Development of an allele-specific functional marker for studying Hd1 effect on flowering time of rice

ABSTRACT: Photoperiodic control of flowering is one of the most significant components of the interaction between plants and their environment. Hd1 promotes floral transition from vegetative to reproductive growth under short-day (SD) conditions. An indel-specific functional marker in Hd1 first exon was developed and tested in a collection of 44 rice indica cultivars with different flowering times to evaluate its association with the trait. Results showed that the Hd1 indel-specific marker produced three allelic forms A, B and C as expected, with frequencies of 43.2, 47.7 and 9.1 percent, respectively. A high negative correlation (r=-0.556) was detected between flowering time and functional Hd1 indel. Interval mapping (IM) analysis showed that Hd1 had a negative additive effect (~4.5 days) on flowering time and the gene explained 27.4 percent of phenotypic variation of the trait. Our results indicated the role of Hd1 in determining the time of flowering in rice and suggest applicability of Hd1 indel-specific marker in molecular breeding of early flowering.