INTERGEN beyond Bayesian and genomics: Iteration on data and approximate accuracies capabilities for large-scale genetic analysis in animal and plant breeding

ABSTRACT The INTERGEN package has been under constant development for the last two decades using the Fortran 90/95 programming language. The latest version of INTERGEN includes three different binaries: intergen, intergeniod, and intergenacc. Intergen has been consistently expanded to include the Best Linear Unbiased Prediction (BLUP) genomic module in recent years. The intergeniod and intergenacc binaries are new and aim to estimate genetic merit using iteration on data (IOD) and approximate accuracy. The present study aimed to provide a high-level overview of INTERGEN functionalities and to assess the reliability of the IOD genomic new module included in the intergeniod. Single-step GBLUP (ssGBLUP) models using beef cattle growth and conformation traits were used to estimate breeding values using intergeniod and compared with benchmarking software (intergen). The rank correlation for the breeding values between intergeniod and intergen was equal to the unit. The INTERGEN package can be applied to the genetic analysis of large-scale datasets using intergen, intergeniod, or intergenacc.