Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations

Howard, Jeremy T., Maltecca, Christian, Haile-Mariam, Mekonnen, Hayes, Ben J. and Pryce, Jennie E. (2015) Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations. BMC Genomics, 16 1: . doi:10.1186/s12864-015-1352-4

Author Howard, Jeremy T.
Maltecca, Christian
Haile-Mariam, Mekonnen
Hayes, Ben J.
Pryce, Jennie E.
Title Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2015-03-15
Year available 2015
Sub-type Article (original research)
DOI 10.1186/s12864-015-1352-4
Open Access Status DOI
Volume 16
Issue 1
Total pages 13
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Dairy cattle breeding objectives are in general similar across countries, but environment and management conditions may vary, giving rise to slightly different selection pressures applied to a given trait. This potentially leads to different selection pressures to loci across the genome that, if large enough, may give rise to differential regions with high levels of homozygosity. The objective of this study was to characterize differences and similarities in the location and frequency of homozygosity related measures of Jersey dairy cows and bulls from the United States (US), Australia (AU) and New Zealand (NZ).


The populations consisted of a subset of genotyped Jersey cows born in US (n = 1047) and AU (n = 886) and Jersey bulls progeny tested from the US (n = 736), AU (n = 306) and NZ (n = 768). Differences and similarities across populations were characterized using a principal component analysis (PCA) and a run of homozygosity (ROH) statistic (ROH45), which counts the frequency of a single nucleotide polymorphism (SNP) being in a ROH of at least 45 SNP. Regions that exhibited high frequencies of ROH45 and those that had significantly different ROH45 frequencies between populations were investigated for their association with milk yield traits. Within sex, the PCA revealed slight differentiation between the populations, with the greatest occurring between the US and NZ bulls. Regions with high levels of ROH45 for all populations were detected on BTA3 and BTA7 while several other regions differed in ROH45 frequency across populations, the largest number occurring for the US and NZ bull contrast. In addition, multiple regions with different ROH45 frequencies across populations were found to be associated with milk yield traits.

Multiple regions exhibited differential ROH45 across AU, NZ and US cow and bull populations, an interpretation is that locations of the genome are undergoing differential directional selection. Two regions on BTA3 and BTA7 had high ROH45 frequencies across all populations and will be investigated further to determine the gene(s) undergoing directional selection.
Keyword Dairy cattle
Runs of homozygosity
Signature of selection
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
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Citation counts: TR Web of Science Citation Count  Cited 4 times in Thomson Reuters Web of Science Article | Citations
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