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

Abstract

The traditional rice cultivars are genetic resources in breeding programs that possess variable of DNA sequence of genes, but variants of gene of these resources have been limited in Thailand. Therefore, DNA sequence variation of the heading date 1 (Hd1) gene was explored in these 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 coding sequence (exon2) and there are four SNPs in noncoding sequence of the gene. First nonsynonymous 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 northern region. Whereas the allele G (GGT:Glycine) was mostly found in indica rice from northeastern region. In addition, two traditional cultivars from the northern, a premature stop codon at exon2 was identified. Furthermore, 2 others nonsynonymous 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. The muations may affect Hd1 gene structures and may contribute to intraspecific flowering time adaptations.