Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2019
Publication Date: 2/28/2019
Citation: Faria, D., Pavia, S., Wilson, C.S., Blackburn, H.D. 2019. Assessing Sus scrofa diversity among continental United States, and Pacific Islands populations using molecular markers from a gene banks collection. Scientific Reports. 9:3173. https://doi.org/10.1038/s41598-019-39309-9.
Interpretive Summary: Livestock genetic diversity is the basis for genetic change leading to increases in productivity. Gene banks have the potential to collect, save, and use genetically diverse samples at some point in the future. Therefore understanding the genetic variation captured and the relationship among populations of any given species informs collection management and potential stakeholders wishing to use the collection. In this study germpalsm or tissue samples from 500 pigs, representing 19 distinct populations were evaluated with genetic markers. Samples were derived from pigs in the continental US, US Pacific islands, and three Chinese breeds imported into the US during the 1980's. The research presented demonstrated the unique genetic structure among American breeds, in particular the Duroc. Feral populations on Pacific islands showed a unique ancestry from breeds now found in the continental US, China, and a third source thought to come from southern Asia as part of the Polynesian settlement. The results demonstrate that US swine populations are genetically diverse and the samples are generally unrelated thereby assuring that a broad range of genetic variation has been captured and available for use by a broad range of stakeholders.
Technical Abstract: Human migration and trade have facilitated domesticated livestock movement, gene flow and development of genetically diverse subpopulations (breeds) upon which agriculture is based. Because these factors and a range of ecological conditions the United States has a diverse set of livestock populations. However, quantifying genetic diversity of these populations is incomplete. This paper quantifies the genetic diversity captured in the national gene bank and explores the genetic structure and differences among 19 pig populations including feral populations in the Pacific Ocean, continental US rare and commercial breeds, and Chinese breeds imported to the US during the late 1980’s using 70,231 SNP on samples from 500 animals. Among breeds found on the continental US 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 populations from Pacific islands was identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian (H5) waves of gene flow. Quantifying the diversity and potential origin of Pacific populations provides insight as to future uses of such populations and the need for their preservation. Viewing the various diversity measures in terms of a collection held by a gene bank we encouragingly found a lack of inbreeding within breeds suggesting the collection represents widely sampled individual breeds.