SoyPedi: A searchable pedigree‐linked web interface for phenotypic data of soybean cultivars

• Published in: Crop science Vol. 62; no. 6; pp. 2319 - 2331
• Main Authors: Jeong, Min‐Gyun, Lee, Chaeyoung, Kim, Jin‐Hyun, Park, Joo‐Seok, Choi, Yoram, Kim, Hye Jeong, Chung, Young‐Soo, Choi, Hong‐Kyu
• Format: Journal Article
• Language: English
• Published: 01-11-2022
• ISSN: 0011-183X; 1435-0653
• DOI: 10.1002/csc2.20826

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.
Core Ideas
SoyPedi is a web‐based bioinformatic interface for phenotype search and investigation of soybean cultivars.
This interface will play a practical role for breeding design via pedigree‐associated cultivar information and selection of crossing lines.
SoyPedi allows users to readily compare the phenotype of cultivars through visualization system.
SoyPedi provides dual phenotype search modes, pedigree module, and tabular format.