July 19, 2019  |  

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

Authors: Zhang, Jianwei and Chen, Ling-Ling and Xing, Feng and Kudrna, David A and Yao, Wen and Copetti, Dario and Mu, Ting and Li, Weiming and Song, Jia-Ming and Xie, Weibo and Lee, Seunghee and Talag, Jayson and Shao, Lin and An, Yue and Zhang, Chun-Liu and Ouyang, Yidan and Sun, Shuai and Jiao, Wen-Biao and Lv, Fang and Du, Bogu and Luo, Meizhong and Maldonado, Carlos Ernesto and Goicoechea, Jose Luis and Xiong, Lizhong and Wu, Changyin and Xing, Yongzhong and Zhou, Dao-Xiu and Yu, Sibin and Zhao, Yu and Wang, Gongwei and Yu, Yeisoo and Luo, Yijie and Zhou, Zhi-Wei and Hurtado, Beatriz Elena Padilla and Danowitz, Ann and Wing, Rod A and Zhang, Qifa

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

Journal: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1611012113
Year: 2016

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