Assessment of genetic diversity in Thai upland rice varieties using SSR markers

Abstract

Upland rice (Oryza sativa L.) is precious genetic resource containing some valuable alleles not common in modern germplasm. In this study, genetic diversity and population structure of 98 upland rice varieties from northern part of Thailand were examined using nine simple sequence repeat markers. Number of alleles detected by the above primers was 50 with a minimum and maximum frequency of 2 to 10 alleles per locus, respectively. The polymorphic information content (PIC) values ranged from 0.375 to 0.714 with an average of 0.605 for the primers RM164 and RM1, respectively. Dendrogram cluster analysis of the SSR data distinctly classified all genotypes into three major groups (I, II and III), which corresponded to their places of collection. Population structure divided these genotypes into two distinct subpopulations. Subpopulation 1 consisted of upland rice varieties that collected from Chiang Rai province while the majority of subpopulation 2 were collected from Phayao and Phitsanulok provinces. Analysis of molecular variance revealed 68% variance among two subpopulations and 32% variance within subpopulations, suggesting a high genetic differentiation between the two subpopulations. The huge genetic variability of upland rice in northern part of Thailand can be used to complement the gene pool of modern genotypes in rice breeding program.

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

“…To effectively utilize this germplasm, an assessment and classification of the diversity is necessary. While studies on genetic diversity are available for many rice collections around the world [19,20], those for Thai rice germplasm have been conducted on limited sets of accessions [21][22][23][24][25]. According to the previous studies on the genetic structure of Thai rice evaluated using indel and simple sequence repeat (SSR) markers, two distinct groups of rice accessions have been revealed to correspond to indica and japonica groups [23,24].…”