Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle

Authors: LOZADA-SOTO, EMMANUEL - North Carolina State University; MALTECCA, CHRISTIAN - North Carolina State University; JIANG, JICAI - North Carolina State University; COLE, JOHN - Former ARS Employee; Vanraden, Paul; TIEZZI, FRANCESCO - North Carolina State University

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2022
Publication Date: 11/1/2022
Citation: Lozada-Soto, E.A., Maltecca, C., Jiang, J., Cole, J.B., Van Raden, P.M., Tiezzi, F. 2022. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. Journal of Dairy Science. 105(11):8956-8971. https://doi.org/10.3168/jds.2022-22116.
DOI: https://doi.org/10.3168/jds.2022-22116

Interpretive Summary: This study leveraged a large dataset of genotyped US dairy cattle to characterize autozygosity and inbreeding in five populations. We compared the location, size, quantity of genomic stretches of homozygosity across breeds to assess potential differences in selective history. Within breed we also calculated pedigree and genomic inbreeding coefficients and estimated several metrics of genetic diversity to evaluate how the recent introduction of genomic selection has contributed to loss or gain of genetic diversity. This study showed substantial heterogeneity in the patterns and overall state of inbreeding across breeds and identified populations at risk of further loss in genetic diversity.

Technical Abstract: Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in five breeds of US dairy cattle. We analyzed a sizeable genomic dataset containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity larger than 1Mb were identified in each animal. The within-breed means for number and the combined length of runs of homozygosity ranged were highest in Jerseys (65.87 +- 8.52 ROH and 431.77 +- 83.49 Mb, respectively) and lowest in Ayrshires (39.20 +- 8.47 ROH and 268.39 +- 85.11 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using three different approaches, pedigree-based (F_PED), marker-based using a genomic relationship matrix (F_GRM), and segment-based using ROH (F_ROH). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using F_PED, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using F_GRM, and from 0.11 in Ayrshires to 0.17 in Jerseys using F_ROH. In addition, the effective population size at past generations (from 5 to 100 generations ago), the yearly rate of inbreeding, and the effective population size in three recent periods (2000-2009, 2010-2014, and 2015-2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the impact of the recent implementation of genomic selection on inbreeding accumulation.