AquaGS: An integrated GUI pipeline for genomic selection in aquaculture breeding

Aquaculture contributes significantly to the global economy and has become the key to global food security and nutrition strategies. In order to supply sustainable and equitable aquatic food, studies on aquaculture genomics, genetics and selective breeding are required. Genomic selection (GS) captures diversity and estimates breeding values based on genome-wide distributed markers enhancing aquaculture production efficiency, sustainability, product quality, and profitability. However, the application of GS in aquaculture is still in its initial stage compared with that in plants and livestock. The complex preprocessing, quality control and postprocessing steps, complicated statistical models, fussy file format conversions between various interfaces and frequent switches among different running environments prevent smooth and large-scale applications. In this study, we have developed AquaGS, an open-source Graphic User Interface (GUI) Genomic Selection pipeline offering click-by-click running from inputting raw data for phenotype and genotype to the final mate allocation scheme. AquaGS is a C++ based application that uses QT to create a GUI and integrates the functions needed for the GS process by calling various programs and specific tools in the background, such as C++, Python, R, PLINK and AlphaMate. AquaGS includes phenotype preprocessing, quality control, testing the significance of effects, breeding value predictions, cross-validation and mating allocation scheme generation, integrated from widely-used standalone methods and tools, such as BLUP, GBLUP, SSBLUP, Bayes A, Bayes B, Bayes Cπ, and Bayesian Lasso model. Additionally, AquaGS includes a mating design module based on optimum contribution selection to avoid inbreeding depression and maximize genetic gains. To accommodate various application scenarios, AquaGS offers a flexible, interactive and customized processing pipeline.