Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets
Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., ‘Gene mapping’, ‘Co-expression’, ‘KEGG/GO Enrichment’ analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through ‘GWAS’, which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
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Format: | Journal Article biblioteca |
Language: | English |
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Wiley
2023-08-02
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Subjects: | functional genomics, abiotic stress, millets, databases, plant breeding, biotechnology, |
Online Access: | https://hdl.handle.net/10568/131513 https://doi.org/10.1111/pbi.14136 |
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dig-cgspace-10568-1315132023-10-18T07:00:12Z Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets Min Sun Haidong Yan Aling Zhang Yarong Jin Chuang Lin Lin Luo Bingchao Wu Yuhang Fan Shilin Tian Xiaofang Cao Zan Wang Jinchan Luo Yuchen Yang Jiyuan Jia Puding Zhou Qianzi Tang Jones, Christopher S. Varshney, R.K. Srivastava, R.K. Min He Zheni Xie Xiaoshan Wang Guangyan Feng Gang Nie Dejun Huang Xinquan Zhang Fangjie Zhu Linkai Huang functional genomics abiotic stress millets databases plant breeding biotechnology Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., ‘Gene mapping’, ‘Co-expression’, ‘KEGG/GO Enrichment’ analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through ‘GWAS’, which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets. 2023-08-02 2023-08-09T10:59:12Z 2023-08-09T10:59:12Z Journal Article Min Sun, Haidong Yan, Aling Zhang, Yarong Jin, Chuang Lin, Lin Luo, Bingchao Wu, Yuhang Fan,Shilin Tian, Xiaofang Cao, Zan Wang, Jinchan Luo, Yuchen Yang, Jiyuan Jia, Puding Zhou, Qianzi Tang, Jones, C.S., Varshney, R.K., Srivastava, R.K., Min He, Zheni Xie, Xiaoshan Wang, Guangyan Feng, Gang Nie, Dejun Huang, Xinquan Zhang, Fangjie Zhu and Linkai Huang. 2023. Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets. Plant Biotechnology Journal 1467-7652 https://hdl.handle.net/10568/131513 https://doi.org/10.1111/pbi.14136 en CC-BY-NC-ND-4.0 Open Access Wiley Plant Biotechnology Journal |
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functional genomics abiotic stress millets databases plant breeding biotechnology functional genomics abiotic stress millets databases plant breeding biotechnology |
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functional genomics abiotic stress millets databases plant breeding biotechnology functional genomics abiotic stress millets databases plant breeding biotechnology Min Sun Haidong Yan Aling Zhang Yarong Jin Chuang Lin Lin Luo Bingchao Wu Yuhang Fan Shilin Tian Xiaofang Cao Zan Wang Jinchan Luo Yuchen Yang Jiyuan Jia Puding Zhou Qianzi Tang Jones, Christopher S. Varshney, R.K. Srivastava, R.K. Min He Zheni Xie Xiaoshan Wang Guangyan Feng Gang Nie Dejun Huang Xinquan Zhang Fangjie Zhu Linkai Huang Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
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Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., ‘Gene mapping’, ‘Co-expression’, ‘KEGG/GO Enrichment’ analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through ‘GWAS’, which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets. |
format |
Journal Article |
topic_facet |
functional genomics abiotic stress millets databases plant breeding biotechnology |
author |
Min Sun Haidong Yan Aling Zhang Yarong Jin Chuang Lin Lin Luo Bingchao Wu Yuhang Fan Shilin Tian Xiaofang Cao Zan Wang Jinchan Luo Yuchen Yang Jiyuan Jia Puding Zhou Qianzi Tang Jones, Christopher S. Varshney, R.K. Srivastava, R.K. Min He Zheni Xie Xiaoshan Wang Guangyan Feng Gang Nie Dejun Huang Xinquan Zhang Fangjie Zhu Linkai Huang |
author_facet |
Min Sun Haidong Yan Aling Zhang Yarong Jin Chuang Lin Lin Luo Bingchao Wu Yuhang Fan Shilin Tian Xiaofang Cao Zan Wang Jinchan Luo Yuchen Yang Jiyuan Jia Puding Zhou Qianzi Tang Jones, Christopher S. Varshney, R.K. Srivastava, R.K. Min He Zheni Xie Xiaoshan Wang Guangyan Feng Gang Nie Dejun Huang Xinquan Zhang Fangjie Zhu Linkai Huang |
author_sort |
Min Sun |
title |
Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
title_short |
Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
title_full |
Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
title_fullStr |
Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
title_full_unstemmed |
Milletdb: A multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
title_sort |
milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets |
publisher |
Wiley |
publishDate |
2023-08-02 |
url |
https://hdl.handle.net/10568/131513 https://doi.org/10.1111/pbi.14136 |
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