Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops
Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help t...
| Autores principales: | , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163999 |
| _version_ | 1855542254822752256 |
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| author | Han, Zhenyun Li, Fei Qiao, Weihua Zheng, Xiaoming Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Yang, Qingwen |
| author_browse | Cheng, Yunlian Fan, Weiya Guo, Wenlong Han, Zhenyun Huang, Jingfen Li, Fei Liu, Ziran Lou, Danjing Nie, Yamin Qiao, Weihua Wang, Shizhuang Wang, Yanyan Xing, Meng Yang, Qingwen Zhang, Lifang Zheng, Xiaoming |
| author_facet | Han, Zhenyun Li, Fei Qiao, Weihua Zheng, Xiaoming Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Yang, Qingwen |
| author_sort | Han, Zhenyun |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs. |
| format | Journal Article |
| id | CGSpace163999 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1639992025-12-08T10:29:22Z Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops Han, Zhenyun Li, Fei Qiao, Weihua Zheng, Xiaoming Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Yang, Qingwen genomes transcription factors wrky weedy rice Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs. 2023-01-10 2024-12-19T12:53:19Z 2024-12-19T12:53:19Z Journal Article https://hdl.handle.net/10568/163999 en Open Access Frontiers Media Han, Zhenyun; Li, Fei; Qiao, Weihua; Zheng, Xiaoming; Cheng, Yunlian; Zhang, Lifang; Huang, Jingfen; Wang, Yanyan; Lou, Danjing; Xing, Meng; Fan, Weiya; Nie, Yamin; Guo, Wenlong; Wang, Shizhuang; Liu, Ziran and Yang, Qingwen. 2023. Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops. Front. Plant Sci., Volume 13 |
| spellingShingle | genomes transcription factors wrky weedy rice Han, Zhenyun Li, Fei Qiao, Weihua Zheng, Xiaoming Cheng, Yunlian Zhang, Lifang Huang, Jingfen Wang, Yanyan Lou, Danjing Xing, Meng Fan, Weiya Nie, Yamin Guo, Wenlong Wang, Shizhuang Liu, Ziran Yang, Qingwen Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| title | Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| title_full | Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| title_fullStr | Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| title_full_unstemmed | Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| title_short | Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| title_sort | global whole genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops |
| topic | genomes transcription factors wrky weedy rice |
| url | https://hdl.handle.net/10568/163999 |
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