Abstract
A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.
Highlights
In the swine industry, crossbreeding has been widely used to exploit the phenomenon of heterosis, or hybrid vigor
As Korean native pig breed (KNP) is an indigenous pig breed that has been adapted to the local environment of South Korea for a long period, we suggest that CRTAM might be a candidate gene that is associated with local adaptation of KNP and WRH populations
The purpose of using DUC in the crossing scheme includes complementing the body size and reproductive traits of KNP; we suggest that ADAMTSL3 and Cytoplasmic Polyadenylation Element Binding Protein 1 (CPEB1), which are located in runs of homozygosity (ROH) islands of DUC and WRH, might be associated with production and reproductive traits in both populations
Summary
In the swine industry, crossbreeding has been widely used to exploit the phenomenon of heterosis, or hybrid vigor. The LYD system resulted in higher productivities, including increased growth rate, by taking advantage of crossbreeding (Jin et al, 2006; Choi et al, 2016). KNP is known to have great meat qualities, such as high glucose content and a high unsaturated/saturated fatty acid ratio. Because it has economically unfavorable characteristics, such as slow growth rate, late maturity, and light carcass weight, it has low productivity compared with the commercial breeds; the population has decreased (Park et al, 2007; Hur et al, 2013). WRH preserved the characteristics of KNP, including superior meat quality, and had an improved growth rate compared with KNP (Kim et al, 2016)
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