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 Xu & 1 others Wenfu Chen

Research output: Contribution to journalArticle

1 Citation (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

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Metagenomics
genomics
rice
Genome
Oryza
genome
domestication
genetic improvement
DNA Shuffling

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Plant Science

Cite this

Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. / Sun, Jian; Ma, Dianrong; Tang, Liang; Zhao, Minghui; Zhang, Guangchen; Wang, Wenjia; Song, Jiayu; Li, Xiang; Liu, Zimeng; Zhang, Wenxing; Xu, Quan; Zhou, Yuncheng; Wu, Jianzhong; Yamamoto, Toshio; Dai, Fei; Lei, Yan; Li, Song; Zhou, Gang; Zheng, Hongkun; Xu, Zhengjin; Chen, Wenfu.

In: Molecular Plant, Vol. 12, No. 5, 06.05.2019, p. 632-647.

Research output: Contribution to journalArticle

Sun, J, Ma, D, Tang, L, Zhao, M, Zhang, G, Wang, W, Song, J, Li, X, Liu, Z, Zhang, W, Xu, Q, Zhou, Y, Wu, J, Yamamoto, T, Dai, F, Lei, Y, Li, S, Zhou, G, Zheng, H, Xu, Z & Chen, W 2019, 'Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game', Molecular Plant, vol. 12, no. 5, pp. 632-647. https://doi.org/10.1016/j.molp.2019.01.019
Sun, Jian ; Ma, Dianrong ; Tang, Liang ; Zhao, Minghui ; Zhang, Guangchen ; Wang, Wenjia ; Song, Jiayu ; Li, Xiang ; Liu, Zimeng ; Zhang, Wenxing ; Xu, Quan ; Zhou, Yuncheng ; Wu, Jianzhong ; Yamamoto, Toshio ; Dai, Fei ; Lei, Yan ; Li, Song ; Zhou, Gang ; Zheng, Hongkun ; Xu, Zhengjin ; Chen, Wenfu. / Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. In: Molecular Plant. 2019 ; Vol. 12, No. 5. pp. 632-647.
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AU - Wang, Wenjia

AU - Song, Jiayu

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