Identification and Fine Mapping of Semidwarf Gene iga-1 in Rice

To understand the genetic mechanism of the semidwarf rice (Oryza sativa L.) mutant, iga-1, isolated by mutagenesis of outer space treatment, the mutant gene was identified through genetic analysis and molecular marker-aided fine mapping. Two iga-1 lines, CHA-2 and CHA-2N, showed great variations in agronomic traits compared to their wild-type parent Texianzhan 13, but their internodes had normal ratio in length, which indicated that they are dn type of dwarfing. Exogenous gibberellic acid (GA₃) could neither restore the wild-type plant height in CHA-2 and CHA-2N nor elongate plants of both lines as tall as Huiyang Zhenzhuzao and Aijiaonante treated with the same concentrations of GA₃; the concentrations of endogenous GA₃ in both iga-1 lines were not affected by the presence of iga-1 gene; and the activities of α-amylase in endosperm of both iga-1 lines were enhanced the same as their wild-type parent. Thus, iga-1 gene proved to be independent of GA₃. Using a large F₂ population (3000 individuals) derived from the cross between CHA-2 and a semidwarf japonica rice variety, 02428 (sd1sd1Iga-1Iga-1), the iga-1 gene was fine mapped between the insert/deletion (InDel) markers DL18 and DL19 on chromosome 5, with the physical distance of 32.01 kb. In this region, 5 open reading frames were predicted, including the gibberellin-insensitive dwarf mutant gene D1. However, D1 gene was not the candidate locus of iga-1 because there was no sequence difference between Texianzhan 13 and CHA-2 or CHA-2N.