Abstract
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 language | English |
|---|---|
| Article number | 500 |
| Number of pages | 13 |
| Journal | Animals |
| Volume | 10 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 1 Mar 2020 |
Funding
Funding: This project has received funding from the European Union’s Seventh Framework Program for research, technological development and demonstration under grant agreement no. 613689. Acknowledgments: The authors would like to acknowledge the support provided by the European Commission under the Seventh Framework Program for the GplusE Projects. However, the views expressed in this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. List of authors within the GplusE consortium: Niamh McLoughlin, Alan Fahey, Elizabeth Matthews, Andreia Santoro, Colin Byrne, Pauline Rudd, Roisin O’Flaherty, Sinead Hallinan, Claire Wathes, Zhangrui Cheng, Ali Fouladi, Geoff Pollott, Dirk Werling, Beatriz Sanz Bernardo, Alistair Wylie, Matt Bell, Mieke Vaneetvelde, Kristof Hermans, Geert Opsomer, Sander Moerman, Jenne De Koster, Hannes Bogaert, Jan Vandepitte, Leila Vandevelde, Bonny Vanranst, Johanna Hoglund, Susanne Dahl, Soren Ostergaard, Janne Rothmann, Mogens Krogh, Else Meyer, Charlotte Gaillard, Jehan Ettema, Tine Rousing, Federica Signorelli, Francesco Napolitano, Bianca Moioli, Alessandra Crisà, Luca Buttazzoni, Jennifer McClure, Daragh Matthews, Francis Kearney, Andrew Cromie, Matt McClure, Shujun Zhang, Xing Chen, Huanchun Chen, Junlong Zhao, Liguo Yang, Guohua Hua, Chen Tan, Guiqiang Wang, Michel Bonneau, Andrea Pompozzi, Armin Pearn, Arnold Evertson, Linda Kosten, Anders Fogh, Thomas Andersen, Matthew Lucey, Chris Elsik, Gavin Conant, Jerry Taylor, Nicolas Gengler, Michel Georges, Frédéric Colinet, Marilou Ramos Pamplona, Hedi Hammami, Catherine Bastin, Haruko Takeda, Aurelie Laine, Anne-Sophie Van Laere, Martin Schulze, Sergio Palma Vera, Conrad Ferris, Cinzia Marchitelli.
Keywords
- Calving interval
- Genome-wide association study
- Holstein