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

Abstract

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.

PERSEUS: an interactive and intuitive web-based tool for pedigree visualization

“…To solve this problem, R packages such as Kinship2 ( Sinnwell et al . 2014 ), software programs like PEDHUNTER ( Agarwala et al 1998 ), Pelican ( Dudbridge et al 2004 ), CraneFoot ( Mäkinen et al 2005 ), HaploPainter ( Thiele and Nürnberg 2005 ), Graphviz ( Zhao 2006 ), PyPedal ( Cole 2007 ), GeneaQuilts ( Bezerianos et al 2010 ), PedVis ( Tuttle et al 2010 ), Pedimap ( Voorrips et al 2012 ), Helium ( Shaw et al 2014 ), and E-Brida ( E-Brida 2018 ), and web-based tools for family trees like The Pedigree Tool ( Lachmund et al 2004 ) or for crops like maize and soybean such as PedigreeNet ( Braun et al 2019 ) and SoyPedi ( Jeong et al 2022 ) have been already developed for visualizing pedigrees. The majority of these visualization tools have been designed for breeding purposes, reason why some of them require attached databases, perform genetic calculations, and permit the upload of marker allele data.…”