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Open AccessArticle

A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach

1
Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium
2
Department of Animal Science, Shiraz University, Shiraz 71441, Iran
3
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
4
School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
5
Department of Farm Animal Health, University of Utrecht, Yalelaan 7, 3584 CL Utrecht, The Netherlands
*
Author to whom correspondence should be addressed.
All the authors from the consortium are listed in the Acknowledgemtns.
Animals 2020, 10(3), 500; https://doi.org/10.3390/ani10030500
Received: 23 January 2020 / Revised: 13 March 2020 / Accepted: 14 March 2020 / Published: 17 March 2020
(This article belongs to the Special Issue Farm Animal Gene Exploration)
Reproductive performance is an important factor, which determines productive life and drives culling decisions in dairy herds. There are strong motives for including reproductive performance in genetic selection programs of dairy cows; however, low heritability estimates reported for reproductive performance measures limit the genetic selection efficiency. More effective genetic selection could be achieved using genomic information. The aim of this study was to identify genomic region(s) associated with the length of the calving interval in Holstein cows. The accuracies of genomic estimated breeding values (GEBVs) with single-step genomic BLUP (ssGBLUP) and the pedigree-based BLUP were compared as well. The results showed that the accuracies of GEBVs using the single-step genomic BLUP were much higher than those estimated using the pedigree-based BLUP. We identified three genomic regions (BTA3, BTA6, and BTA7) associated with the length of the calving interval in Holstein dairy cows.
The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows. View Full-Text
Keywords: genome-wide association study; Holstein; calving interval genome-wide association study; Holstein; calving interval
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MDPI and ACS Style

Atashi, H.; Salavati, M.; De Koster, J.; Crowe, M.A.; Opsomer, G.; Hostens, M.; The GplusE Consortium. A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach. Animals 2020, 10, 500.

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