Cargando…

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

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) ge...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhang, Wenying, Tan, Cong, Hu, Haifei, Pan, Rui, Xiao, Yuhui, Ouyang, Kai, Zhou, Gaofeng, Jia, Yong, Zhang, Xiao‐Qi, Hill, Camilla Beate, Wang, Penghao, Chapman, Brett, Han, Yong, Xu, Le, Xu, Yanhao, Angessa, Tefera, Luo, Hao, Westcott, Sharon, Sharma, Darshan, Nevo, Eviatar, Barrero, Roberto A., Bellgard, Matthew I., He, Tianhua, Tian, Xiaohai, Li, Chengdao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9829399/
https://www.ncbi.nlm.nih.gov/pubmed/36054248
http://dx.doi.org/10.1111/pbi.13917
_version_ 1784867460263968768
author Zhang, Wenying
Tan, Cong
Hu, Haifei
Pan, Rui
Xiao, Yuhui
Ouyang, Kai
Zhou, Gaofeng
Jia, Yong
Zhang, Xiao‐Qi
Hill, Camilla Beate
Wang, Penghao
Chapman, Brett
Han, Yong
Xu, Le
Xu, Yanhao
Angessa, Tefera
Luo, Hao
Westcott, Sharon
Sharma, Darshan
Nevo, Eviatar
Barrero, Roberto A.
Bellgard, Matthew I.
He, Tianhua
Tian, Xiaohai
Li, Chengdao
author_facet Zhang, Wenying
Tan, Cong
Hu, Haifei
Pan, Rui
Xiao, Yuhui
Ouyang, Kai
Zhou, Gaofeng
Jia, Yong
Zhang, Xiao‐Qi
Hill, Camilla Beate
Wang, Penghao
Chapman, Brett
Han, Yong
Xu, Le
Xu, Yanhao
Angessa, Tefera
Luo, Hao
Westcott, Sharon
Sharma, Darshan
Nevo, Eviatar
Barrero, Roberto A.
Bellgard, Matthew I.
He, Tianhua
Tian, Xiaohai
Li, Chengdao
author_sort Zhang, Wenying
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9829399
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-98293992023-01-10 Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley Zhang, Wenying Tan, Cong Hu, Haifei Pan, Rui Xiao, Yuhui Ouyang, Kai Zhou, Gaofeng Jia, Yong Zhang, Xiao‐Qi Hill, Camilla Beate Wang, Penghao Chapman, Brett Han, Yong Xu, Le Xu, Yanhao Angessa, Tefera Luo, Hao Westcott, Sharon Sharma, Darshan Nevo, Eviatar Barrero, Roberto A. Bellgard, Matthew I. He, Tianhua Tian, Xiaohai Li, Chengdao Plant Biotechnol J Research Articles 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. John Wiley and Sons Inc. 2022-11-16 2023-01 /pmc/articles/PMC9829399/ /pubmed/36054248 http://dx.doi.org/10.1111/pbi.13917 Text en © 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Research Articles
Zhang, Wenying
Tan, Cong
Hu, Haifei
Pan, Rui
Xiao, Yuhui
Ouyang, Kai
Zhou, Gaofeng
Jia, Yong
Zhang, Xiao‐Qi
Hill, Camilla Beate
Wang, Penghao
Chapman, Brett
Han, Yong
Xu, Le
Xu, Yanhao
Angessa, Tefera
Luo, Hao
Westcott, Sharon
Sharma, Darshan
Nevo, Eviatar
Barrero, Roberto A.
Bellgard, Matthew I.
He, Tianhua
Tian, Xiaohai
Li, Chengdao
Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
title Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
title_full Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
title_fullStr Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
title_full_unstemmed Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
title_short Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
title_sort genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9829399/
https://www.ncbi.nlm.nih.gov/pubmed/36054248
http://dx.doi.org/10.1111/pbi.13917
work_keys_str_mv AT zhangwenying genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT tancong genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT huhaifei genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT panrui genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT xiaoyuhui genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT ouyangkai genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT zhougaofeng genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT jiayong genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT zhangxiaoqi genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT hillcamillabeate genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT wangpenghao genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT chapmanbrett genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT hanyong genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT xule genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT xuyanhao genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT angessatefera genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT luohao genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT westcottsharon genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT sharmadarshan genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT nevoeviatar genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT barrerorobertoa genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT bellgardmatthewi genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT hetianhua genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT tianxiaohai genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley
AT lichengdao genomearchitectureanddivergedselectionshapingpatternofgenomicdifferentiationinwildbarley