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Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)
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  • Qing-Lin Meng,
  • Qiang Chenggen,
  • Ji-Long Li,
  • Mu-Fan Geng,
  • Ning-Ning Ren,
  • Zhe Cai,
  • Mei-Xia Wang,
  • Zi-Hui Jiao,
  • Fu-Min Zhang,
  • JIanxin Song,
  • Song Ge
Qing-Lin Meng
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Qiang Chenggen
Institute of Botany Chinese Academy of Sciences
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Ji-Long Li
Institute of Botany, Chinese Academy of Sciences, China
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Mu-Fan Geng
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Ning-Ning Ren
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Zhe Cai
Chinese Academy of Sciences
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Mei-Xia Wang
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Zi-Hui Jiao
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Fu-Min Zhang
Chinese Academy of Sciences
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JIanxin Song
Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Song Ge
Chinese Academy of Sciences

Corresponding Author:gesong@ibcas.ac.cn

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Abstract

Ecological divergence due to habitat difference plays a prominent role in the formation of new species but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild rice species (O. rufipogon and O. nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolved linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two wild rice species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and helps effective manipulation of specific genes or gene cluster in rice breeding.
21 Sep 2023Submitted to Molecular Ecology
22 Sep 2023Submission Checks Completed
22 Sep 2023Assigned to Editor
22 Sep 2023Review(s) Completed, Editorial Evaluation Pending
23 Sep 2023Reviewer(s) Assigned