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W529: Walking on the wild side using pangenomics for accelerated crop improvement in chickpea

Khan, A.W., Garg, V., Roorkiwal, M., Bayer, P.E., Thudi, M., Chitikineni, A., Upadhaya, H.D., Nguyen, H.T., Edwards, D. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2019) W529: Walking on the wild side using pangenomics for accelerated crop improvement in chickpea. In: Plant & Animal Genome Conference XXVII, 12 - 16 January 2019, San Diego, CA


The wild accessions of chickpea have huge genetic diversity which can be exploited for increasing genetic gains in the crop. Several large scale re-sequencing efforts have been carried out to identify variants in chickpea, but the complete genetic repertoire has not been captured as these efforts involve mapping of reads on single chickpea reference genome. We report the construction of chickpea pangenome by sequencing and de novo assembly of accessions from eight different annual chickpea wild species. These accessions were sequenced at ~180X coverage using Illumina platform, generating a total of 1.14 Tbp data. The de novo assemblies for these species resulted in size varying from 512.3 Mbp to 927.0 Mbp with high N50 values. Comparisons of these assemblies identified genes exhibiting copy number variations and presence absence variations, some of which show evidence of positive selection and might have association with important agronomic traits. The chickpea pangenome will serve as a valuable genomics resource and will have broad implications in chickpea breeding.

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