Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat
Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for...
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MDPI AG
2023-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/12/10217 |
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| author | Tianbao Li Chuizheng Kong Pingchuan Deng Chengdao Li Guangyao Zhao Hongjie Li Lifeng Gao Dangqun Cui Jizeng Jia |
| author_facet | Tianbao Li Chuizheng Kong Pingchuan Deng Chengdao Li Guangyao Zhao Hongjie Li Lifeng Gao Dangqun Cui Jizeng Jia |
| author_sort | Tianbao Li |
| collection | DOAJ |
| description | Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat. |
| first_indexed | 2024-03-11T02:21:38Z |
| format | Article |
| id | doaj.art-96df179e09b9424685e4de90b411193c |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T02:21:38Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-96df179e09b9424685e4de90b411193c2023-11-18T10:50:23ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-06-0124121021710.3390/ijms241210217Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in WheatTianbao Li0Chuizheng Kong1Pingchuan Deng2Chengdao Li3Guangyao Zhao4Hongjie Li5Lifeng Gao6Dangqun Cui7Jizeng Jia8The College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, ChinaWestern Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, AustraliaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaThe College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, ChinaThe College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, ChinaCrop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat.https://www.mdpi.com/1422-0067/24/12/10217wheat genomegene duplicationhomolog diversitysubgenome divergencetransposable elements |
| spellingShingle | Tianbao Li Chuizheng Kong Pingchuan Deng Chengdao Li Guangyao Zhao Hongjie Li Lifeng Gao Dangqun Cui Jizeng Jia Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat International Journal of Molecular Sciences wheat genome gene duplication homolog diversity subgenome divergence transposable elements |
| title | Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat |
| title_full | Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat |
| title_fullStr | Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat |
| title_full_unstemmed | Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat |
| title_short | Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat |
| title_sort | intra varietal diversity and its contribution to wheat evolution domestication and improvement in wheat |
| topic | wheat genome gene duplication homolog diversity subgenome divergence transposable elements |
| url | https://www.mdpi.com/1422-0067/24/12/10217 |
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