Embryonic lethality due to recessive alleles is a major concern in livestock breeding programs. The Online Mendelian Inheritance in Animal (OMIA) is a database of reported recessive mutations in livestock that helps breeders to manage the segregation of these mutations in their population. Recessive alleles are lethal in the offspring of two carrier parents; therefore, identifying and eliminating carrier animals are critical for maintaining the breed. Hanwoo cattle is native to the Korean peninsula and is of great economic importance to Korea. Due to geographical constraints and the controlled breeding program with very few proven bulls, if not monitored periodically, the threat of segregation of recessive lethal alleles in the population remains high. Therefore, identifying potential carriers of lethal recessive alleles is critical in Hanwoo. In this regard, we genotyped 17,325 animals using bovine 50K Illumina SNP chip and also sequenced a further 311 animals which was mapped against the bovine reference genome sequence. We then used the OMIA database to identify reported recessive alleles and calculated the allele frequency of these mutations in the population to determine potential lethal alleles carried by the animals.

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP × Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (|log2FC| > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.