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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 #396483

Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

Title: Current state of inbreeding, genetic diversity, and selection history in all major breeds of U.S. dairy cattle

item LOZADA-SOTO, EMMANUEL - North Carolina State University
item MALTECCA, CHRISTIAN - North Carolina State University
item COLE, JOHN - Former ARS Employee
item Vanraden, Paul
item TIEZZI, FRANCESCO - University Of Florence

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/10/2022
Publication Date: 6/19/2022
Citation: Lozada-Soto, E.A., Maltecca, C., Cole, J.B., Van Raden, P.M., Tiezzi, F. 2022. Current state of inbreeding, genetic diversity, and selection history in all major breeds of U.S. dairy cattle [abstract]. Journal of Dairy Science. 105(Suppl. 1):188(abstr. 1475V).

Interpretive Summary:

Technical Abstract: This study aimed to characterize autozygosity, assess the current state of pedigree and genomic inbreeding, and identify trends in genetic diversity in five breeds of U.S. dairy cattle. Pedigree information and imputed genotypes for 76,389 autosomal markers were obtained for 4,173,679 animals of the Ayrshire (AY), Brown Swiss (BS), Guernsey (GU), Holstein (HO), and Jersey (JE) breeds. Inbreeding was calculated using pedigree information (FPED), genomic information via a marker-based approach (FGRM), and genomic information using runs of homozygosity (FROH). The average pedigree inbreeding ranged from 0.06 (AY, BS) to 0.08 (JE), FGRM ranged from 0.22 (HO) to 0.29 (GU, JE), and FROH ranged from 0.11 (AY) to 0.17 (JE). In addition, we assessed genetic diversity for sires and dams born before genomic selection (P1; 2000-2009), during the implementation of genomic selection (P2; 2010-2014), or after the widespread adoption of GS (P3; 2015-2018). The rate of yearly inbreeding accumulation ('Fyear) and effective population size (Ne) were calculated in each period. For AY, BS, and GU, no clear trends in 'Fyear and Ne were observed between periods. For HO and JE sires and dams, we observed a significant increase in inbreeding rate after genomic selection, resulting in effective population sizes that ranged from 14 to 29 for HO sires, from 20 to 55 for HO dams, from 35 to 74 for JE sires, and from 102 to 276 for JE dams. We performed QTL enrichment of genomic regions with high autozygosity. We found evidence of selection for milk, production, and health in all five breeds, for exterior traits in three breeds (except HO and GU), for meat and carcass in three breeds (except BS and HO), and for reproduction in all breeds except GU. We show how recent selection strategies have contributed to the observed levels of autozygosity, rate of inbreeding accumulation, and genetic diversity in the major U.S. dairy populations.