Population Structure of Nation-Wide Rice in Thailand

Abstract

Background Thailand 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. Results The 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. Conclusion The 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.

WITHDRAWN: Glycaemic index and glycaemic load values of Thai geographical indication rice cultivars

“…Thailand is also a country with large diversity in rice varieties due to its rich and diverse ecology. Rice ecologies in Thailand can be classi ed as irrigated, rainfed lowland, deep water, and upland ecosystems [3].…”

“…Thailand ensures GI protection through the enforcement of the law on GIs, the Protection of Geographical Indications Act B.E.2546 (AD2003). This Act lumps the hundreds of potential GI products in the country into three major categories: (1) general protection, (2) GI protection for speci c goods, and (3) protection for foreign products. Special GI products include: (1) rice, (2) silk, (3) wines and (4) spirits.…”

“…This Act lumps the hundreds of potential GI products in the country into three major categories: (1) general protection, (2) GI protection for speci c goods, and (3) protection for foreign products. Special GI products include: (1) rice, (2) silk, (3) wines and (4) spirits. The introduction of legal protection to GIs for speci c goods also re ects a keen sense of consideration to emphasize the importance of some special products, such as rice, which represents a signi cant portion of the Thai economy and labor force.…”

Genome-Wide Analysis of Amino Acid Transporter Gene Family Revealed That the Allele Unique to the Aus Variety Is Associated with Amino Acid Permease 17 (OsAAP17) Amplifies Both the Tiller Count and Yield in Indica Rice (Oryza sativa L.)

“…Using OsAAP17 SNPs and In/Dels, a random forest classifier was used to classify the rice genotypes into different ecotypes. This analysis was carried out in the same manner as previously reported by Vejchasarn et al [75], and OsAAP17 genetic variants and genotype ecotype information from the rice SNP seek database were used to assess the classification error using random forest classifier models. Furthermore, the random forest classifier's varImp function was used to assess variant importance.…”

“…Prior research has also employed a random forest classifier to categorize rice genotypes into various subpopulations, including India and Japonica groups, via the utilization of a set of 268 predictive SNPs. These SNPs are likely to have been subjected to selection pressures and are distributed across multiple chromosomes within the rice genome [75]. Among the total of 389 SNPs present in OsAAP17, seventeen were found to potentially be under the influence of selection pressures, which could impact the classification as well as the trait responses across distinct rice ecotypes.…”