An assessment of Wx microsatellite allele, alkali degradation and differentiation of chloroplast DNA in traditional black rice (Oryza sativa L.) from Thailand and Lao PDR

Unearthed New Indel in the Waxy Gene in Glutinous Rice Landraces from Thailand

<b>Background and Objective:</b> Glutinous rice landraces have played important role in northeastern and northern region of Thailand and the Lao People's Democratic Republic (PDR) by ethnic groups in this area, both as staple food and ritual in rice culture since ancient times. At a present number of these rice, cultivars have decreased and disappeared from villages without considerations and/or explore DNA variation. This study compared target DNA sequences of <i>waxy</i> genes of a collection of glutinous rice landraces both upland and lowland rice. <b>Materials and Methods:</b> A collection of 50 glutinous rice landraces was explored DNA variation in the <i>Waxy</i> gene by re-sequencing DNA of the two segments (i.e., promoter, exon1 and intron1) of a gene. <b>Results:</b> New InDel of two deletion G at position 11 (GG-) and C at position 15 (CC-) were observed in DNA sequences of the promoter region and 5'untranslalted region of both upland and lowland rice accessions. Further, the (CT)<sub>17</sub> and (CT)<sub>18</sub> were two alleles in these glutinous rice landraces from northern and northeastern Thailand. All glutinous rice landraces exhibited a characteristic of low amylose content or glutinous rice: T Single Nucleotide Polymorphisms (SNP) (AGTTATA) in the first intron splice site. <b>Conclusion:</b> New InDel in DNA sequences of the promoter region of the <i>waxy</i> gene in glutinous rice landraces was first reported. This implies that it may reflect the status of genetic background in glutinous rice landraces in Thailand.