD-416):
The project will genotype a representative chickpea minicore collection of 200 germplasm lines, and 90 wild crop relatives of chickpea we have assembled at Pullman, with a 768 SNP (single nucleotide polymorphism) genotyping assay developed by UCD and ICRISAT, according to published criteria and in consultation with the ADOR. Illumina GoldenGate based genotyping developed by UCD and ICRISAT and the collaborative genotyping represents substantial savings over a stand alone project. This collaboration will allow ARS Pullman to gain genomics technologies, foster integration into an international consortium in chickpea genomics, and identify specific follow on research avenues of interest to chickpea breeding in the Pacific Northwest production area.


3.Progress Report:

A total of 222 cultivated accessions were assayed (128 were from the USDA mini-core you sent; another 94 from reference set of ICRISAT), along with 100 wild annuals (99 annuals, 1 perennial; all wilds from USDA). High quality data were obtained for 538 SNPs of 768 SNPs present in the genotyping assay. The genotype x molecular allele data were analyzed in DARwin and Structure, which supports a single origin for the cultivated form with C. reticulatum as the progenitor wild species, and is also in agreement with the known taxonomic relationships. We can discern at least six sub-groups within the cultivated germplasm. Three clases with accessions from the Indian sub-continent, a fourth from Iran, a fifth with Ethiopian accessions, and the sixth with accessions from Western Asia (Syria, Iran). We can also discern the extent of a mixture (historical and probably natural gene flow) within at least wild reticulatum and echinospermum accessions.

Kabuli accessions are polyphyletic; though they are of the highest frequency in the Western Asia group, they occur in at least two other clades (organization with same ancestor), one of the Indian ones and the Ethiopian one. We took a candidate approach to identify gene(s) underlying light colored seed and flower of the Kabuli type, and identified mutations in a bHLH transcription factor that is orthologous to the pea 'A' gene. All kabulis we have looked at have one of the five variants alleles that are likely to be loss-of-function (based on in silico analysis of the nucleotide changes, but also more directly from looking at gene expression of downstream transcriptional targets of this). These research results support CRIS 5348-21000-026-00D Objective 3: to Strategically characterize (“genotype”) and evaluate (“phenotype”) crop core subsets and other priority germplasm for molecular markers, morphological descriptors, and key agronomic or horticultural traits, such as general adaptation, phenology, and growth potential and also supports CRIS 5348-21000-026-00D Sub-objective 3.A. to accomplish with cooperators, apply existing and newly developed DNA genetic marker technology to phylogenetic and genetic diversity analyses of priority crops and microbial symbionts, emphasizing core subsets of Cicer.


Last Modified: 7/30/2014
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