Population Structure Analysis and Genome-Wide Association Study of Rice Landraces from Qiandongnan, China, using Specific–Locus Amplified Fragment Sequencing

Abstract

Uncovering the genetic basis of rice landraces has important applications in breeding. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of the agronomic traits of 60 rice species in Southeast Guizhou. We obtained a total of 178,287,776 reads, 314,065 SLAFs, and 571,521 single nucleotide polymorphisms (SNPs). A neighbor-joining phylogenetic tree, admixture proportions, and principal component analyses revealed that the investigated landraces were divided into japonica (heterozygosity rate 0.062) and indica (heterozygosity rate 0.073) groups. The groupings were consistent with the local classifications of ―He‖ and ―Gu‖ based on the resistance to seed shattering, and the SNPs clustered in the qSH1 gene. The GWAS of eight agronomic traits revealed that the signal peaks at four locations were closely related to previously reported genes or gene regions. This study demonstrates that the SLAF sequencing method combined with a GWAS may be effective for investigating the evolution of rice and identifying genes regulating complex traits in rice landraces cultivated in relatively isolated regions.