Fine Mapping Of The Rice Photoperiod-sensitive Genic Male Sterile Gene Pms3

Photoperiod-sensitive genie male sterility rice (PSGMS) Nongken 58S, which under long-day condition is sterile while under short-day condition is fertile, is a very important germplasm to develop the "two-line" hybrid in rice breeding program. Previous studies have established that the sterility of Nongken 58S is controlled by one or two loci, depending on the genetic backgrounds of the material used in the crosses, and the locus located on rice chromosome 12 designated pms3 is the one at which the original mutation occurred in the cultivar Nongken 58 to give rise to Nongken 58S. Using an F₂ population from a cross between Nongken 58S and DH80, in which the fertility trait showed a typical single-locus segregation at the pms3 locus, the pms3 gene was mapped to two molecular markers C751 and M36, with the genetic distance of about 1.6 cM each.The overall goal of this study was to clone the pms3 gene following a map-based cloning method. Firstly, we got 892 highly sterile individuals from Nongken 58S/DH80 F₂ population and then genotyped them by using C751 and M36. The two markers identified 17 and 43 recombinants respectively. Based on the whole genomic physical map information released, we anchored the pms3 gene to one possible Nipponbare BAC contig. Combining the DNA fingerprinting with the 60 recombination individuals analysis by molecuar markers, the physical map of the pms3 gene region containing 13 BACs was identified.157 BAC subclones were then used as probes to reveal the polymorphisms between Nongken 58S and DH80 and hence analyze the recombination plants. 4 markers were found to be closely linked to pms3 with M2 and P9 limiting the pms3 to two overlapping BACs 73M2 and 71J16. By shotgun sequencing method, 73M2 was sequenced and assembled into 3 contigs with a total length of 162 kb. By searching the sequence data provided by Monsanto Company, we got additional 108 kb DNA sequence and extended the contiguous sequence to 268 kb. Sequence analysis of the two RFLP markers P9 and M2 showed that they were located on 230 kb apart in the 268 kb range. Additional 11 polymorphic probes from the 49 ones spaced at distance of one clone per ～5 kb in the...