Abstract
BackgroundIt has been suggested that traits with low heritability, such as fertility, may have proportionately more genetic variation arising from non-additive effects than traits with higher heritability, such as milk yield. Here, we performed a large genome scan with 408,255 single nucleotide polymorphism (SNP) markers to identify chromosomal regions associated with additive, dominance and epistatic (pairwise additive × additive) variability in milk yield and a measure of fertility, calving interval, using records from a population of 7,055 Holstein cows. The results were subsequently validated in an independent set of 3,795 Jerseys.ResultsWe identified genomic regions with validated additive effects on milk yield on Bos taurus autosomes (BTA) 5, 14 and 20, whereas SNPs with suggestive additive effects on fertility were observed on BTA 5, 9, 11, 18, 22, 27, 29 and the X chromosome. We also confirmed genome regions with suggestive dominance effects for milk yield (BTA 2, 3, 5, 26 and 27) and for fertility (BTA 1, 2, 3, 7, 23, 25 and 28). A number of significant epistatic effects for milk yield on BTA 14 were found across breeds. However on close inspection, these were likely to be associated with the mutation in the diacylglycerol O-acyltransferase 1 (DGAT1) gene, given that the associations were no longer significant when the additive effect of the DGAT1 mutation was included in the epistatic model.ConclusionsIn general, we observed a low statistical power (high false discovery rates and small number of significant SNPs) for non-additive genetic effects compared with additive effects for both traits which could be an artefact of higher dependence on linkage disequilibrium between markers and causative mutations or smaller size of non-additive effects relative to additive effects. The results of our study suggest that individual non-additive effects make a small contribution to the genetic variation of milk yield and fertility. Although we found no individual mutation with large dominance effect for both traits under investigation, a contribution to genetic variance is still possible from a large number of small dominance effects, so methods that simultaneously incorporate genotypes across all loci are suggested to test the variance explained by dominance gene actions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0241-9) contains supplementary material, which is available to authorized users.
Highlights
It has been suggested that traits with low heritability, such as fertility, may have proportionately more genetic variation arising from non-additive effects than traits with higher heritability, such as milk yield
Fuerst and Solkner [9] reported a higher proportion of the phenotypic variance explained by dominance and additive × additive epistatic effects than heritability estimated in the narrow sense for calving interval (CI)
Additive marker effects Manhattan plots of all additive single nucleotide polymorphism (SNP) effects for milk yield (MY) and CI in study populations are presented in Figs 1 and 2
Summary
It has been suggested that traits with low heritability, such as fertility, may have proportionately more genetic variation arising from non-additive effects than traits with higher heritability, such as milk yield. We performed a large genome scan with 408,255 single nucleotide polymorphism (SNP) markers to identify chromosomal regions associated with additive, dominance and epistatic (pairwise additive × additive) variability in milk yield and a measure of fertility, calving interval, using records from a population of 7,055 Holstein cows. Hoeschele [10] estimated additive and non-additive genetic variance for a number of cow fertility measures in US Holsteins and obtained broad sense heritabilities that were at least twice as large as narrow sense heritabilities, albeit with large standard errors. Fuerst and Solkner [9] reported a higher proportion of the phenotypic variance explained by dominance and additive × additive epistatic effects than heritability estimated in the narrow sense for calving interval (CI). Druet et al [11] observed similar values for additive and dominance variances in analyses of fertility traits for Austrian Simmental and Brown Swiss dairy cattle and Palucci et al [12] estimated non-additive genetic effects of sizable magnitude for a number of fertility measures in Canadian Holstein heifers and cows and suggested including non-additive genetic effects in models for estimating genetic merit of animals
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