Nucleic Acids Research
Abstract
To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.
| 论文编号: | DOI:10.1093/nar/gkz921 |
| 论文题目: | MBKbase for Rice: An Integrated Omics Knowledgebase for Molecular Breeding in Rice |
| 英文论文题目: | MBKbase for Rice: An Integrated Omics Knowledgebase for Molecular Breeding in Rice |
| 第一作者: | Hua Peng, Kai Wang, Zhuo Chen, Yinghao Cao, Qiang Gao, Yan Li, Xiuxiu Li, Hongwei Lu, Huilong Du, Min Lu, Xin Yang, Chengzhi Liang |
| 英文第一作者: | Hua Peng, Kai Wang, Zhuo Chen, Yinghao Cao, Qiang Gao, Yan Li, Xiuxiu Li, Hongwei Lu, Huilong Du, Min Lu, Xin Yang, Chengzhi Liang |
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| 发表年度: | 2019-10-23 |
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| 摘要: | To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding. |
| 英文摘要: | To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding. |
| 刊物名称: | Nucleic Acids Research |
| 英文刊物名称: | Nucleic Acids Research |
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| 其它备注: | Hua Peng, Kai Wang, Zhuo Chen, Yinghao Cao, Qiang Gao, Yan Li, Xiuxiu Li, Hongwei Lu, Huilong Du, Min Lu, Xin Yang, Chengzhi Liang. MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. Nucleic Acids Research. DOI:10.1093/nar/gkz921 |
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