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Article

Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle

1
Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
2
National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
3
Faculty of Animal Science, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Kraków, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Martino Cassandro
Animals 2022, 12(9), 1127; https://doi.org/10.3390/ani12091127
Received: 11 February 2022 / Revised: 25 April 2022 / Accepted: 26 April 2022 / Published: 27 April 2022
(This article belongs to the Section Animal Genetics and Genomics)
Traits related to the calving abilities and workability of cows are essential both for the dairy economy and for the welfare of cows. We analysed the direct and maternal components of calving ease, direct and maternal components of stillbirth, milking speed, and temperament by looking for SNPs, gene ontologies, and metabolic pathways significantly associated with the additive genetic variability of those traits. At the genetic level, 150 significant SNPs were identified whereas at the functional level we found 45 significant gene ontology terms and 5 metabolic pathways.
The goal of our study was to identify the SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability traits in dairy cattle. We analysed direct (DCE) and maternal (MCE) calving ease, direct (DSB) and maternal (MSB) stillbirth, milking speed (MSP), and temperament (TEM) based on a Holstein-Friesian dairy cattle population consisting of 35,203 individuals. The number of animals, depending on the trait, ranged from 22,301 bulls for TEM to 30,603 for DCE. We estimated the SNP effects (based on 46,216 polymorphisms from Illumina BovineSNP50 BeadChip Version 2) using a multi-SNP mixed model. The SNP positions were mapped to genes and the GO terms/KEGG pathways of the corresponding genes were assigned. The estimation of the GO term/KEGG pathway effects was based on a mixed model using the SNP effects as dependent variables. The number of significant SNPs comprised 59 for DCE, 25 for DSB and MSP, 17 for MCE and MSB, and 7 for TEM. Significant KEGG pathways were found for MSB (2), TEM (2), and MSP (1) and 11 GO terms were significant for MSP, 10 for DCE, 8 for DSB and TEM, 5 for MCE, and 3 for MSB. From the perspective of a better understanding of the genomic background of the phenotypes, traits with low heritabilities suggest that the focus should be moved from single genes to the metabolic pathways or gene ontologies significant for the phenotype. View Full-Text
Keywords: calving traits; gene ontology; metabolic pathways; mixed model calving traits; gene ontology; metabolic pathways; mixed model
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MDPI and ACS Style

Jakimowicz, M.; Szyda, J.; Zarnecki, A.; Jagusiak, W.; Morek-Kopeć, M.; Kosińska-Selbi, B.; Suchocki, T. Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle. Animals 2022, 12, 1127. https://doi.org/10.3390/ani12091127

AMA Style

Jakimowicz M, Szyda J, Zarnecki A, Jagusiak W, Morek-Kopeć M, Kosińska-Selbi B, Suchocki T. Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle. Animals. 2022; 12(9):1127. https://doi.org/10.3390/ani12091127

Chicago/Turabian Style

Jakimowicz, Michalina, Joanna Szyda, Andrzej Zarnecki, Wojciech Jagusiak, Małgorzata Morek-Kopeć, Barbara Kosińska-Selbi, and Tomasz Suchocki. 2022. "Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle" Animals 12, no. 9: 1127. https://doi.org/10.3390/ani12091127

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