SNP determination and breeding values

How are SNPs determined in the laboratory?

SNP-chips are used in laboratory analysis. SNP-chips are available from different manufacturers and in different versions (number of SNPs which are analysed per sample). Standard at the outset for cattle (dairy breeds) was the Illumina® BovineSNP50 BeadChip, with which over 54,000 SNPs were determined simultaneously on 12 samples. There are now others with fewer SNPs called low-density chips (LD-chips) and others with over 777,000 SNP, described as high-density chips (HD-chips). Added to this are chips which, in addition to SNPs, also offer hereditary defect tests (e.g. SMA, Weaver, BLAD, CVM) for estimating breeding values and some tests for certain monogenically inherited characteristics (e.g. red factor, kappa-casein, polledness for certain breeds). Genotypes of LD-chips can be projected through imputing on a higher density (standard chip or even HD-chip). HD-chips are currently only used in research projects because they do not deliver any significant benefit for breeding value estimation.

From SNPs to breeding values

Most SNPs, as determined in the laboratory, tell us nothing initially about the hereditary potential of an animal. Only through statistical methods are the connections between SNPs and the characteristics of interest for breeding exposed. The necessary data often deliver proven bulls whose hereditary patterns are well-known. To this end, many studied proven bulls are required, presumably over a thousand; the more the better. Cows with reliable breeding values can also make a contribution.

Once the relationships have been determined, using SNP studies in combination with the information about their parents, breeding values for young animals can be determined which are significantly more reliable than pure lineage breeding values. How reliable these genomic breeding values are, depends primarily on how well the relationship between SNPs and breeding values can be estimated and which heritability the trait manifests.

How reliable are genomic optimized breeding values (GOBV) in comparison to traditional breeding values (BW)? There have been various studies on this, for example, by Van Doormaal (2009) for a selection of traits on Canadian Holsteins:

Breeding value reliability (coefficient of determination, B%) Holstein Canada (Van Doormaal, 2009)

The inclusion of SNP information, primarily for calves, delivers a significant increase in reliability in comparison to the previous method. But cows can also be assessed more reliably with SNP information than was possible in the traditional way of estimating breeding values based on individual yield and progenitor information. For bulls that have been proven in Switzerland, on the other hand, there is no further increase in reliability to be achieved.