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

BACKGROUND: Duroc is one of the most popular terminal sire pig breeds worldwide due to its greater growth rate, meat quality, feed efficiency, and carcass characteristics compared to other breeds. Despite the breed's 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 of Duroc subpopulations from Europe, North America, and Australia, and of other pig breeds. RESULTS: The studied pig populations were differentiated into five subgroups(European and North American Durocs, Australian Durocs, Asian-Pacific pig breeds, and two other breed 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 140,713 runs of homozygosity (ROHs) were identified across all individuals, with 98,039 ROHs in Durocs and 42,674 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 in all the studied pig populations. A total of 43, 18, 27, 37, and 20 candidate genes were identified in the ROH islands for European and North American Durocs, Australian Durocs, Asian-Pacific pigs, OBP1, and OBP2 pigs, respectively. The significant KEGG pathways were mainly related to growth, metabolism, immune system, cellular processes, and signal transduction. CONCLUSIONS: 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. Functional enrichment analyses of shared ROH islands provide new insights into biological pathways shaped by selection decisions in the past decades, especially those related to the immune system and energy metabolism.