Diversity of Heading date 1 (Hd1) gene that conditions flowering time in traditional tropical japonica and traditional Indica rice from Thailand

The traditional rice cultivars are genetic resources in breeding programs that possess variable DNA sequence of genes, but variants of genes of these resources have been limited in Thailand. Therefore, DNA sequence variation of the Heading date 1 (Hd1) gene was explored in the rice cultivars collected from north (tropical japonica rice) and northeastern (indica rice) regions of the country. Results from re-sequencing of the Hd1 gene, identified 3 non-synonymous SNPs in the coding sequence (exon2) and there are four SNPs in the non-coding sequence of the gene. For coding sequences, the first non-synonymous SNP, AGT/GGT leading to amino acid sequence changes in Hd1 protein at position 339 of 407 residues. The allele S (AGT:Serine) of Hd1 gene were dominant in tropical japonica rice in the northern region, whereas the allele G (GGT: Glycine) was mostly found in indica rice from the northeastern region. In addition, in two traditional cultivars from the northern, a premature stop codon at exon2 was identified. Furthermore, 2 others non-synonymous SNPs was distributed in both populations, including allele S (AGC:Serine) was dominant in tropical japonica rice, while the allele A (AGA:Arginine) were mostly found in indica rice.