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Background  Genome wide association studies are now widely used in the livestock sector to estimate the association among single nucleotide polymorphisms (SNPs) distributed across the whole genome and one or more trait. As computational power increases, the use of machine learning techniques to analyze large genome wide datasets becomes possible.    Methods  The objective of this study was to identify SNPs associated with the three traits simulated in the 16th MAS-QTL workshop dataset using the Random Forest (RF) approach. The approach was applied to single and multiple trait estimated breeding values, and on yield deviations and to compare them with the results of the GRAMMAR-CG method.    Results  The two QTL mapping methods used, GRAMMAR-CG and RF, were successful in identifying the main QTLs for trait 1 on chromosomes 1 and 4, for trait 2 on chromosomes 1, 4 and 5 and for trait 3 on chromosomes 1, 2 and 3.    Conclusions  The results of the RF approach were confirmed by the GRAMMAR-CG method and validated by the effective QTL position, even if their approach to unravel cryptic genetic structure is different. Furthermore, both methods showed complementary findings. However, when the variance explained by the QTL is low, they both failed to detect significant associations.

Genome wide association analysis of the 16th QTL- MAS Workshop dataset using the Random Forest machine learning approach