Fine Mapping Of A Major Indica-japonica Rice Hybrid Sterility Locus QS12 Located In A Recent Duplicated Segment In Rice Genome

The cultivated Asian rice, Oryza saliva L., is one of the earliest domesticated crop species. For both of the natural and artificial selection, a broad range of genetic variability and genetically structured populations have been documented in O. sativa, and there were many hypotheses long being debated on several issues in the histroy of rice domestication. For thousands of years diversification of the two subspecies of Oryza sativa, dozens of reproductive barriers had been developed between indica and japonica, and partial hybrid sterility is common in hybrids between interspecific crosses. Therefore, it is problematic when attempting to apply positive heterosis, an application that significantly increases rice grain yield. Large chromosomal segment duplications are considered very important in organism evolution, providing material of the development of speciation genes. Besides an ancient genome duplication which serve a significant role in divergence of grasses, a likely young duplicated DNA segment also was identified in rice and several other cereal genomes. Although rapid revolution and expression differentiation of genes in this recent duplicated segments were also observed, its impact on the phenotypic evolution of rice was still unknown. In this study, using a set of chromosome segment substitution lines (CSSLs) and several near-isogenic lines (NILs), the hybrid sterility phenotype associated with this recent duplicated segment was confirmed. We hope it would contribute to our molecular understanding of evolutionary diversification and heterosis utilization in Oryza sativa.The main results were as followings:1. Three hybrid sterility QTLs have been detected from the CSSLs population. Using a set of 40 CSSLs crossed with the initial parents Nipponbare and 9311,74 heterozygous lines were obtained, which were divided into two different populations. Taking the spikelet fertility score of the heterozygous lines as phenotypes,3 hybrid sterility QTLs qS3, qS6 and qS12 were detected on chromosome 3,6 and 12 in rice genome, respectively. Considering the large percentage of phenotypic variance explained, qS6 and qS12 were seemed as two major QTLs. Analysis with several related CSSLs, the physical position of qS6 was found near the cloned hybrid sterility gene S5, and qS12 were located on the recent duplicated segment on chromosome 12.2. The major hybrid sterility locus qS12 was mapped in a～400kb region. A series NILs were devoloped from the cross between CSSLs which carried the hybrid sterility locus and background parent Nipponbare. Adopted the NILs, the major QTL(qS12) resulting in hybrid sterility was mapped within a～400kb region adjacent to the recent duplicated segment on the short arm of chromosome 12. From the segregation ratio results in the two separate populations and pollen fertility assays of the plants from near-isogenic lines we found that qS12 is also a significant segregation distortion locus with male semi-sterility. 3. Comparison of Nipponbare and 9311 genomes, several chromosome arrangements had been detected in the candidate region of qS12. And the tested result of the molecular marker XF28401 revealed that the two sides of the candidate region in japonica cultivar Nipponbare were inverted from indica cultivar 9311. Among 47 of the 111 rice genotypes evaluated by molecular markers, the inverted sides were detected, and found completely homologous to indica cultivar 9311. These results suggested the two inverted sides protect the sequence in the qS12 regions from recombination.4. Idetified with polymophic markes, all the 20 wild rice accessions were found similar to Nipponbare, not inverted in the two sides of the candidate region of qS12. It suggested that the inverted sides like 9311, which might not generated from wild rice, were appeared later in the domestication process of the cutivated rice. And detected results of other 6 markers within the region of qS12 revealed that there were many differences between wild and cultivated rice, which impled that several recombiantion events had occoured between alleles during the domestication histroy of rice.