Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley

Wenying Zhang, Cong Tan, Haifei Hu, Rui Pan, Yuhui Xiao, Kai Ouyang, Gaofeng Zhou, Yong Jia, Xiao Qi Zhang, Camilla Beate Hill, Penghao Wang, Brett Chapman, Yong Han, Le Xu, Yanhao Xu, Tefera Angessa, Hao Luo, Sharon Westcott, Darshan Sharma, Eviatar NevoRoberto A. Barrero, Matthew I. Bellgard, Tianhua He, Xiaohai Tian, Chengdao Li

Research output: Contribution to journalArticlepeer-review

Abstract

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Original languageEnglish
JournalPlant Biotechnology Journal
DOIs
StateAccepted/In press - 2022

Bibliographical note

Funding Information:
This work was supported by the National Natural Science Foundation of China (31471496), Grain Research and Development Corporation (9176507), and Yangtze University Scientific and Technological Innovation Team Foundation. We thank Claire Mérot and Peter Civáň for constructive comments on an earlier version of this paper.

Publisher Copyright:
© 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Keywords

  • chromosome inversion
  • cis-regulatory mutation
  • drought response
  • evolution canyon
  • flowering time
  • local principal component analysis

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science

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