Characterization of genomic diversity and population structure of worldwide Duroc subpopulations and other pig breeds

Authors: WEN, HUI - Purdue University; Blackburn, Harvey; MULIM, H - Purdue University; OLIVERIA, H - Purdue University; HERMESCH, S - University Of New England; CHEN, CHING-YI - Genus; HOLL, JUNSTIN - Genus; SCHINCKEL, ALLAN - Purdue University; BRITO, LUIZ - Purdue University

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2025
Publication Date: 12/16/2025
Citation: Wen, H., Blackburn, H.D., Mulim, H.A., Oliveria, H.R., Hermesch, S., Chen, C., Holl, J., Schinckel, A.P., Brito, L.F. 2025. Characterization of genomic diversity and population structure of worldwide Duroc subpopulations and other pig breeds. Genetics Selection Evolution. https://doi.org/10.1186/s12711-025-01017-6.
DOI: https://doi.org/10.1186/s12711-025-01017-6

Interpretive Summary: Duroc pigs were developed in the U.S. and play a predominant role in global pork production due to their production characteristics. Therefore, understanding genetic diversity among global Duroc populations is critically important. We obtained genotypes from four U. S., three Canadian, 3 Australian, and 1 European corporate populations plus non-corporate samples from the ARS/National Animal Germplasm Program’s collection of Durocs for evaluation. In total 1,409 Durocs were included in the study. Thirteen additional breeds (n = 449) were included in the study to aid in exploring genetic diversity in Duroc. All Duroc populations evaluated were genetically distinct, likely due to differing selection protocols and genetic drift. However, North American and European populations were more closely associated with one another when compared to Australian Durocs. The effective population size for Duroc subpopulations ranged from 17 to 47 suggesting breeding companies need to monitor their populations using genetic diversity measures like effective population size and/or inbreeding levels. That said, when all the subpopulations were merged together and evaluated the effective population size for the breed was 172 animals. This finding suggests substantial genetic variation exists for the breed. It also suggests that breeding companies could possibly turn to each other’s populations to introduce new genetic variation. While genetic variation among Duroc is high there are several measures of genetic diversity for some populations suggesting breeding companies need to vigilantly monitor their population's genetic diversity and employ tactics to support selection goals while maintaining sufficient within population genetic diversity.

Technical Abstract: Duroc is one of the most popular terminal sire pig breeds worldwide due to its greater growth rate, meat quality, feed efficiency, carcass characteristics, and resilience to environmental stressors as compared to other breeds. Despite the breed popularity, its developmental history, genetic diversity, and genetic relationships with other pig breeds remain largely unknown. Therefore, the primary objective of this study was to investigate population structure and genetic diversity in Duroc subpopulations from Europe, North America, and Australia, and other selected pig breeds. The studied pig populations were differentiated into five subgroups – North American Durocs, Australian Durocs, Asian-Pacific pig breeds, and two other breed pig groups (OBP1 and OBP2) – consistent with their geographical origins, as revealed by population structure analyses. The estimated effective population size (Ne) of Duroc subpopulations ranged from 17 to 47 while the Ne for the combined Duroc subpopulations was 172. A total of 130,558 runs of homozygosity (ROHs) were identified across all individuals, with 90,357 ROHs in Durocs and 40,201 in other pig breeds. Durocs had a greater number and proportion of longer ROHs (> 8 Mb) compared to other pig breeds. The ROH-based inbreeding (FROH) values were significantly greater in Durocs than in most of the other breeds, indicating the need for better management of genetic diversity in the breed. We observed strong correlations (> 0.65) between different inbreeding metrics (e.g., FHOM1 and FUNI, FHOM1 and FHOM2, FGRM and FUNI) in all the studied pig populations. A total of one, 76, 181, and 674 candidate genes overlapping with the ROH islands were identified for North American Durocs, Australian Durocs, Asian-Pacific pigs, and OBP2 pigs, respectively. The identified KEGG pathways are mainly related to metabolism, the immune system, cellular processes, and signal transduction. Significant differences exist in genetic diversity, population structure, and ancestry within Duroc subpopulations and between Duroc and other pig breeds. The observed inbreeding levels in Duroc subpopulations indicate the need for better management of genetic diversity within the breed. The functional enrichment analyses of shared ROH islands and FST from pig populations provide new insights into the consequences of selection in the past decades, including the identification of many pathways related to the immune system and energy metabolism.