solGS: a web-based tool for genomic selection

BMC Bioinformatics

Isaak Y Tecle⁵  Jeremy D Edwards⁵  Naama Menda⁵  Chiedozie Egesi¹  Ismail Y Rabbi⁴  Peter Kulakow⁴  Robert Kawuki³  Jean-Luc Jannink²  Lukas A Mueller⁵ 

[1] National Root Crops Research Institute (NRCRI), Umudike, Nigeria

[2] USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, USA

[3] National Crops Resources Research Institute, Kampala, Uganda

[4] International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria

[5] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA

关键词: Web-based tool;    Database;    Bioinformatics;    RR-BLUP;    Genomic selection;   

Others  :  1084348
DOI  :  10.1186/s12859-014-0398-7

 received in 2014-07-12, accepted in 2014-11-26,  发布年份 2014

【 摘 要 】

Background

Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders.

Results

We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs webcite.

Conclusions

solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program.

【 授权许可】

   
2014 Tecle et al.; licensee BioMed Central Ltd.

【 图 表 】

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