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United States Department of Agriculture

Agricultural Research Service


Location: Plant Germplasm Introduction and Testing Research

Title: Multi-locus molecular phylogeny and allelic variation in a transcription factor gene suggest the multiple independent origins of kabuli chickpea

item Penmetsa, R
item Carrasquilla-garcia, N
item Sarma, B
item Bergmann, E
item Vance, L
item Castro, B
item Kassa, M
item Datta, S
item Dubey, A
item Gujaria, N
item Baek, J
item Woodward, J
item Farmer, A
item Coyne, Clarice - Clare
item Wettberg, E
item Varshney, R
item Cook, D

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/26/2012
Publication Date: 10/3/2012
Citation: Penmetsa, R.V., Carrasquilla-Garcia, N., Sarma, B.K., Bergmann, E.M., Vance, L.C., Castro, B.M., Kassa, M.T., Datta, S., Dubey, A., Gujaria, N., Baek, J.M., Woodward, J.E., Farmer, A.D., Coyne, C.J., Wettberg, E.J., Varshney, R.K., Cook, D.R. 2012. Multi-locus molecular phylogeny and allelic variation in a transcription factor gene suggest the multiple independent origins of kabuli chickpea. Meeting Abstract. Proceedings of VI International Legume Genomic & Genetics Conference Oct. 2-7, 2012 Hyderabad, India.

Interpretive Summary: none

Technical Abstract: To examine the patterns of molecular diversity in wild crop relatives and the cultivated gene pool of chickpea we genotyped a set of 98 wild annual and 224 cultivated accessions with a 768 feature assay that monitored SNPs in low-copy orthologous loci. Analyses of the resulting multi-locus genotyping data - which is deeper for both molecular markers and for representation of wild annual relatives - recapitulated the taxonomic relationships between cultivated chickpea and its wild crop relatives. We identified gene flow both within the primary gene pool, but also hybrid accessions between the primary and secondary pools that could serve as genetic bridges for introgression of wild traits from the secondary pool into cultivated chickpea. Cultivated accessions typically had high levels of admixture but could be resolved into coherent geographic origin-based clades from low-admixed subsets. Contrary to the traditional two-way subdivision of chickpea into ‘desi’ and ‘kabuli’ types, our multi-locus analyses finds ‘kabuli’ to be polyphyletic. Moreover, from candidate pathways, syntenic relationships and genetic association we identified a candidate transcription factor for the B locus of chickpea that governs several ‘kabuli’ traits. Three of five of its variant alleles result in frameshift alterations, whose loss-of-function effect is reflected in the attenuated expression of transcriptional targets in petals and seed coats of ‘kabuli’ but not ‘desi’ types. The absence of nesting among variant alleles at the candidate gene, and the pattern of their occurrence within germplasm together suggest that the ‘kabuli’ type arose independently multiple times during chickpea’s crop evolutionary history.

Last Modified: 10/19/2017
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