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

Jian Sun, Dianrong Ma, Liang Tang, Minghui Zhao, Guangchen Zhang, 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 XuWenfu Chen

    Research output: Contribution to journalArticlepeer-review

    18 Citations (Scopus)

    Abstract

    Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy 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 rice. We 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 weediness. To 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 genomes. Multiple 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. Multiple lines of evidence suggest that differentiation between weedy rice at Asian high latitudes (WRAH) and cultivated rice was initiated by the genetic improvement of cultivated rice. The essence of weediness of weedy rice arose through semi-domestication and can be modeled as an evolutionary game. The reference genome published herein will benefit rice molecular breeding by accelerating the discovery of favorable alleles from weedy rice.

    Original languageEnglish
    Pages (from-to)632-647
    Number of pages16
    JournalMolecular Plant
    Volume12
    Issue number5
    DOIs
    Publication statusPublished - May 6 2019

    Keywords

    • comparative genomics
    • de novo assembly
    • evolutionary game
    • population genomics
    • weedy rice

    ASJC Scopus subject areas

    • Molecular Biology
    • Plant Science

    Fingerprint

    Dive into the research topics of 'Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game'. Together they form a unique fingerprint.

    Cite this