Abstract
Single nucleotide polymorphism (SNP) data of 7384 Fleckvieh bulls was analyzed to identify epistatic interactions influencing stillbirth. Deregressed breeding values were used as phenotypes. The epistatic effects were identified as significant interaction terms from pairwise linear regressions performed for each SNP after accounting for multiple testing. Majority of the detected epistatic effects were located in the 9-31Mb region of chromosome 14, corresponding to the most significant region from the genome wide association. Additional epistatic SNPs at 50.5Mb and 80.5 Mb at the same chromosome were detected. The region around 25 Mb contained genes connected to height and body size such as PLAG1, CHCHD7, LYN, RDHE2 (SDR16C5) and PENK. The other interesting region at 50.5Mb contained the TRPS1 gene influencing bone malformations. Both regions have been identified as candidates influencing stillbirth.
Highlights
Epistasis is commonly defined as interaction between loci, when the phenotypic effect of a locus is influenced by the genotype of the second locus
Single nucleotide polymorphism (SNP) genotypes from 7384 Fleckvieh bulls were considered in the study, initially from both versions of BovineSNP50 BeadChips and the Illumina HD chip
Since all pairwise combinations for all SNPs were analyzed, it was common that neighboring SNPs from a given genomic region were showing significant interaction to other neighboring, or even the same SNP in another region, most likely describing the same connection
Summary
Epistasis is commonly defined as interaction between loci, when the phenotypic effect of a locus is influenced by the genotype of the second locus. These interactions could be present between two or more loci (Carlborg and Haley 2004). These interactions are known to influence a plethora of quantitative traits, see Cordell (2002) and Mackay (2014) for review, the topic is not extensively studied in animal genetics. Our particular aim was to analyze epistatic effects influencing stillbirth in cattle
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