作物表型组数据库研究进展及展望

Research progress and prospect on crop phenomics database

关键词:  作物  表型组  数据库  构建标准  数据管理

Key words:  crop  phenomics  database  construction standard  data management

摘要:

目的 总结归纳作物表型数据库的研究进展，对作物表型数据库的构建进行展望。方法 采用文献综述法，从Web of Science、NCBI的PubMed和中国知网等常用公共文献数据库中对已发表的作物表型组学相关研究文献进行检索，据此对国内外作物表型组学研究现状进行分析，并基于其中的数据库研究，对目前的作物表型相关数据库进行了介绍。最后对作物表型组数据库构建标准及要求进行了介绍。结果 不同于基因组学已有许多大型的、公认的、成熟的公共数据库，有关作物表型组学的数据库虽已有一些，但综合性较强、普适性较广的通用标准数据库却不是很多。因此，构建综合性作物表型组标准数据库或构建特定作物的表型组数据库，将成为该领域相关研究人员的工作重点。结论 农业信息化是现代农业的一个必然发展趋势，作物表型组数据库的构建也是顺应时代发展的产物。今后，在充分利用各种综合和专用数据库的基础上，研究人员应在实际研究中构建自己的作物表型组数据库，增强数据管理和共享。

Abstract:

Purpose During the past few years，crop phenomics has emerged as a fast growing and data intensive discipline，under which the related research techniques and analysis methods have resulted in a large number of phenotypic information. The phenotypic data are usually multiple dimensional and in different data types. For example，the image data covers a wide range of spectral information，including RGB，hyperspectral，near-infrared，thermal and fluorescent. Moreover，the plant physiological data contains various physiological indicators and other data during plant growth. Consequently，the development of biological models and data management systems in this field requires a rational use of these complex，dynamic and large-scale phenotypic data.Methods The article reviews the published studies on crop phenomics in recent years，by consulting the public literature databases including Web of Science，PubMed of NCBI and China National Knowledge Infrastructure（CNKI）. According to the search results，the research status of crop phenomics both in China and overseas are analyzed. At the same time，the current crop phenomics related databases obtained from the above search results are categorized into planteome，plant genomics and phenomics research data repository，and OPTIMAS-DW. At the end of the paper，the standards and requirements for constructing the crop phenomics related database are proposed.Results In the genomics research field，there are many large，well-recognized and mature public databases，including GDB，Ensembl，and GenBank. While in the crop phenomics，although there are already some available databases，the general-purpose standardized databases with strong comprehensiveness and wide universality are still lacking. Despite a total of 300 case studies on crop phenomics have been coded，there are only about 20 studies relevant to database construction. This number is much smaller than the number of existing genomic databases. Given most of these crop phenomics databases can be classified by species，constructing a comprehensive and standardized crop phenomics database，or building a phenomics database for a specific crop，would be of research interests in future studies.Conclusion Agricultural informatization accelerates the development of modern agriculture，which also provides opportunities for the construction of crop phenomics databases. In the future，by fully using the integrated and specialized databases，researchers should build their own crop phenomics databases in their specific studies. Building a database can not only help researchers better manage their phenotypic data，but also can benefit the data sharing among researchers.