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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 #389457
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

Author
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 - North Carolina State University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/15/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: This study aimed to identify trends in inbreeding accumulation and genetic diversity in five breeds of U.S. dairy cattle. Pedigree and genotypic information were available for 4,010,718 animals of the Holstein (HO), Jersey (JE), Brown Swiss (BS), Ayrshire (AY), and Guernsey (GU) breeds. Inbreeding was calculated using pedigree information (F_PED), genomic information via a marker-based approach (F_GRM), and genomic information using runs of homozygosity (F_ROH). Genetic diversity was assessed at two time points, for animals born before (preGS; 2000-2009) and after (postGS; 2010-2020) the approximate implementation of genomic selection. The rate of yearly inbreeding accumulation (F_year), the effective number of remaining founder genomes (fg_e), and effective population size (N_e) were some of the genetic diversity metrics calculated within breed and birth year cohorts. All metrics of diversity in most breeds and timepoints indicated a decrease in genetic diversity in the last decade, especially in HO where current Ne estimates ranged from 23 to 32 depending on the inbreeding coefficient used. In addition, within breed we identified signatures of selection using a smoothed F_ST statistic and region-specific inbreeding using ROH. We found regions under selection and with high inbreeding in chromosomes 10 and 20 for HO, 2, 3, 7, and 20 for JE, 5, 6, and 16 for BS, 6 and 8 for AY, and 13, 15, and 19 for GU. These results show how the selection history of a breed and recent selection strategies contribute to the observed inbreeding load, rate of inbreeding accumulation, and genetic diversity of the population.