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

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DOI

  • H. Atashi, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium, Department of Animal Science, Shiraz University, Shiraz 71441-65186, Iran , Belgium
  • Mazdak Salavati, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
  • Jenne De Koster, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium, Belgium
  • Mark Crowe, University College Dublin, Dublin, Ireland
  • Gert Opsomer, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium, Belgium
  • Miel Hostens, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium, Department of Farm Animal Health, University of Utrecht, Yalelaan 7, 3584 CL Utrecht, The Netherlands, Belgium
  • GplusE Consortium, Genotype Plus Environment Consortium (www.gpluse.eu)
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.
Original languageEnglish
Article number500
JournalAnimals
Volume10
Issue3
Pages (from-to)1-13
Number of pages13
ISSN2076-2615
DOIs
Publication statusPublished - Mar 2020

    Research areas

  • genome-wide association study, Holstein, calving interval, PREIMPLANTATION MOUSE EMBRYOS, IDENTIFICATION, FERTILITY, ACID-TRANSPORT REGULATION, QUANTITATIVE TRAIT LOCI, IN-VITRO, HERDS, REPRODUCTIVE TRAITS, GENETIC-PARAMETERS, AMINO-ACIDS

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