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Journal article
Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
Plant biotechnology journal, Vol.21(1), pp.46-62
2023
PMID: 36054248
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.
Details
- Title
- Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley
- Authors/Creators
- Wenying Zhang - Yangtze UniversityCong Tan - Murdoch UniversityHaifei Hu - Murdoch UniversityRui Pan - Yangtze UniversityYuhui Xiao - GrandomicsKai Ouyang - GrandomicsGaofeng Zhou - Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, AustraliaYong Jia - Department of Primary Industries and Regional DevelopmentXiao-Qi Zhang - Murdoch University, Centre for Crop and Food InnovationCamilla Beate Hill - Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, AustraliaPenghao Wang - Murdoch University, Centre for Crop and Food InnovationBrett Chapman - Murdoch University, Centre for Crop and Food InnovationYong Han - Department of Primary Industries and Regional DevelopmentLe Xu - Yangtze UniversityYanhao Xu - Yangtze UniversityTefera Angessa - Murdoch University, Centre for Crop and Food InnovationHao Luo - Murdoch University, Centre for Crop and Food InnovationSharon Westcott - Department of Primary Industries and Regional DevelopmentDarshan Sharma - Department of Primary Industries and Regional DevelopmentEviatar Nevo - University of HaifaRoberto A Barrero - Queensland University of TechnologyMatthew I Bellgard - Queensland University of TechnologyTianhua He - Murdoch University, Centre for Crop and Food InnovationXiaohai Tian - Yangtze UniversityChengdao Li - Murdoch University, Centre for Crop and Food Innovation
- Publication Details
- Plant biotechnology journal, Vol.21(1), pp.46-62
- Publisher
- Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
- Identifiers
- 991005573469607891
- Copyright
- © 2022 The Authors.
- Murdoch Affiliation
- Food Futures Institute; State Agricultural Biotechnology Centre; Western Crop Genetics Alliance
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1543 Flow Cytometry
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science