Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Michalina Jakimowicz
ORCID logo ,
Barbara Kosińska-Selbi
* ,
Tomasz Suchocki
* ,
Andrzej Zarnecki
,
Wojciech Jagusiak
,
Małgorzata Morek-Kopeć
ORCID logo ,
Joanna Szyda
ORCID logo
Version 1 : Received: 11 February 2022 / Approved: 14 February 2022 / Online: 14 February 2022 (15:50:54 CET)

A peer-reviewed article of this Preprint also exists.

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. 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.

Abstract

(1) Background: The goal of our study was to identify SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability; (2) Methods: Based on the EuroGenomics reference data set, we analyzed direct (DCE) and maternal (MCE) calving ease, direct (DSB), and maternal (MSB) stillbirth, milking speed (MSP), and temperament (TEM). We estimated SNP effects using a multi-SNP mixed-model. Further, SNP positions were mapped to genes, and GO terms/KEGG pathways of the corresponding genes were assigned. The estimation of GO term/KEGG pathway effects was based on a mixed-model using SNP effects as dependent variables; (3) Results: 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), while 11 GO terms were significant for MSP, 10 for DCE, 8 for DSB and TEM, 5 for MCE, and 3 for MSB.; (4) Conclusions: 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 metabolic pathways or gene ontologies significant for the phenotype.

Keywords

GO: terms; GWAS; KEGG; SNP

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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