Rice novel useful semidwarf gened60on chromosome 2 causing pleiotropically gamete abortion

Abstract

Rice semidwarf gened60is inherited according to a unique mode because it causes pleiotropically gamete abortion in the case of coexistence with the gamete lethal genegal. Namely, F2progenies of Koshihikari (D60D60galgal, long stem) × Hokuriku 100 (d60d60GalGal, short stem) segregated in the ratio of 1 semidwarf (1d60d60GalGal):2 tall and quarter sterile (2D60d60Galgal):6 tall (2D60d60GalGal:1D60D60GalGal:2D60D60Galgal:1D60D60galgal), which is skewed from the Mendelian 1 semidwarf:3 tall ratio. Firstly, genetic linkage was tested on the basis that the segregation ratios of the phenotypic marker genes linked tod60do not fit Mendelian ratio. F2of Koshihikari d60 line (d60d60GalGal)× lines carryingd30orgh2on chromosome 2, the segregation ratios of these alleles were deviated from 1:3 but well fitted to 5:4 whend30 and gh2were closely linked toD60. We then conducted molecular fine mapping ofd60by using DNA polymorphisms in F2of Koshihikari d60 line × line carrying the indica chromosome 2 segment in Koshihikari. As a result,d60was tightly linked with RM12970 by a recombination value 0.0 at the region 10.3 Mb away from the distal end of the short arm of chromosome 2. Whole genome sequencing of Koshihikari d60 revealed no SNPs and Indels around the 10.3 Mb region. RT-qPCR for ent-copalyl diphosphate synthase-like gene on 10.3 Mb indicated its transcription was reduced compared to that of Koshihikari.