Whole‐genome resequencing‐based QTL ‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

Rakesh Kumar, Pasupuleti Janila, Manish K. Vishwakarma, Aamir W. Khan, Surendra S. Manohar, Sunil S. Gangurde, Murali T. Variath, Yaduru Shasidhar, Manish K. Pandey, Rajeev K. Varshney

Research output: Contribution to journalArticlepeer-review

48 Citations (Scopus)


The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human‐made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy‐to‐use genetic markers enables early‐generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL‐seq approach for identification of key genomic regions and candidate genes. Whole‐genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta‐SNP index and identified a total of 10,759 genomewide high‐confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes—RING‐H2 finger protein and zeaxanthin epoxidase—were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL‐seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.
Original languageEnglish
Pages (from-to)992-1003
Number of pages12
JournalPlant Biotechnology Journal
Issue number4
Publication statusPublished - 1 Apr 2020
Externally publishedYes


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