Single nucleotide polymorphisms of the KIT and KITLG genes in pigs

Here, we report the variability in the KIT tyrosine kinase receptor and its ligand KITLG genes by determining single nucleotide polymorphisms (SNPs) in 384 individuals including 11 pig breeds, two synthetic-line cross pigs, two cross breeds, and one Japanese wild boar. SNPs and indels within the coding sequence regions of KITLG and KIT and their 5'-flanking regions were detected by aligning sequences from eight pigs, and subsequently the SNPs were genotyped using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS). Principal component analysis using allele frequencies in the SNP locus showed a distant relationship between Asian and Euro-American pig groups, except for Berkshire and Tokyo X breeds. These breeds were located within the mid-portion of the distribution in the first principal component. The Hampshire breed was distant from the other pig groups on the axis of the second principal component. Haplotype frequencies that were deduced using non-synonymous substitutions of the KIT gene revealed the uniqueness of Landrace, Large White, Middle White, and three-way cross pigs (LWD) and of the Hampshire breed. On the other hand, the haplotypes of KITLG and KIT detected in the Berkshire breed were prevalent in Asian pig groups. This tendency is different from that observed in other Euro-American pig breeds.