Lost genome segments associate with trait diversity during rice domestication
DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to e...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2023
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/163990 |
| _version_ | 1855528887335780352 |
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| author | Zheng, Xiaoming Zhong, Limei Pang, Hongbo Wen, Siyu Li, Fei Lou, Danjing Ge, Jinyue Fan, Weiya Wang, Tianyi Han, Zhenyun Qiao, Weihua Pan, Xiaowu Zhu, Yebao Wang, Jilin Tang, Cuifeng Wang, Xinhua Zhang, Jing Xu, Zhijian Kim, Sung-Ryul Kohli, Ajay Ye, Guoyou Olsen, Kenneth M. Fang, Wei Yang, Qingwen |
| author_browse | Fan, Weiya Fang, Wei Ge, Jinyue Han, Zhenyun Kim, Sung-Ryul Kohli, Ajay Li, Fei Lou, Danjing Olsen, Kenneth M. Pan, Xiaowu Pang, Hongbo Qiao, Weihua Tang, Cuifeng Wang, Jilin Wang, Tianyi Wang, Xinhua Wen, Siyu Xu, Zhijian Yang, Qingwen Ye, Guoyou Zhang, Jing Zheng, Xiaoming Zhong, Limei Zhu, Yebao |
| author_facet | Zheng, Xiaoming Zhong, Limei Pang, Hongbo Wen, Siyu Li, Fei Lou, Danjing Ge, Jinyue Fan, Weiya Wang, Tianyi Han, Zhenyun Qiao, Weihua Pan, Xiaowu Zhu, Yebao Wang, Jilin Tang, Cuifeng Wang, Xinhua Zhang, Jing Xu, Zhijian Kim, Sung-Ryul Kohli, Ajay Ye, Guoyou Olsen, Kenneth M. Fang, Wei Yang, Qingwen |
| author_sort | Zheng, Xiaoming |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. Results In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice. |
| format | Journal Article |
| id | CGSpace163990 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1639902025-05-14T10:24:14Z Lost genome segments associate with trait diversity during rice domestication Zheng, Xiaoming Zhong, Limei Pang, Hongbo Wen, Siyu Li, Fei Lou, Danjing Ge, Jinyue Fan, Weiya Wang, Tianyi Han, Zhenyun Qiao, Weihua Pan, Xiaowu Zhu, Yebao Wang, Jilin Tang, Cuifeng Wang, Xinhua Zhang, Jing Xu, Zhijian Kim, Sung-Ryul Kohli, Ajay Ye, Guoyou Olsen, Kenneth M. Fang, Wei Yang, Qingwen agronomic characters domestication dna genomes oryza sativa phenotypes varieties wild rice DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. Results In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice. 2023-02-01 2024-12-19T12:53:18Z 2024-12-19T12:53:18Z Journal Article https://hdl.handle.net/10568/163990 en Open Access Springer Zheng, Xiaoming; Zhong, Limei; Pang, Hongbo; Wen, Siyu; Li, Fei; Lou, Danjing; Ge, Jinyue; Fan, Weiya; Wang, Tianyi; Han, Zhenyun; Qiao, Weihua; Pan, Xiaowu; Zhu, Yebao; Wang, Jilin; Tang, Cuifeng; Wang, Xinhua; Zhang, Jing; Xu, Zhijian; Kim, Sung Ryul; Kohli, Ajay; Ye, Guoyou; Olsen, Kenneth M.; Fang, Wei and Yang, Qingwen. 2023. Lost genome segments associate with trait diversity during rice domestication. BMC Biol, Volume 21, no. 1 |
| spellingShingle | agronomic characters domestication dna genomes oryza sativa phenotypes varieties wild rice Zheng, Xiaoming Zhong, Limei Pang, Hongbo Wen, Siyu Li, Fei Lou, Danjing Ge, Jinyue Fan, Weiya Wang, Tianyi Han, Zhenyun Qiao, Weihua Pan, Xiaowu Zhu, Yebao Wang, Jilin Tang, Cuifeng Wang, Xinhua Zhang, Jing Xu, Zhijian Kim, Sung-Ryul Kohli, Ajay Ye, Guoyou Olsen, Kenneth M. Fang, Wei Yang, Qingwen Lost genome segments associate with trait diversity during rice domestication |
| title | Lost genome segments associate with trait diversity during rice domestication |
| title_full | Lost genome segments associate with trait diversity during rice domestication |
| title_fullStr | Lost genome segments associate with trait diversity during rice domestication |
| title_full_unstemmed | Lost genome segments associate with trait diversity during rice domestication |
| title_short | Lost genome segments associate with trait diversity during rice domestication |
| title_sort | lost genome segments associate with trait diversity during rice domestication |
| topic | agronomic characters domestication dna genomes oryza sativa phenotypes varieties wild rice |
| url | https://hdl.handle.net/10568/163990 |
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