Evaluation of the agronomic and genotypic diversity of Thailand local rice (Oryza sativa L.) varieties under lowland conditions

Local Thai varieties of rice contain high levels of genetic diversity. Thus, understanding the genetic structure and relationships among local varieties will be useful for parent selection in rice breeding programs. This study aimed to evaluate the agronomic and genetic variation in a collection of 82 local Thai germplasms from 4 regions of Thailand. The agronomic traits and the Shannon-Weaver index (H') were used to determine phenotypic diversity. In addition, a set of 82 diverse local varieties were genotyped using 75 SNP markers to assess the structural analysis and phylogenetic tree. The results showed that phenotypic variation among 82 varieties was found in all traits. Most local Thai varieties were photosensitive varieties, the plant height was tall to very tall (> 140 cm), the panicle number was low (10-20 panicles), the panicle length was long (> 25 cm), and the grain shape was slender. A moderate H' index was found for panicle number, panicle length, and grain weight. The structural analysis was classified into 5 subpopulations. It was clear to separate glutinous rice (group II) and non-glutinous rice (group I, III, IV, and V). In addition, it is sufficient to be able to differentiate by region in some groups, but it cannot be classified according to the ecology (upland and lowland) and grain shape. Moreover, the results of the phylogenetic tree were associated with the analysis of the structure. Therefore, local Thai rice varieties may be beneficial in terms of rice germplasm that can be used in breeding programs.