Breeding dairy cows has changed a lot in recent years. Nowadays, it often involves using genetic markers from SNP chips. This method is pretty standard in the industry. But, is it the best way to predict important traits in dairy cows? This is what a recent study tried to find out.

        The study looked at how well different types of genetic variants could predict things like fat and protein content in milk, as well as the total amount of milk produced. These predictions were compared to those made using generic SNP markers from a common 50k SNP chip.

        The study used five different classes of functional variants. These variants were found through various methods. Some were identified through Genome-Wide Association Studies (GWAS). Others came from RNA sequencing, Histone modification ChIP-seq, or ATAC-seq. Additionally, some were coding variants. Each of these methods looks at different aspects of the genome, providing a more detailed picture.

        The results showed that using these specific functional variants could improve the accuracy of predictions. This is important because it means breeders might be able to make better decisions. By focusing on these specific variants, they could potentially select cows that produce better milk. But, it's not all good news. Using these variants can be more complex and costly.

        The study also compared the accuracy of predictions made using these functional variants to those made using randomly selected SNPs from the 50k chip. The idea was to see if the extra effort of identifying functional variants was worth it. The findings suggest that, in some cases, it might be. But, the benefits vary depending on the trait being predicted.

        So, what does this all mean for dairy cow breeding? It suggests that there might be better ways to predict important traits. But, it also shows that these methods come with their own challenges. Breeders will need to weigh the benefits against the costs and complexity. In the end, the goal is to produce better milk. But, how to get there is still up for debate.

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