Abstract
BackgroundIn the 1980s, Korean native black pigs from Jeju Island (Jeju black pigs) served as representative sample of Korean native black pigs, and efforts were made to help the species rebound from the brink of extinction, which occurred as a result of the introduction of Western pig breeds. Geographical separation of Jeju Island from the Korean peninsula has allowed Jeju black pigs not only to acquire unique characteristics but also to retain merits of rare Korean native black pigs.ResultsTo further analyze the Jeju black pig genome, we performed whole-genome re-sequencing (average read depth of 14×) of 8 Jeju black pig and 6 Korean pigs (which live on the Korean peninsula) to compare and identify putative signatures of positive selection in Jeju black pig, the true and pure Korean native black pigs. The candidate genes potentially under positive selection in Jeju black pig support previous reports of high marbling score, rare occurrence of pale, soft, exudative (PSE) meat, but low growth rate and carcass weight compared to Western breeds.ConclusionsSeveral candidate genes potentially under positive selection were involved in fatty acid transport and may have contributed to the unique characteristics of meat quality in JBP. Jeju black pigs can offer a unique opportunity to investigate the true genetic resource of once endangered Korean native black pigs. Further genome-wide analyses of Jeju black pigs on a larger population scale are required in order to define a conservation strategy and improvement of native pig resources.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0160-1) contains supplementary material, which is available to authorized users.
Highlights
In the 1980s, Korean native black pigs from Jeju Island (Jeju black pigs) served as representative sample of Korean native black pigs, and efforts were made to help the species rebound from the brink of extinction, which occurred as a result of the introduction of Western pig breeds
We retained a total of ~15.91 million (M) SNPs, comparable to recent studies of 18.68 M, 9.49 M and 6.79 M SNPs identified from diverse pig breeds [9,29,30] (Additional file 1: Table S2)
Assuming two source populations (K = 2), the program assigns all individuals to either JBP or KP (Figure 1A). This genetic clustering analysis provided no concrete support in favor of population admixture between JBP and KP
Summary
In the 1980s, Korean native black pigs from Jeju Island (Jeju black pigs) served as representative sample of Korean native black pigs, and efforts were made to help the species rebound from the brink of extinction, which occurred as a result of the introduction of Western pig breeds. The economic value of this breed is well appreciated, KNBP shows a relatively slower growth rate and lighter carcass weight [2], which has led to the introduction of improved breeds such as Hampshire and Berkshire pigs for both growth and lean meat production since the 1970’s [3]. This massive influx of industrial pig breeds has JBP is considered as the rare representative of true KNBP [4], of which genetic resources are of prime importance in industrial breeding programs. The biological basis for these characteristics of JBP has not been clearly demonstrated
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