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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #404930
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: Characterization of additive, dominance, and runs of homozygosity effects inbreeds of dairy cattle

Author
item BEN ZAABZA, HAFEDH - University Of Vermont
item Neupane, Mahesh
item JAAFAR, M - Cornell University
item SRIKANTH, K - Cornell University
item MCKAY, STEPHANIE - University Of Vermont
item Miles, Asha
item STRANDEN, I - Natural Resources Institute Finland (LUKE)
item HUSON, HEATHER - Collaborator
item Blackburn, Harvey
item Van Tassell, Curtis - Curt

Submitted to: European Association of Animal Production Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 6/1/2023
Publication Date: 8/26/2023
Citation: Ben Zaabza, H., Neupane, M., Jaafar, M., Srikanth, K., Mckay, S., Miles, A.M., Stranden, I., Huson, H.J., Blackburn, H.D., Van Tassell, C.P. 2023. Characterization of additive, dominance, and runs of homozygosity effects inbreeds of dairy cattle [abstract]. European Association of Animal Production Proceedings. p. 806.

Interpretive Summary:

Technical Abstract: The global application of genomic selection in dairy cattle has raised interest in characterizing dominance effects for a better understanding of inbreeding depression (IB). We believe that a richer understanding of additive (ADD), dominance (DOM), and runs of homozygosity (ROH) effects in purebred and crossbred dairy cattle will help to understand the impact of these factors on IB and heterosis. To identify and localize genomic regions associated with ADD, DOM, and ROH effects we performed a single-SNP GWAS analysis, where SNPs were fit as fixed effects for the ADD, DOM, and ROH one locus at a time. The current analysis has been performed using 125,000 US Holstein cows genotyped on 79,294 SNP markers. We have analyzed 3 production traits, 3 fertility traits, and somatic cell score (SCS). For the production traits, SNPs on BTA14 had the largest ADD effects. For fertility traits, SNPs on BTA1 had the most significant ADD effects. SCS had no significant DOM effects. Few DOM effects were detected for production traits and these effects had lower significance than ADD effects. Estimates of fertility trait DOM were detected with similar statistical significance as the ADD effects. The ROH revealed less prominent -log10(P) peaks than the ADD effects for all traits. Genome-wide inbreeding depression will be examined for all traits. Correlations between ROH and ADD effects were close to 0. Correlations between ROH and DOM effects calculated by ADD-DOM model were 0.006. However, correlations between ROH and DOM effects calculated by ADD-DOM-ROH model were 0.31. These findings suggest that confounding exists between ADD and ROH effects – and that DOM and ROH components capture the same variance. This study will be further extended to a genomic dataset comprising over 4 million (1 million) genotyped purebred Holstein (Jersey) cows and all available crossbreds.