Rice Chloroplast Genome Variation, Diversity and Phylogenetic Dissection in Diverse Oryza Species Suggested By Whole Genome Resequencing

Chloroplast genome variations have been detected even in its overall conserved structure, which was valuable for plant population genetics and evolutionary studies. In current report, we deeply detected the chloroplast variations of 364 rice accessions with diverse region and different ecotypes, including O. sativa indica and japonica, O. rufipogon, O. nivara, O. glaberrima and others. Total 583 single nucleotide polymorphisms (SNPs) and 67 Indels across the chloroplast genome was identified, but with only 217 high quality (no missing and heterozygotes) ones, in which wild type rice shown more abundant variations than other cultivated groups. Chloroplast genome nucleotide diversity, genetic distanc, and the Tajima’s D value were also investigated, which revealed a high diversity in wild rice. In expectation, African cultivated rice (O.galberrima) revealed low level of breeding and connectivity with the other groups. Population structure clustering and principal component analysis revealed the existence of three clear groups (indica, japonica and O.glaberrima) and admixture group, but with several mis-clustered accessions among indica and japonica. Phylogenetic analysis based on Maximum likelihood (ML) and Bayesian inference (BI) methods suggested and supported the independent origin of indica and japonica. Meanwhile, the O.glaberrima were defined has separated domestication with the Asian cultivated rice.

Keywords: Chloroplast, diversity, phylogenetic, rice, resequencing, variation