{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T03:51:03Z","timestamp":1767844263439,"version":"3.49.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T00:00:00Z","timestamp":1571356800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Strategic Priority Research Program","award":["XDA08020302"],"award-info":[{"award-number":["XDA08020302"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u20132 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.<\/jats:p>","DOI":"10.1093\/nar\/gkz921","type":"journal-article","created":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T08:17:03Z","timestamp":1570522623000},"source":"Crossref","is-referenced-by-count":32,"title":["MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice"],"prefix":"10.1093","author":[{"given":"Hua","family":"Peng","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Kai","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Zhuo","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Yinghao","family":"Cao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Qiang","family":"Gao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Yan","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Xiuxiu","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Hongwei","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Huilong","family":"Du","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Min","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]},{"given":"Xin","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Chengzhi","family":"Liang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}]}],"member":"286","published-online":{"date-parts":[[2019,10,18]]},"reference":[{"key":"2019101802090416600_B1","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1126\/science.253.5022.833","article-title":"Resources of plant germplasm","volume":"253","author":"Abelson","year":"1991","journal-title":"Science"},{"key":"2019101802090416600_B2","doi-asserted-by":"crossref","first-page":"D1003","DOI":"10.1093\/nar\/gkw755","article-title":"EURISCO: the European search catalogue for plant genetic resources","volume":"45","author":"Weise","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019101802090416600_B3","doi-asserted-by":"crossref","first-page":"D26","DOI":"10.1093\/nar\/gkp996","article-title":"NBRP databases: databases of biological resources in Japan","volume":"38","author":"Yamazaki","year":"2010","journal-title":"Nucleic Acids 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Biol."},{"key":"2019101802090416600_B5","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1104\/pp.108.129205","article-title":"Cereal germplasm resources","volume":"149","author":"Sachs","year":"2009","journal-title":"Plant Physiol."},{"key":"2019101802090416600_B6","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.plantsci.2019.01.007","article-title":"High-throughput phenotyping for crop improvement in the genomics era","volume":"282","author":"Mir","year":"2019","journal-title":"Plant Sci."},{"key":"2019101802090416600_B7","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.tplants.2015.10.018","article-title":"Analytical and decision support tools for genomics-assisted breeding","volume":"21","author":"Varshney","year":"2016","journal-title":"Trends Plant Sci."},{"key":"2019101802090416600_B8","doi-asserted-by":"crossref","first-page":"221","DOI":"10.3389\/fgene.2016.00221","article-title":"Genomic selection in the era of next generation sequencing for complex traits in plant breeding","volume":"7","author":"Bhat","year":"2016","journal-title":"Front. Genet."},{"key":"2019101802090416600_B9","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1111\/pbi.12645","article-title":"Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application","volume":"15","author":"Scheben","year":"2017","journal-title":"Plant Biotechnol. J."},{"key":"2019101802090416600_B10","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/s12870-019-1754-6","article-title":"Genome-wide association studies of seven agronomic traits under two sowing conditions in bread wheat","volume":"19","author":"Jamil","year":"2019","journal-title":"BMC Plant Biol."},{"key":"2019101802090416600_B11","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/nbt.3096","article-title":"Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean","volume":"33","author":"Zhou","year":"2015","journal-title":"Nat. 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Plant Sci."},{"key":"2019101802090416600_B20","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.3389\/fpls.2018.01226","article-title":"Genome-wide association studies of photosynthetic traits related to phosphorus efficiency in soybean","volume":"9","author":"Lu","year":"2018","journal-title":"Front. Plant Sci."},{"key":"2019101802090416600_B21","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/S1360-1385(03)00134-1","article-title":"Breeding by design","volume":"8","author":"Peleman","year":"2003","journal-title":"Trends Plant Sci."},{"key":"2019101802090416600_B22","doi-asserted-by":"crossref","first-page":"15324","DOI":"10.1038\/ncomms15324","article-title":"Sequencing and de novo assembly of a near complete indica rice genome","volume":"8","author":"Du","year":"2017","journal-title":"Nat. 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