blupADC: An R package and shiny toolkit for comprehensive genetic data analysis in animal and plant breeding

Abstract

Summary Genetic analysis is a systematic and complex procedure in animal and plant breeding. With fast development of high-throughput genotyping techniques and algorithms, animal and plant breeding has entered into a genomic era. However, there is a lack of software, which can be used to process comprehensive genetic analyses, in the routine animal and plant breeding program. To make the whole genetic analysis in animal and plant breeding straightforward, we developed a powerful, robust and fast R package that includes genomic data format conversion, genomic data quality control and genotype imputation, breed composition analysis, pedigree tracing, analysis and visualization, pedigree-based and genomic-based relationship matrix construction, and genomic evaluation. In addition, to simplify the application of this package, we also developed a shiny toolkit for users. Availability and implementation blupADC is developed primarily in R with core functions written in C++. The development version is maintained at https://github.com/TXiang-lab/blupADC. Supplementary information Supplementary data are available online