Cloning and mutation sites analysis of a putative hd3a-like gene in eleven foxtail millet cultivars

Abstract

Heading date 3a (Hd3a), a rice ortholog of FT gene, promotes transition to flowering under short-day conditions. Here a putative Hd3a-like gene was cloned in eleven foxtail millet cultivars including “8322-14”, “An04-5014”, Jigu1, Jigu27, “Jiyecong4”, Longgu26, “Xianzihui”, Yugu1, Zheng8041, Zhenggu2 and Zhengzhou12. Totally 26 mutation sites including 23 SNPs and 3 Indels were found among 11 Hd3a-like gene sequences. All the mutation sites arose only from the variation of two cultivars, Jigu27 and “An04-5014”, which led to a premature termination at Aa107 of Jigu27 Hd3a protein and quite a few frame-shift mutations after Aa137 of “An04-5014” Hd3a protein. LD analysis found a large LD structure which included 15 SNP sites and 2 Indel sites. Finally, association analysis between 26 mutation sites and eight phenotypic traits including plant height (PH), heading date (HD), panicle length (PL), ear diameter (ED), panicle weight (PW), spikelet number (SN), grain number per branch (GN) and 1000-grain weight (1000-GW) was performed, only PH was correlated with 18 mutation sites (p<0.05).