Polymorphism Analysis of Heading Date Exon 2 Gene Region in Japonica Rice

Nguyen Pha, Le Linh, Nguyen Thang, Nguyen Kieu Tien, Tran Thach and Tran Gioi

Background and Objective: Temperate japonica rice varieties when grown in tropical climates have short daylight periods and high temperatures, so the heading date will be very early without enough panicles development, leading to low grain yields. This study aims to investigate the divergence of the Hd1 exon 2 gene region related to the flowering time serving japonica rice breeding for the tropics. Materials and Methods: Forty-one japonica rice varieties (Oryza sativa L.) were used to evaluate flowering phenotypes and agronomic characteristics combined with sequencing of the heading date (Hd1) exon 2 gene region to determine the relationship between genotype and phenotype of the target trait. Results: The phenotypic assessment categorized 41 japonica rice varieties into four groups based on growth duration. Late varieties exhibited higher yields compared to early ones. Polymorphism analysis of Hd1 exon 2 in 7 rice varieties revealed four Single Nucleotide Polymorphisms (SNPs) at positions 897, 1120, 1131 and 1159. The very early variety AKP4 showed no variation, while early varieties (Wc2811 and J16) had SNPs at positions A897C and G1131C, resulting in amino acid changes R299S and Q377H. Medium and long-duration varieties (A2 and B groups), in addition to the SNP at position A897C, might also have 1-2 SNPs at positions G1120A and G1159A that changed amino acids E374K and G387S, respectively. Conclusion: The SNP at G1120A and G1159A positions that changed amino acids E374K and G387S, respectively, may help to inactivate the Hd1 gene function leading to the adaptation of temperate japonica rice to tropical regions.

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