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Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection - PubMed

  • ️Tue Jan 01 2019

Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection

D A Faria et al. Sci Rep. 2019.

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Population structure of all US, Pacific Islands, and China populations analyzed revealed by Principal component analysis. The graph represents a 3D scatterplot of the 3 firsts PCAs, explaining 20.34, 10.76, and 8.47% of the genetic variance among the populations, respectively. BE – Berkshire, CW – Chester White, DU – Duroc, FE – Fengjing, GI – Guam Island, GH – Guinea Hog, HS – Hampshire, HI – Hawaii island, KI – Kauai island, HF – Hereford, LA – Landrace, LB – Large Black, MA – Mangalitsa, ME – Meishan, MI – Minzhu, OI – Ossabaw Island, SP – Spotted, TA – Tamworth, YK – Yorkshire.

Figure 2
Figure 2

Population Structure of all US, Pacific Islands and China populations revealed by Admixture assignment proportions, where K is the number of assumed ancestral clusters that ranged from 2 to 21. BE – Berkshire, CW – Chester White, DU – Duroc, FE – Fengjing, GI – Guam Island, GH – Guinea Hog, HS – Hampshire, HI – Hawaii island, KI – Kauai island, HF – Hereford, LA – Landrace, LB – Large Black, MA – Mangalitsa, ME – Meishan, MI – Minzhu, OI – Ossabaw Island, SP – Spotted, TA – Tamworth, YK – Yorkshire.

Figure 3
Figure 3

Population Structure of minor, feral, Pacific Islands and China populations revealed by Admixture assignment proportions where K is the number of assumed ancestral clusters that ranged from 2 to 9. GI – Guam island, GH – Guinea Hog, HI – Hawaii island, KI – Kauai island, LB – Large Black, MA – Mangalitsa, MI – Minzhu, OI – Ossabaw island, and, SP – Spotted.

Figure 4
Figure 4

(A) Frequency distribution of five Y chromosome haplotypes from sampled pig populations by geographic origin. (B) Median-joining network of Y chromosome haplotypes in all US, Pacific Islands and China populations.

Figure 5
Figure 5

Ancestral and recent effective population size of swine populations place in 10 groups for 60 previous generations. BE – Berkshire, CW – Chester White, DU – Duroc, Chinese (ME – Meishan, MI – Minzhu, FE – Fengjing), Pacific islands (GI – Guam Island, HI – Hawaii island, KI – Kauai island), Minor breeds (GH – Guinea Hog, LB – Large Black, MA – Mangalitsa, OI – Ossabaw Island, SP – Spotted, TA – Tamworth), HF – Hereford, HS – Hampshire, LA – Landrace, YK – Yorkshire.

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