Chickpea HapCat/PanGenome Hub

The DivSeek International thematic HapCat and PanGenome Hub aims to use chickpea as the case species, the proposed Hub will develop and refine tools for haplotypes catalogue (HapCat) and pangenome (PanGenome) analysis to provide a common and scalable data analysis platform and community focal point for researchers primarily generating sequencing data with an aim to utilize genetic diversity in crop improvement programs.

Co-leads:  Rajeev K Varshney, ICRISAT, India; Dave Edwards, The University of Western Australia Australia and Kuldeep Singh, ICAR- National Bureau of Plant Genetic Resources, India

2021 update on Activities:
  • Optimizing and developing tools/pipeline for HapCat and PanGenome
  • \Pangenome is developed using the iterative mapping and assembly approach combining the available reference genomes and resequencing data of different accessions for a given crop.
  • We are now working to optimize the different parameters and integrate all these different tools into a single workflow for construction of pangenome.
  • A haplo-pheno analysis pipeline is being developed that takes SNPs calls and phenotypic data as input and reports the superior haplotypes for the trait of interest.
  • Establishing a HapCat and PanGenome as use case in chickpea
    • A chickpea pan-genome (592 Mb ) has been developed using the iterative mapping and an assembly approach
    • Using extensive phenotyping and sequencing data, 205 trait associated SNPs present in 79 unique genes with a putative function were used to identify 350 haplotypes.
  • By using 19.10 million haplo-pheno combinations, 24 consistent and stable superior haplotypes for 20 genes were identified.