On Wednesday, June 18, 2025, the Workshop on Statistical Machine Learning Methods for Genomic Prediction Using R Program on the second day started at 10:00-13:00 WIB in the FMIPA UNY Ballroom. In this workshop, Professor Osval Antonio Montesinos López, Ph.D. from Universidad de Colima, Mexico delivered advanced materials covering three main materials. First, computational genetics material that discusses genetic markers from genotype data, the process of recoding marker information according to the rules, to calculating the Minor Allele Frequency (MAF). Second, a systematic method for calculating the genomic relationship matrix was discussed, which is important for understanding the genetic relationship between individuals. Third, various regression analysis methods such as ridge regression, lasso regression, and logistic penalized regression were presented. This material was presented starting from the definition and basic concepts, the statistical models used, to their application in real life, both through manual calculations and with the help of RStudio software.