Population Structure of Nation-Wide Rice in Thailand

Phanchita Vejchasarn,Arissara Suthanthangjai,Varapong Chamarerk,Usawadee Chaiprom,Yotwarit Phansenee,Jirapong Jairin,Chainarong Amornbunchornvej,Jeremy R Shearman,Tatpong Tulyananda

doi:10.1186/s12284-021-00528-2

Abstract

BackgroundThailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.ResultsThe result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure.ConclusionThe population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.

Highlights

Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology
To fill gaps in the literature, our study mainly focused on the population structure of 300 rice accessions, 277 of which are grown in diverse ecological systems in Thailand and 23 obtained from International Rice Research Institute (IRRI) germplasm collection
300 rice accessions (277 rice accessions from all across Thailand and 23 IRRI rice accessions) were sequenced to identify SNP variants allowing for the population-structure to be explored

Summary

Introduction

Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. Thailand has large diversity in ecological systems (Chakhonkaen et al 2012). Due to the diverse ecology in Thailand, rice varieties need to be adapted to their intended growth region and there is some degree of association between genetic variation and geographical origin of Thai rice (Pusadee et al 2019). There is a higher level of diversity in Thai rice accessions compared to selected rice accessions obtained from International Rice Research Institute (IRRI) germplasm based on InDel markers (Chakhonkaen et al 2012). Limited data shows that Upland Thai rice forms a cluster of tropical japonica (Pathaichindachote et al 2019; Chakhonkaen et al 2012; Kladmook et al 2012), while lowland rice forms indica clusters

Methods

Results

Discussion

Conclusion