Integrating Bioinformatics and Machine Learning for Genomic Prediction in Chickens

Abstract

Genomic prediction plays an increasingly important role in modern animal breeding, with predictive accuracy being a crucial aspect. The classical linear mixed model is gradually unable to accommodate the growing number of target traits and the increasingly intricate genetic regulatory patterns. Hence, novel approaches are necessary for future genomic prediction. In this study, we used an illumina 50K SNP chip to genotype 4190 egg-type female Rhode Island Red chickens. Machine learning (ML) and classical bioinformatics methods were integrated to fit genotypes with 10 economic traits in chickens. We evaluated the effectiveness of ML methods using Pearson correlation coefficients and the RMSE between predicted and actual phenotypic values and compared them with rrBLUP and BayesA. Our results indicated that ML algorithms exhibit significantly superior performance to rrBLUP and BayesA in predicting body weight and eggshell strength traits. Conversely, rrBLUP and BayesA demonstrated 2–58% higher predictive accuracy in predicting egg numbers. Additionally, the incorporation of suggestively significant SNPs obtained through the GWAS into the ML models resulted in an increase in the predictive accuracy of 0.1–27% across nearly all traits. These findings suggest the potential of combining classical bioinformatics methods with ML techniques to improve genomic prediction in the future.