Analysis of SNPs in the KIT gene of cattle with different coat colour patterns and perspectives to use these markers for breed traceability and authentication of beef and dairy products

Abstract

The identification of the breed of origin of farm animals has recently assumed particular relevance as increasing interests in marketing mono-breed labelled lines of beef and dairy products have created the need to protect them from frauds. In order to develop DNA based breed traceability and authentication protocols, the first step is the identification of breed specific markers with high discriminatory power among breeds. We analysed two single nucleotide polymorphisms identified in exon 2 (g.72779776C>T) and exon 3 (g.72783182A>G) of the KIT gene (a candidate gene for the spotting locus) in seven cattle breeds with different coat colour patterns (Italian Holstein-Friesian, no. = 61; Italian Brown, no. = 60; Italian Simmental, no. = 78; Jersey, no. = 60; Rendena, no. = 51; Reggiana, no. = 128; and Modenese, no. = 52). The two alleles of both SNPs were detected in all analysed breeds making their use unsuitable in breed traceabilty with a deterministic approach. Italian Simmental was almost fixed for the most common alleles (g.72779776C and g.72783182A). Haplotype analysis showed that spotted breeds (Italian Holstein-Friesian and Italian Simmental) had only two haplotypes with one of them ([C:A]) with high frequency (~90% and ~99%, respectively). Analysis of molecular variance (AMOVA) averaged over the two loci indicated that genetic variation between spotted and non-spotted groups of breeds amounted to 25.3% (P<0.05) supporting a possible involvement of the KIT gene in influencing the spotted phenotype, but probably not determining it, as we previously suggested. Pairwise Fst values indicated significant differences between almost all pair of investigated breeds. The high discriminatory power of the analysed SNPs is an important characteristic for the inclusion of these markers in SNP panels useful for breed allocation and traceability based on probabilistic approaches

Association of 20 candidate gene markers with milk production and composition traits in sires of Reggiana breed, a local dairy cattle population

“…In Holstein, allele C was associated with decreased MY (the opposite was observed in Reggiana) and PP (Leonard et al, 2005). KIT gene markers investigated in this study were previously associated with the spotted phenotype but not with any production traits (Fontanesi et al, 2010a(Fontanesi et al, , 2010b. Another marker in this gene was associated with milk somatic cell count but not with any other milk production traits (Fontanesi et al, 2014).…”

Combined use of principal component analysis and random forests identify population‐informative single nucleotide polymorphisms: application in cattle breeds

“…These genes are located in the QTL region for the spotted locus and are associated with spotted phenotypes and proportion of black in Holstein (Reinsch et al 1999;Fontanesi et al 2010b;Fan et al 2014). Markers in the KIT gene have been already proposed for breed traceability (Fontanesi et al 2010a). Another SNP (Hapmap26308-BTC-057761) was within the LAP3 Table S3 Order gene that is located in a region of BTA6 associated with milk production traits in dairy cattle and with feed intake, gain, meat and carcass traits in beef cattle (e.g.…”

The Effect of a Coat Colour-Associated Genes Polymorphism on Animal Health – A Review

“…In cattle large number of mutation in KIT gene, located on chromosome 6, were identified in all of 21 exons, resulting in different pigmentation patterns (Fontanesi et al, 2010). KIT gene has been suspected to be associated with hereditary gonadal hypoplasia (predominantly left-sided in both sexes) in Finncattle and Swedish Mountain cattle, while this disorder occurs only in animals that are in 60-100% white coloured (Venhoranta et al, 2013).…”

“…This protein plays a very important function in controlling differentiation, proliferation and survival of melanocytes and mast cells, and also participates in gametogenesis, hematopoiesis and T cell differentiation (Johansson et al, 2005;Fontanesi et al, 2010;Haase et al, 2009). The dominant allele of the KIT gene encodes defective transmembrane protein, unable to transmit signal, which disrupts melanocyte migration.…”