No abstract

Oryza rufipogon Griff. (common wild rice; CWR) is the ancestor of Asian cultivated rice (Oryza sativa L.). Investigation of the genetic structure and diversity of CWR in China will provide information about the origin of cultivated rice and the grain quality and yield. In this study, we used 36 simple sequence repeat (SSR) markers to assay 889 accessions, which were highly representative of whole germplasm in China. The analysis revealed a hierarchical genetic structure within CWR. First, CWR has diverged into two ecotypic populations, a south subtropical population (SSP) and a middle subtropical population (MSP), probably owing to natural selection by the different climates. The distribution of specific alleles and haplotypes indicated that Chinese CWR had both indica-like and japonica-like variations; the SSP was an indica-like type, whereas the MSP was more japonica-like. The SSP and MSP further diverged into five (HN, GD-GX1, GX2, FJ and YN) and two (JX-HuN1 and HuN2) geographical populations, respectively. The genetic data suggest the isolation by distance, although water systems also appear to play an important role in the formation of homogenous populations, and occasionally landscape was also involved. The population GD-GX1, which grew widely in Guangdong and Guangxi provinces, was the largest geographical population in China. It had a high level of genetic diversity (GD) and the closest genetic relationship with other inferred populations. The population HN, with the smallest SSR molecular weights and the highest level of GD, may be the most ancestral population.

Stigma characteristics are important factors affecting the seed yield of hybrid rice per unit area. Natural variation of stigma characteristics has been reported in rice, but the genetic basis for this variation is largely unknown. We performed a genome-wide association study on three stigma characteristics in six environments using 1.3 million single-nucleotide polymorphism (SNPs) characterized in 353 diverse accessions of Oryza sativa. An abundance of phenotypic variation was present in the three stigma characteristics of these collections. We identified four significant SNPs associated with stigma length, 20 SNPs with style length (SYL), and 17 SNPs with the sum of stigma and style length, which were detected repeatedly in more than four environments. Of these SNPs, 28 were novel. We identified two causal gene loci for SYL, OsSYL3 and OsSYL2; OsSYL3 was co-localized with the grain size gene GS3. The SYL of accessions carrying allele OsSY-L3 AA was significantly longer than that of those carrying allele OsSYL3 CC. We also demonstrated that the outcrossing rate of female parents carrying allele OsSYL2 AA increased by 5.71% compared with that of the isogenic line carrying allele OsSYL2 CC in an F 1 hybrid seed production field. The allele frequencies of OsSY-L3 AA and OsSYL2 AA decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement in stigma characteristics of parents of hybrid rice.