Development of a PCR-based marker for studying allelic variation of Hd3a in rice and its effect on flowering time

ABSTRACT: Time of flowering is a key factor affecting both quantity and quality of rice grain production. Among several genes, Hd3a is an important factor associated with flowering time in rice. An Hd3a-specific marker was developed and utilized in a panel of 44 rice indica cultivars with different flowering times to evaluate allelic frequencies and their effect on the trait. Results showed that newly developed marker produced two allelic forms A and B as expected, which had frequencies of 84.1 and 15.9 percent, respectively. Difference between flowering time of cultivars with alleles A and B was significantly large (9.6 days). A relatively high correlation (r=0.408) was detected between flowering time and Hd3a gene. Interval mapping (IM) analysis showed that Hd3a had a positive additive effect (4.8 days) on flowering time and the gene explained 16.2 percent of phenotypic variation of the trait. Our results indicated the applicability of Hd3a-specific marker in studying allelic variation and confirmed previous reports on association of Hd3a with flowering time in rice.