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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 #400864

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

Location: Animal Genomics and Improvement Laboratory

Title: Characterization and localization of within and across breed as indications of 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 STRANDEN, ISMO - Natural Resources Institute Finland (LUKE)
item Blackburn, Harvey
item Van Tassell, Curtis - Curt

Submitted to: Advances in Genome Biology and Technology
Publication Type: Abstract Only
Publication Acceptance Date: 2/28/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: With the global adoption of genomic selection, the annual level of inbreeding in dairy cattle has rapidly increased. Inbreeding raises homozygosity throughout the genome and can lead to inbreeding depression in fitness traits. Characterization of dominance effects improves our understanding of the genetic architecture of inbreeding depression. Runs of homozygosity (ROH) are currently considered to provide an effective measure of genomic inbreeding. To identify and localize the genomic landscape of the genomic regions associated with additive, dominance, and ROH effects in 2 breeds of US dairy cattle, we carried out a single-SNP genome-wide association study (GWAS) analysis, fitting SNPs as fixed effects for additive, dominance, and ROH effects one locus at a time. We used a small data set containing 180, 437 pedigreed and genotyped cows born between 2015 and 2020. Genotypes were imputed to approximately 78k. The analysis was conducted only on yield deviation for 305-d milk yield, but other low heritably traits such as fertility and health will also be analyzed later. We found that the regions with the most pronounced additive effects were located on chromosomes 14 between 0 and 2Mb and on chromosome 6 between 20 and 30Mb. Dominance effects had less pronounced -log_10(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. One SNP on chromosome 14 also had a large dominance effect. Similarly, ROH effects revealed less prominent -log_10(P) peaks than additive effects, although higher than dominance effects. In fact, some high, narrow ROH peaks were found on chromosome 14. Chromosome 21 also had one SNP with a large ROH effect. This present study will be further extended to a sizable genomic dataset comprising over 4 million pedigreed and genotyped purebred Holstein cows, nearly 1 million pedigreed and genotyped Jersey cows, and all available crossbreds.