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

Authors

Wenying Zhang, Yangtze University, China
Cong Tan, Murdoch University
Haifei Hu, Murdoch University
Rui Pan, Yangtze University, China
Yuhui Xiao, Grandomics Biotechnology Co Ltd
Kai Ouyang, Grandomics Biotechnology Co Ltd
Yong Jia, Murdoch University
Xiao-Qi Zhang, Murdoch University
Camilla Hill, Murdoch University
Penghao Wang, Murdoch University
Brett Chapman, Murdoch University
Yong Han, Department of Primary Industries and Regional Development, Western AustraliaFollow
Gaofeng Zhou, Murdoch University
Le Xu, Yangtze University, China
Yanhao Xu, Yangtze University, China
Tefera Angessa, Murdoch University
Hao Luo, Murdoch University
Sharon Westcott, Department of Primary Industries and Regional Development, Western AustraliaFollow
Darshan Sharma, Department of Primary Industries and Regional Development, Western AustraliaFollow
Eviatar Nevo, University of Haifa
Roberto Barrero, Queensland University of Technology
Matthew I. Bellgard, Queensland University of Technology
Tianhua He, Murdoch University
Xiaohai Tian, Yangtze University, China
Chengdao Li, Murdoch UniversityFollow

Document Type

Article

Publication Date

8-19-2022

Journal Title

Plant Biotechnology Journal

ISSN

1467-7644

Keywords

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

Disciplines

Agricultural Science | Agriculture | Agronomy and Crop Sciences | Plant Breeding and Genetics

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 theHvWRKY45gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influenceHvCO5expression 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.

Recommended Citation

Zhang, W, Tan, C, Hu, H, Pan, R, Xiao, Y, Ouyang, K, Jia, Y, Zhang, X, Hill, C, Wang, P, Chapman, B, Han, Y, Zhou, G, Xu, L, Xu, Y, Angessa, T, Luo, H, Westcott, S, Sharma, D, Nevo, E, Barrero, R, Bellgard, M I, He, T, Tian, X, and Li, C. (2022), Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley. Plant Biotechnology Journal, 21 (1), 46-62.
https://library.dpird.wa.gov.au/fc_researchart/7