Associations for whole-exome sequencing profiling with carcass traits in crossbred pigs

Jae Young  Yoo1   Sang-Mo  Kim2,3   Dong Hyun  Lee2   Gye-Woong Kim2   Jong-Young  Lee3,*   

1Division of Biobank, National Biobank of Korea, Cheongju 28160, Korea
2Department of Animal Resources Science, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea
3Oneomics Ltd., Bucheon 14585, Korea


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.

Figures & Tables

Fig. 1. The analytical framework for the identification of carcass traits genes in crossbred pigs. The diagram shows the processes used to filter the variants identified by whole exome sequencing. KASP, Kompetitive allele-specific polymerase chain reaction; KIF5B, kinesin family member 5B; GLI2, GLI family zinc finger 2; KIF26B, kinesin family member 26B; CIE, International Commission on Illumination; L*, indicates lightness.