Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows

Aliloo, Hassan, Pryce, Jennie E., Gonzalez-Recio, Oscar, Cocks, Benjamin G. and Hayes, Ben J. (2015) Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows. BMC Genetics, 16 . doi:10.1186/s12863-015-0241-9


Author Aliloo, Hassan
Pryce, Jennie E.
Gonzalez-Recio, Oscar
Cocks, Benjamin G.
Hayes, Ben J.
Title Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows
Journal name BMC Genetics   Check publisher's open access policy
ISSN 1471-2156
Publication date 2015-07-22
Sub-type Article (original research)
DOI 10.1186/s12863-015-0241-9
Open Access Status DOI
Volume 16
Total pages 16
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background: 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. 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.
Results: We 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.
Conclusions: In 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.
Keyword Dairy cow
Fertility
Genome-wide association study
Non-additive genetic effect
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number 89

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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