Genetic And Evolution Studies For Japonica Cultivated Rice And Its Coexisting Weedy Rice In Northeast China

Inter-subspecific hybridization combined with utilization of ideal plant type has led to the development of high-yielding rice (Oryza sativa L. var. japonica) in northeast China and made great contributions to worldwide food production. Based on simple sequence repeat markers (SSR), we analyzed genetic diversity variation and kinship among japonica rice in northeast China from different breeding phase and ecological regions. The result indicates that since1990the genetic diversity among northeast japonica cultivars was enriched. The varieties genetic background from three main japonica rice producing areas, Liaoning, Jilin, Heilongjiang, is relatively independent. Several differentiation genomic segments from Liaoning japonica rice was scanned by haplotype matrix which constructed based on japonica core Single Nucleotide Polymorphisms (SNPs). These segments differentiation might be derived from the selection difference that involved in fertility, heading date., and plant architecture.Subspecies-specific Indel and Subspecies-Specific Intron Length Polymorphism (SSILP) markers showed indica-allele frequencies were significantly increased in the cultivars bred after1990, and were significantly positively correlated with spikelet number per panicle and significantly negatively correlated with panicle number per plant. To obtain richer subspecies differentiation markers, we screened and synthesized genotyping chip with366Subspecies-Specific SNPs (SSS). It will contribute to genome-wide haplotype-based selection for inter-subspecific hybridization breeding with its high throughput and efficiency compared with PCR-based genotyping.Among eight genes controlling agronomic traits, Gnla and gs3were partially fixed in the genome of northern japonica cultivars. In contrast, Waxy and qSHl were eliminated, whereas deol and qsw5were retained. The studies above has enhanced our understanding about molecular basis of heterosis from inter-subspecific hybridization.As a weed of rice paddy fields, weedy rice (Oryza. sativa f. spontanea) has spread worldwide. Its evolutionary history and mechanisms are poorly understood. Firstly, the japonica background was revealed by subspecies-specific Indel and SSILP. Molecular evolution from three key genes, atpB-rbcL p-VATPase and SAM, were successfully interpreted the domestication scenario of O. sativa L. On the basis of haplotype phylogenetic analysis of above three key genes, we established evolutionary relationships between weedy rice and O. sativa L. from worldwide. At the same time, we did not detect any novel haplotypes at the three loci and the vast majority of weedy rice samples shared consistent haplotypes and molecular evolution status with ancient japonica rice varieties.Genetic divergence appears in the domestication related traits between japonica cultivated rice and its coexisting weedy rice in northeast China. Although ancestral-type frequency of9domestication related genes in weedy rice was closed to wild rice and indica rice, the defined-gene sh4of weedy rice as a strong evidence demonstrated that weed rice in northern China is not directly derived from closely-related wild Oryza species. Our observations regarding haplotypes at Rc, another defined-gene of weedy feature, also do not support the hypothesis that weedy rice in northeast China was derived simply from introgression of indica. The genomic evidence above imply that the evolution of weedy rice is multiple introgression event from exotic gene pool to local cultivars. Genes involved in rice domestication were evaluated for their potential roles in weedy rice seed longevity on the basis of classic genetic analysis. And hence explored new biological significance, fitness, for these domesticated related genes. Introgression with local cultivars coupled with selection that maintained weedy identity shaped evolution of weedy rice in northern China.Compared with long-term evolutionary events, such as cultivated rice domestication, successful japonica super-rice breeding in northern China has occurred over a very short time span, which could be considered as super-domestication. On the contrary, weedy rice has spread rapidly forced by natural selection and rarely artificial selection with the application of direct seeding and simplified cultivation practices, which would treat as de-domestication. Different directions of selection pressure from artificial and natural acting on the same japonica gene pool in northeast China. During this process, different alleles were fixed in the genome of japonica cultivar and its coexisting weedy rice populations respectively and reproduction in their own way. This finding provides a new research perspective for the domestication scientific issues. And it also reflects the plasticity of japonica in northeast China. After severe natural selection, weedy rice owned excellent genetic advantage such as drought, cold and blast resistance, etc., which could be used as effective genetic resources for improving japonica cultivar in northeast China.