Abstract
Human migration and trade facilitated domesticated livestock movement, gene flow and development of diverse populations upon which agriculture is based. In addition, varying USA ecological conditions has led to a diverse set of livestock populations to utilize. Quantifying genetic diversity of these populations is incomplete. This paper quantifies genetic diversity captured by the National Animal Germplasm Program and explores genetic structure and differences among 19 pig populations (feral populations from Pacific islands, continental US, and Chinese breeds) using 70,231 SNP from 500 animal samples. Among continental US breeds Fis was consistently low suggesting genetic variability is sufficiently available for breeders to use. A unique population structure using principal component analysis illustrated clear distinctions between Duroc, Yorkshire, Hampshire, breeds of Chinese origin, and feral Pacific Island populations were identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian waves of gene flow. Quantifying diversity and potential origin of Pacific populations provides insight for future uses, and the need for preservation. Viewing gene bank holdings in context of diversity measures we found a lack of inbreeding within breeds, suggesting the collection represents a wide sampling of individual breeds.
Highlights
The objective of this study was to quantify the genetic diversity of a substantial number of pig breeds found in the United States (US) as previous assessments tend to be focused on Europe and Asia[1,2,3,4]
Large and substantial genetic differences in pig populations dispersed across the continental US, Pacific Islands and Chinese breeds were found
Results suggest that feral populations from Pacific islands have a combination of European, East Asian and potentially South East Asian origin
Summary
The objective of this study was to quantify the genetic diversity of a substantial number of pig breeds found in the United States (US) as previous assessments tend to be focused on Europe and Asia[1,2,3,4]. McCann et al.[8] suggested animals sampled in the Hawaiian Islands originated from Europe, China, Papua-New Guinea, Vanuatu, and shared haplotypes with other domestic-feral pigs and S. verrucosus (from Java). The Duroc in particular is an interesting example as its foundation breeds have not been shown to have strong genetic linkages with other European breeds[1,3]. These authors have suggested that the breed may have been comprised, in part, of Guinea Hog from Africa (among other breeds) due to its red color. A better understanding of the genetic diversity among these U.S populations has a number of uses, including: general management of genetic diversity by public and private sectors, targeting future germplasm collections, and providing input into policies concerning feral pig populations on Pacific islands
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