• Korean Journal of Agricultural Science
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• v.49 no.3
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• pp.595-606
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• 2022

Industrial pig breeding has used the Duroc breed and terminal sires in a three-way crossbred system in Korea. This study identified the gene variation patterns related to carcass quality in crossbred pigs ([Landrace × Yorkshire] × Duroc) using whole-exome sequencing (WES). This study used crossbred pigs and divided them into two groups (first plus grade, n = 5; second grade, n = 5). Genomic DNA samples extracted from the loin muscles of both groups were submitted for WES. A set of validated single-nucleotide polymorphisms (SNPs: n = 102) were also subjected to the Kompetitive allele-specific polymerase chain reaction (KASP) to confirm the WES results in the loin muscles. Based on the WES, SNPs associated with meat quality were found on chromosomes 5, 10, and 15. We identified variations in three of the candidate genes, including kinesin family member 5B (KIF5B), GLI family zinc finger 2 (GLI2), and KIF26B, that were associated with meat color, marbling score, and backfat thickness. These genes were associated with meat quality and the mitogen-activated protein kinase (MAPK) and Hedgehog (Hh) signaling pathways in the crossbred pigs. These results may help clarify the mechanisms underlying high-quality meat in pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.4
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• pp.462-469
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• 2017

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.