Genome-Wide Association Study of Xian Rice Grain Shape and Weight in Different Environments

Abstract

Drought is one of the key environmental factors affecting the growth and yield potential of rice. Grain shape, on the other hand, is an important factor determining the appearance, quality, and yield of rice grains. Here, we re-sequenced 275 Xian accessions and then conducted a genome-wide association study (GWAS) on six agronomic traits with the 404,411 single nucleotide polymorphisms (SNPs) derived by the best linear unbiased prediction (BLUP) for each trait. Under two years of drought stress (DS) and normal water (NW) treatments, a total of 16 QTLs associated with rice grain shape and grain weight were detected on chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12. In addition, these QTLs were analyzed by haplotype analysis and functional annotation, and one clone (GSN1) and five new candidate genes were identified in the candidate interval. The findings provide important genetic information for the molecular improvement of grain shape and weight in rice.

Genome-Wide Association Analysis of Rice Leaf Traits

“…In this study, we obtained 1,872,276 SNPs (MAF > 0.05) and 8 sets of phenotypic data. The mixed linear model (MLM) implemented in TASSEL [45] was used to correlate the phenotypic data with the corresponding SNP loci. A Manhattan map was generated by using the R language.…”

“…By calculation, p = 1.22 × 10 −6 was selected as the threshold for a significant association of SNP markers with traits. In addition, a 200 kb region was chosen as the overlap recognition marker-trait-associated signal range [45]. If there was one or more significant SNP in the 200 kb region, these SNPs were considered as one QTL.…”