Genomic insights into positive selection during barley domestication
Abstract Background Cultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process. Results...
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-022-03655-0 |
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| author | Wenjing Tao Jianxin Bian Minqiang Tang Yan Zeng Ruihan Luo Qinglin Ke Tingting Li Yihan Li Licao Cui |
| author_facet | Wenjing Tao Jianxin Bian Minqiang Tang Yan Zeng Ruihan Luo Qinglin Ke Tingting Li Yihan Li Licao Cui |
| author_sort | Wenjing Tao |
| collection | DOAJ |
| description | Abstract Background Cultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process. Results The rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley. Conclusions Our comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley. |
| first_indexed | 2024-04-12T14:09:48Z |
| format | Article |
| id | doaj.art-7f17121d36ed4ccc9720df3ea205b5d8 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-12T14:09:48Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-7f17121d36ed4ccc9720df3ea205b5d82022-12-22T03:29:56ZengBMCBMC Plant Biology1471-22292022-06-0122111910.1186/s12870-022-03655-0Genomic insights into positive selection during barley domesticationWenjing Tao0Jianxin Bian1Minqiang Tang2Yan Zeng3Ruihan Luo4Qinglin Ke5Tingting Li6Yihan Li7Licao Cui8College of Bioscience and Engineering, Jiangxi Agricultural UniversityPeking University Institute of Advanced Agricultural SciencesCollege of Forestry, Hainan UniversityCollege of Bioscience and Engineering, Jiangxi Agricultural UniversityCollege of Bioscience and Engineering, Jiangxi Agricultural UniversityCollege of Bioscience and Engineering, Jiangxi Agricultural UniversityCollege of Bioscience and Engineering, Jiangxi Agricultural UniversityCollege of Bioscience and Engineering, Jiangxi Agricultural UniversityCollege of Bioscience and Engineering, Jiangxi Agricultural UniversityAbstract Background Cultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process. Results The rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley. Conclusions Our comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley.https://doi.org/10.1186/s12870-022-03655-0BarleyDomesticationPositively selected geneGene compactnessExpression patternGenetic diversity |
| spellingShingle | Wenjing Tao Jianxin Bian Minqiang Tang Yan Zeng Ruihan Luo Qinglin Ke Tingting Li Yihan Li Licao Cui Genomic insights into positive selection during barley domestication BMC Plant Biology Barley Domestication Positively selected gene Gene compactness Expression pattern Genetic diversity |
| title | Genomic insights into positive selection during barley domestication |
| title_full | Genomic insights into positive selection during barley domestication |
| title_fullStr | Genomic insights into positive selection during barley domestication |
| title_full_unstemmed | Genomic insights into positive selection during barley domestication |
| title_short | Genomic insights into positive selection during barley domestication |
| title_sort | genomic insights into positive selection during barley domestication |
| topic | Barley Domestication Positively selected gene Gene compactness Expression pattern Genetic diversity |
| url | https://doi.org/10.1186/s12870-022-03655-0 |
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