Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #413161
Research Project: Increasing Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

Title: A million-cow genome-wide association study of productive life in U.S. Holstein cows

Author
item ZUOXIANG, LIANG - University Of Minnesota
item DZIANIS, PRAKAPENKA - University Of Minnesota
item ZAABZA, HAFEDH - Collaborator
item Vanraden, Paul
item Van Tassell, Curtis - Curt
item DA, YANG - University Of Minnesota

Submitted to: Genetic Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/6/2024
Publication Date: 9/26/2024
Citation: Zuoxiang, L., Dzianis, P., Zaabza, H.B., Van Raden, P.M., Van Tassell, C.P., Da, Y. 2024. A million-cow genome-wide association study of productive life in U.S. Holstein cows. Genetic Selection Evolution. 56:67. https://doi.org/10.1186/s12711-024-00935-1.
DOI: https://doi.org/10.1186/s12711-024-00935-1

Interpretive Summary: Productive life (PL) of a cow is the time the cow remains in the milking herd from first calving to exit from the herd due to culling or death and is an important economic trait in U.S. Holstein cattle. The large samples of Holstein genomic evaluation data provided unprecedented opportunity to identify genetic factors affecting PL in Holstein. Utilizing over one million cows, this study identified genetic factors affecting PL including some rare but sharply negative detrimental genotypes to PL for eliminating heifers carrying those genotypes. The results of this study provided high-confidence evidence for the understanding of genetic factors affecting PL.

Technical Abstract: Background Productive life (PL) of a cow is the time the cow remains in the milking herd from first calving to exit from the herd due to culling or death and is an important economic trait in U.S. Holstein cattle. The large samples of Holstein genomic evaluation data that have become available recently provided unprecedented statistical power to identify genetic factors affecting PL in Holstein cows using the approach of genome-wide association study (GWAS). Methods The GWAS analysis used 1,014,718 Holstein cows with phenotypic observations on PL and genotypes of 75,365 single neucleotide polymorthism (SNP) markers. The statistical tests and estimation of SNP additive and dominance effects used the approximate generalized least squares method implemented by the EPISNPmpi computer program. Results The GWAS detected 3,346 significant additive effects of PL distributed over all 29 autosomes and the X-Y nonrecombining region of the X chromosome (Chr31). Two chromosome regions had the most significant and largest cluster of additive effects, the SLC4A4-GC-NPFFR2 (SGN) region of Chr06 with pleiotropic effects for PL, fertility, somatic cell score and milk yield; and the 32-52 Mb region of Chr10 with peak effects for PL in or near RASGRP1 with many important immunity fuctions. The dominance tests detected 33 significant dominance effects including 13 dominance effects with sharply negative homozygous recessive genotypes on Chr18, Chr05, Chr23 and Chr24. A Chr14 region with the DGAT1 gene known to have the most significant effects for milk production traits did not have significant effects for PL. Conclusions The GWAS results showed that highly significant genetic effects for PL were in a chromosome regions known to have highly significant effects for fertility and health and a chromosome region with multiple genes with reproductive and immunity functions. SNPs with rare but sharply negative homozygous recessive genotypes for PL existed and should be used for eliminating heifers with the homozygous recessive genotypes.