Signatures of differential selection in chloroplast genome between japonica and indica

作者：Lin Cheng, Jungrye Nam, Sang‐Ho Chu, Phitaktansakul Rungnapa, Myeong-Hyeon Min, Yuan Cao, Ji-Min Yoo, Jee-Su Kang, Kyu‐Won Kim, Yong‐Jin Park · 发表于：Rice · 年份：2019 · DOI：10.1186/s12284-019-0322-x · 被引用次数：36 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、GABA and Rice Research、Genomics and Phylogenetic Studies

BACKGROUND: The domestication process of Asian rice (Oryza sativa L.) is complicated. It's well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. RESULTS: ) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima's D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. CONCLUSIONS: Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least t...