Open AccessWhole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice
Author(s) -
Gopal Misra,
Saurabh Badoni,
Roslen Anacleto,
Andreas Graner,
Nickolai Alexandrov,
Nese Sreenivasulu
Publication year - 2017
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/s41598-017-12778-6
Subject(s) - indel , biology , synteny , genetics , genome wide association study , single nucleotide polymorphism , locus (genetics) , haplotype , genome , gene , allele , genotype
In this study, we used 2.9 million single nucleotide polymorphisms (SNP) and 393,429 indels derived from whole genome sequences of 591 rice landraces to determine the genetic basis of cooked and raw grain length, width and shape using genome-wide association study (GWAS). We identified a unique fine-mapped genetic region GWi7.1 significantly associated with cooked and raw grain width. Additionally, GWi7.2 that harbors GL7 / GW7 a cloned gene for grain dimension was found. Novel regions in chromosomes 10 and 11 were also found to be associated with cooked grain shape and raw grain width, respectively. The indel-based GWAS identified fine-mapped genetic regions GL3.1 and GWi5.1 that matched synteny breakpoints between indica and japonica . GL3.1 was positioned a few kilobases away from GS 3, a cloned gene for cooked and raw grain lengths in indica . GWi5.1 found to be significantly associated with cooked and raw grain width. It anchors upstream of cloned gene GW 5, which varied between indica and japonica accessions. GWi11.1 is present inside the 3′-UTR of a functional gene in indica that corresponds to a syntenic break in chromosome 11 of japonica . Our results identified novel allelic structural variants and haplotypes confirmed using single locus and multilocus SNP and indel-based GWAS.