Abstract
SummaryThe 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.
Highlights
The life begins in most of the higher plants through seed and regulation of its germination plays a crucial role for plant survival, during unfavourable environmental conditions (Shu et al, 2015)
The dormant parent ICGV 97045 was used as source for dormancy, which has fresh seed dormancy (FSD) up to 15 days, whereas ICGV 00350 was used as nondormant parent which germinate within 48 hours
Among 366 recombinant inbred lines (RIL), 149 lines showed nondormant phenotype, 117 lines showed FSD between 2 and 3 days, 57 lines showed FSD up to 4–7, and 19 showed FSD up to 8– 12 days
Summary
The life begins in most of the higher plants through seed and regulation of its germination plays a crucial role for plant survival, during unfavourable environmental conditions (Shu et al, 2015). Most of the varieties grown in the Asia are Spanish type that lack fresh seed dormancy have significant economic losses due to in-situ germination of seeds during harvest, which affect economic strength of small holder farmers. This reduces the quality of groundnut seeds, thereby limiting their end use and global trade. It is important to cultivate varieties that significantly possess 2–3 weeks of FSD for sustainable agricultural benefit for smallholder farmers and industries
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