Rice novel useful semidwarf gene d60 on chromosome 2 causing pleiotropically gamete abortion

Rice semidwarf gene d60 is inherited according to a unique mode because it causes pleiotropically gamete abortion in the case of coexistence with the gamete lethal gene gal. Namely, F2 progenies of Koshihikari (D60D60galgal, long stem) x Hokuriku 100 (d60d60GalGal, short stem) segregated in the ratio of 1 semidwarf (1 d60d60GalGal):2 tall and quarter sterile (2 D60d60Galgal):6 tall (2 D60d60GalGal:1 D60D60GalGal:2 D60D60Galgal:1 D60D60galgal), 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 to d60 do not fit Mendelian ratio. F2 of Koshihikari d60 line (d60d60GalGal) x lines carrying d30 or gh2 on chromosome 2, the segregation ratios of these alleles were deviated from 1:3 but well fitted to 5:4 when d30 and gh2 were closely linked to D60. We then conducted molecular fine mapping of d60 by using DNA polymorphisms in F2 of Koshihikari d60 line x line carrying the indica chromosome 2 segment in Koshihikari. As a result, d60 was 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.