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SoyPedi: A searchable pedigree-linked web interface for phenotypic data of soybean cultivars
Crop Science ( IF 2.3 ) Pub Date : 2022-08-25 , DOI: 10.1002/csc2.20826
Min‐Gyun Jeong 1 , Chaeyoung Lee 2, 3 , Jin‐Hyun Kim 2, 4 , Joo‐Seok Park 2 , Yoram Choi 1 , Hye Jeong Kim 5 , Young‐Soo Chung 5 , Hong‐Kyu Choi 5
Affiliation  

Pedigrees of crop species reflect genealogical relationships among bred lines and are important resources for breeding design. Recently, as more genomic and phenomic data are being accumulated at an astonishing rate, well-organized pedigrees and database-linked systems have become ever more important. To cope with the prospective future of breeding science, this study aimed to develop a pedigree-centered web interface called SoyPedi for the purpose of searching the phenotypic information of soybean [Glycine max (L.) Merr.] cultivars. SoyPedi employed an integrated pedigree composed of 178 well-defined soybean cultivars and phenotype data. The system was constructed using various bioinformatic tools, such as SQLite3, PHP, and JavaScript. SoyPedi consists largely of three submodules, including a pedigree map, a tabular format database, and single cultivar-dedicated web pages. The pedigree and tabular databases are interconnected by a single page application system, so that users can promptly switch between these two modules. In addition, comparative analysis of whole genome resequencing-derived phylogeny and pedigrees implicated some extent of parallel correlation between these two. SoyPedi was developed with the intention of serving breeders for selecting parental lines in hybridization planning, which will be readily operable and intuitive for users. This system will be potentially expandable by integrating more data in the future and is available at https://tgil.donga.ac.kr/SoyPedi/index.html.

中文翻译:

SoyPedi:一个可搜索的系谱链接网络界面,用于大豆品种的表型数据

作物物种系谱反映了育种系之间的系谱关系,是育种设计的重要资源。最近,随着越来越多的基因组和表型数据以惊人的速度积累,组织良好的谱系和数据库链接系统变得越来越重要。为了应对育种科学的前景,本研究旨在开发一个名为 SoyPedi 的以系谱为中心的网络界面,用于搜索大豆的表型信息 [ Glycine max(L.) Merr.] 品种。SoyPedi 采用了由 178 个定义明确的大豆品种和表型数据组成的综合谱系。该系统是使用各种生物信息学工具构建的,例如 SQLite3、PHP 和 JavaScript。SoyPedi 主要由三个子模块组成,包括系谱图、表格格式数据库和单一品种专用网页。系谱数据库和表格数据库通过单页应用系统互联,用户可以在这两个模块之间快速切换。此外,对全基因组重测序衍生的系统发育和谱系的比较分析表明这两者之间存在一定程度的平行相关。SoyPedi 旨在为育种者在杂交计划中选择亲本系而开发,这对用户来说易于操作和直观。
更新日期:2022-08-25
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