Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game

作     者：Jian Sun Dianrong Ma Liang Tang Minghui Zhao Guangchen Zhangh Wenjia Wang Jiayu Song Xiang Li Zimeng Liu Wenxing Zhang Quan Xu Yuncheng Zhou Jianzhong Wu Toshio Yamamoto Fei Dai Yan Lei Song Li Gang Zhou Hongkun Zheng Zhengjin Xu Wenfu Chen 

作者机构：Rice Research InstituteShenyang Agricultural UniversityShenyangChina College of Information and Electrical EngineeringShenyang Agricultural UniversityShenyangChina Institute of Crop ScienceNational Agriculture and Food Research OrganizationIbarakiJapan lnstitute of Plant Science and ResourcesOkayama UniversityOkayamaJapan Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina Biomarker Technologies CorporationBeijingChina 

出 版 物：《Molecular Plant》 (分子植物（英文版）)

年 卷 期：2019年第12卷第5期

页      面：632-647页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 0901[农学-作物学] 0902[农学-园艺学] 

基　　金：the National Natural Science Foundation of China(grant nos.U1708231 and 31271687) the National Key R&D Program of China(grant no.2017YFD0100501) 

主　　题：weedy rice population genomics de novo assembly comparative genomics evolutionary game 

摘      要：Crop weediness,especially that of weedy rice(Oryza sativa ***),remains *** rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated *** also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice *** identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference *** lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.