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.
ABSTRACT
A total of 101 local rice varieties, composted of 85 glutinous and 16 non-glutinous varieties grown in wet season 2016, were analyzed for tocopherols (TOC), tocotrienols (T3) and γ-oryzanol (Orz). Two popular varieties, RD6 and KDML105, were used as standard checks for glutinous and non-glutinous varieties, respectively. γ-TOC was found in all glutinous varieties (0.47-9.78 mg/kg), which were higher than RD6 (0.16 mg/kg). α-TOC was found in 40 varieties (1.02-6.29 mg/kg), only 6 varities were higher than RD6 (3.95 mg/kg). δ-T3 was found in 81 varieties (0.57-7.00 mg/kg), mostly varities were higher than RD6 (0.67 mg/kg). γ-T3 was found in all glutinous varieties (8.00-22.1 mg/kg), while RD6 contained 13.3 mg/kg. For α-T3, it was found in 39 glutinous varieties (1.52-9.94 mg/kg), mostly varities were higher than RD6 (2.62 mg/kg). Orz was found in all glutinous rice varieties (276-638 mg/kg), while RD6 contained 423 mg/kg. γ-TOC was found in all non-glutinous varieties (0.67-5.21 mg/kg), which were higher than KDML105. α-TOC was found in only 5 varieties (1.92-2.83 mg/kg), while KDML105 contained 2.23 mg/kg. δ-T3 was found in all non-glutinous varieties (1.64-8.87 mg/kg), which were higher than KDML105 (0.71 mg/kg). γ-T3 was also found in all non-glutinous varieties (8.80-17.58 mg/kg), while KDML105 contained 15.8 mg/kg. α-T3 was found in 9 non-glutinous varieties (4.56-8.93 mg/kg),while KDML105 contained only 0.86 mg/kg. Orz was also found in all those non-glutinous varieties (272-469 mg/kg), while KDML105 contained 469 mg/kg. These results indicate that γ-T3 was the highest vitamin E isomer present in all rice samples, while γ-TOC, α-TOC, δ-T3 and α-T3 were present in trace amounts. Orz was found in all local rice varieties.
