Population Genomics of Peanut

Genome‐wide structural and functional features of single nucleotide polymorphisms revealed from the whole genome resequencing of 179 accessions of Arachis

“…About 1% (46,087) of the SNPs had the maximum PIC of 0.375, while 13%, 44% and 42% of the SNPs had high, moderate and low PIC values, respectively. They were previously used (Bhat et al, 2021) to determine the genetic distances (Euclidean) and clustering, which allowed to distinguish between the accessions belonging to A. hypogaea ssp. hypogaea and those of A. hypogaea ssp.…”

“…gov/sra) of 178 accessions (cultivated tetraploids, diploids and a few synthetic amphidiploids) (Bhat et al, 2021). In the current study, we identified the structural and functional features to gain knowledge on their application in peanut genomics.…”

“…Previous effort on the re‐sequencing of 52 accessions consisting of cultivated peanut, wild species and artificial tetraploids revealed a total of 17.16 million non‐redundant SNPs and 4.52 million non‐redundant InDels (Zhuang et al, 2019). We previously identified 4,309,724 SNPs using the WGRS data (https://www.ncbi.nlm.nih.gov/sra) of 178 accessions (cultivated tetraploids, diploids and a few synthetic amphidiploids) (Bhat et al, 2021). In the current study, we identified the structural and functional features to gain knowledge on their application in peanut genomics.…”

“…With the surge in peanut genome sequencing projects and the comparison of multiple related individuals within and between the species of genus Arachis, single nucleotide polymorphisms are being discovered at a faster rate now. In this direction, genotyping by sequencing (GBS) (Wang et al, 2019), tunable genotyping‐by‐sequencing (tGBS) (Zheng et al, 2018), restriction site‐associated DNA sequencing (RAD‐Seq) (Zhao et al, 2016), double‐digested RAD sequencing (ddRAD‐Seq) (Zhou et al, 2014), target amplicon sequencing (TAS) (Shirasawa et al, 2016), specific‐locus amplified fragment sequencing (SLAF‐seq) (Hu et al, 2018; Wang et al, 2020; Zhang et al, 2019), exome capturing (Bertioli et al, 2019), and RNA sequencing (Chopra et al, 2015; Chopra et al, 2016; Li et al, 2021) techniques were used to discover a large number of SNPs, and to employ them for mapping various traits for peanut improvement (see Bhat et al, 2021).…”

“…Recently, population genomics of peanut was reported (Bhat et al, 2021) using the whole genome re-sequencing (WGRS) data of 231 accessions. Also, a total of 4,309,724 SNPs was detected using the preliminary analysis of 179 accessions from different countries.…”