Origin And Domestication History Of Oryza Sativa L. Revealed With Chloroplast Genome Sequences

Oryza sativa L. is the staple food for more than 1/3 of the world human population, and it is alsoone of the model organisms in the research of biology. According to the efforts of biologistsand archaeologists, we have already known that the O.sativa is domesticated from common wild rice(Oryza rufipogon) distributing in South Asia and China about ten thousand years ago. However, severalkey issues about its origin and domestication history still exist controversially. Based ondifferent subjects by using molecular markers, functional genes and nuclear genome sequences, geneflow was one of the important factors during rice domestication. Because chloroplast genome is anindependent circular DNA which is inherited in maternal pathway and its structure and function is bothconservative, comparing differences between O.sativa and its wild relatives to analyze domesticationhistory of rice directly become better by the chloroplast genome using the Next-generationsequencing technology. This study collected 114 representative accessions of cultivated rice and its wildrelatives across the world and sequenced their chloroplast genomes to explore the origin andevolution of O.sativa. The results are showed as below:1. We obtained 66 high quality single nucleotide polymorphisms(SNPs) after comparing thechloroplast genomes from 32 indica varieties, 31 japonica varieties and 51 O. rufipogon accessions.These SNPs composed 95 haplotypes, in which only two haplotypes shared between accessionsof indica and japonica.2. Based on the homology of the chloroplast sequences, these accessions can be clearly dividedinto two groups including indica and japonica through the analysis of structure, network and PrincipalComponent Analysis(PCA), which means that indica and japonica varieties originated from differentpopulations of O. rufipogon.3. We simulated the domestication history of two rice subspecies using isolation and migration(IM)model and found that there is ongoing gene flow between indica and japonica and the gene flow size is 1.4. We performed coalescent simulations of rice domesticationin the presence of gene flowand found that the assessment of diversity parameters on the genome is significantly differentcomparing with the Wrigh-Fisher model. However, the assessments of neutral test were not affected bythe model with gene flow.This study was conducted to analyze the data of high quality chloroplast of O.sativa and found thatthere were existing gene flows during rice domestication. Based on coalescent simulations, we detectedthat gene flow would affect the evaluation of diversity parameters, and we gave direction of thedeviation based on the model with gene flow. The results will reveal impacts of gene flow on speciationand evolution, and lay the foundation for the subsequent studies on domestication history of O.sativausing genome sequence data.