Genome-Wide Association Study of Starch Properties in Local Thai Rice.

Rice (Oryza sativa L.) is the main source of energy for humans and a staple food of high cultural significance for much of the world's population. Rice with highly resistant starch (RS) is beneficial for health and can reduce the risk of disease, especially type II diabetes. The identification of loci affecting starch properties will facilitate breeding of high-quality and health-supportive rice. A genome-wide association study (GWAS) of 230 rice cultivars was used to identify candidate loci affecting starch properties. The apparent amylose content (AAC) among rice cultivars ranged from 7.04 to 33.06%, and the AAC was positively correlated with RS (R2 = 0.94) and negatively correlated with rapidly available glucose (RAG) (R2 = -0.73). Three loci responsible for starch properties were detected on chromosomes 1, 6, and 11. On chromosome 6, the most significant SNP corresponded to LOC_Os06g04200 which encodes granule-bound starch synthase I (GBSSI) or starch synthase. Two novel loci associated with starch traits were LOC_Os01g65810 and LOC_Os11g01580, which encode an unknown protein and a sodium/calcium exchanger, respectively. The markers associated with GBSSI and LOC_Os11g01580 were tested in two independent sets of rice populations to confirm their effect on starch properties. The identification of genes associated with starch traits will further the understanding of the molecular mechanisms affecting starch in rice and may be useful in the selection of rice varieties with improved starch.

Quantification of Tocopherols, Tocotrienols and γ-Oryzanol Contents of Local Rice Varieties in Northeastern Thailand.

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.

Diverse genetic variation in maternal lineages with high heterogeneity among in situ-conserved wild rice (Oryza rufipogon Griff.) developed in Thailand.

Wild rice, Oryza rufipogon, is a genetic resource that can be used to improve cultivated rice, but its populations are now decreasing in terms of both size and number. Extensive research on wild rice has been conducted in Thailand, where two in situ conservation sites have been preserved in natural areas where perennial wild rice predominates. The genetic structure of wild rice populations was investigated by examining both the chloroplast and nucleus genomes at sites of in situ conservation site in Thailand. One accession from an in situ-conserved site was re-sequenced against the chloroplast genome of O. sativa cv. 'Nipponbare' to develop chloroplast insertion/deletion (cpINDEL) markers. These cpINDEL markers revealed unique maternal lineages in the in situ-conserved populations upon comparison with other Asian wild rice accessions. Diverse genetic variation was also detected with SSR markers throughout the genome. Three populations differed from each other and also within single populations. The sub-populations within an in situ-conserved population showed a complex population structure due to their multiple maternal lineages and relatively higher number of haplotypes when they maintained a relatively large population size. Such a heterogeneous population would serve as a unique gene pool for rice breeding.