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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 #399771

Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Characterization and localization within and across breed measures of dominance as observed in inbreeding depression and heterosis

item BEN ZAABZA, HAFEDH - University Of Vermont
item Neupane, Mahesh
item JAAFAR, MOHD - Cornell University
item KRISHNAMOORTHY, SRIKANTH - Cornell University
item MCKAY, STEPHANIE - University Of Vermont
item Miles, Asha
item HUSON, HEATHER - Cornell University
item STRANDÉN, ISMO - Natural Resources Institute Finland (LUKE)
item Blackburn, Harvey
item Van Tassell, Curtis - Curt

Submitted to: Gordon Research Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/7/2022
Publication Date: N/A
Citation: N/A

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 the genetic architecture of inbreeding depression. We believe that a richer understanding of additive, dominance, and runs of homozygosity (ROH) effects in purebred and crossbred dairy cattle will help to understand the impact of these factors on inbreeding depression and heterosis. To identify and localize genomic regions associated with additive, dominance, and ROH effects we performed a single-SNP genome-wide association study (GWAS) analysis, where SNPs were fit as fixed effects for the additive, dominance, and ROH effects one locus at a time. The current analysis has been performed using 125,000 genotyped US Holstein cows born between 2015 and 2020 genotyped on 79,294 SNP markers. We have analyzed only milk yield to date but will analyze production, fertility, and health traits. We found that the regions with the most notable effects were located on chromosomes 14 between 0 and 2Mb and on chromosome 6 between 20 and 30Mb. Dominance effects had less pronounced -log10(P) peaks compared to additive effects, and only a few significant dominance effects were detected. The most notable dominance effect was observed on chromosome 5. Similarly, the effects of ROH revealed less prominent -log10(P) peaks than the additive effects, although higher than dominance effects. Indeed, some narrow ROH peaks occurred on chromosome 14. This study will be extended to use over 4 million purebred Holsteins and nearly 1 million Jersey cattle and all available crossbred cows.