Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): Development of chickpea genomic resources for discovering genes controlling economic traits, via association mapping of germplasm accessions. 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. This progress contributes to the Objective 2 of the parental project: �Conduct genetic characterizations and phenotypic evaluations of genetic resources of the preceding crops and related wild species for priority genetic and agronomic traits�. We have completed genotyping of the chickpea minicore (~220 accessions of cultivated chickpea), together with an additional set of ~100 accessions of annual wild crop relatives from the USDA germplasm repository using a 768-SNP chip and high-throughput Illumina GoldenGate genotyping platform. Principal findings are described in brief below for purposes of this Specific Cooperator Agreement report. An ARS scientist at Pullman, Washington, co-authored manuscript is under preparation for submission in the near future to a peer-reviewed scientific journal. We prepared genomic DNA from the accessions, genotyped them with 768 Single-Nucleotide Polymorphisms (SNP) and obtained high quality data for 538 SNPs across the 322 accessions that served as the basis for further molecular diversity analyses using clustering and ordinal approaches. The program Structure clustered the germplasm into into two groups (a cultivated and a wild group). Further analysis could partitioned loosely or incompletely between the two cultivated market types, �desi� and �kabuli�. Wild annual accessions split into two groups with one cluster containing accessions from the primary and secondary gene pools (C. reticulatum and C. echinospermum, respectively), and another cluster containing all wild annual Cicers from the tertiary gene pool. In addition to analysis of molecular diversity of SNP data, we employed a candidate gene approach to clone the chickpea B locus. This genetically defined locus conditions a key phenotypic difference between �desi� and �kabuli� chickpea: that of light (tan) seed coats and white flowers of the �kabuli� type. From this line of investigation, we identified independent loss-of-function alleles in a basic helix loop helix (bHLH) transcription factor as the molecular basis of seed coat and flower color differences between �desi� and �kabuli� chickpea. Furthermore, and consistent with the findings from our SNP genotyping data described above, the nature and distribution of allelic variation at the bHLH suggests that the �kabuli� market type of chickpea arose multiple times during chickpea�s domestication and breeding history.
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): Development of chickpea genomic resources for discovering genes controlling economic traits, via association mapping of germplasm accessions. 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. 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.
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) Development of chickpea genomic resources for discovering genes controlling economic traits, via association mapping of germplasm accessions. 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. Progress was made to objective 1 from parent project. Seeds samples are ready for shipping to the collaborators and the genotyping team is designing the primers for the 768 SNP (single nucleotide polymorphism) markers for the project. Monitoring of progress was made through conference calls and emails.
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