Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

Abstract

Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to indica and japonica groups. The indica group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise FST showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.

Genetic Diversity and Population Structure of the Peruvian Andean Legume, tarwi (Lupinus mutabilis), With High Quality SNPs

“…Genetic diversity indices of lupin, based on SNPs, is high among the nine populations sampled across the Peruvian Andes, which is concordant for individuals that are landraces, as reported for other landraces of rye [51], pea [52] , maize [53], rice [54,55], squash [56], bean [57], wheat [58]. The wealth and abundance among tarwi landraces can be explained due to their adaptation to local environments and diversity of grower´s choice [49].…”

Molecular diversity of exotic durian (Durio spp.) germplasm: a case study of Kalimantan, Indonesia

“…According to Teixeira and Huber [ 43 ], conservation genetic practice rests on the assumption that measured levels of diversity provide a direct indicator of the degree to which genetic factors contribute to the risk of extinction. For crop improvement, genetic diversity is beneficial for parental selection [ 51 ] or selecting parents with genetically divergent [ 14 ]. In this context, determining populations with a high level of genetic diversity will become a valuable resource for broadening the genetic base or gene pool of germplasm, as this enables the identification of superior alleles for several traits [ 51 ].…”

“…For crop improvement, genetic diversity is beneficial for parental selection [ 51 ] or selecting parents with genetically divergent [ 14 ]. In this context, determining populations with a high level of genetic diversity will become a valuable resource for broadening the genetic base or gene pool of germplasm, as this enables the identification of superior alleles for several traits [ 51 ].…”

Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-Wide Association Study of Thai Rice Populations

“…Thailand has more than 17,000 local rice varieties, conserved at the National Rice Gene Bank of Thailand and these are valuable genetic resources for GWAS [23]. The SNP data obtained from local Thai rice populations can be used to identify the causative genes for the traits of interest.…”