a depth-analysis of organelle genome diversity in 1495 rice hybrids reveals hybrid rice breeding strategy

The genomic architecture for heterosis in rice hybrid has been well elucidated. Since cultivated rice is a self-pollinating plant or an inbreeding crop, the rice male sterility varieties, which are unable to produce functional pollen grains and are used as female parents to avoid self-pollination, are prerequisite for efficiently generating hybrid rice varieties to produce large quantities of hybrid seeds. However, we know little about maternally inherited cytoplasmic genome variations for rice hybrids. In this study, we analyzed the cytoplasmic genomes of a collection of 1495 elite hybrid rice (O. sativa) varieties, and revealed 5 major types of hybrid cytoplasm which were adopted in different hybrid production strategies. We revealed that the appliance of cytoplasmic male sterility associated gene WA352c, a new type of mitochondrial genome from wild rice (O. rufipogon) population was introduced to cultivated rice (O. sativa) population and broaden the organelle resource pool. We also conducted organelle genome assembling for 5 representative hybrids from 5 groups, and revealed variable sequence structure for hybrids mtDNA (mitochondrial DNA) but conservative for cpDNA (chloroplast DNA). The functional effects for group-specific nucleotide variations were also evaluated. In order to figure out the interaction between nuclear and cytoplasm could hinder the cross between nuclear genomes, we analyzed the nucleus-genetic relationship among female lines containing 5 types of organelle. There were 4 subtypes of WA352c-based CMS (cytoplasmic male sterile) lines, and subtype 4 had ‘communicated’ with EGMS (environment sensitive male sterile) lines. They shared genomic similarities as well as composition patterns of heterotic loci. Our results showed that, hybrid cytoplasmic genome also contained polymorphisms. It could imply strategies for hybrids production and helped us get better understanding of hybrid rice.