Haplotype variability in the bovine MITF gene and association with piebaldism in Holstein and Simmental cattle breeds

DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Italy.
Animal Genetics (Impact Factor: 2.21). 06/2012; 43(3):250-6. DOI: 10.1111/j.1365-2052.2011.02242.x
Source: PubMed

ABSTRACT Candidate gene analysis, quantitative trait locus mapping in outbreed and experimental cross-populations and a genomewide association study in Holstein have reported that a few chromosome regions contribute to great variability in the degree of white/black spotting in cattle. In particular, an important region affecting this trait was localized on bovine chromosome 22 in the region containing the microphthalmia-associated transcription factor (MITF) gene. We sequenced a total of 7258 bp of the MITF gene in 40 cattle of different breeds, including 20 animals from spotted breeds (10 Italian Holstein and 10 Italian Simmental) and 20 animals from solid coloured breeds (10 Italian Brown and 10 Reggiana), and identified 17 single nucleotide polymorphisms (SNPs). The allele frequencies of one polymorphism (g.32386957A>T) were clearly different between spotted (A = 0.875; T = 0.125) and non-spotted breeds (A = 0.125; T = 0.875) (P = 8.2E-12). This result was confirmed by genotyping additional animals of these four breeds (P < 1.0E-20). A total of 21 different haplotypes were inferred from the sequenced animals. Considering similarities among haplotypes, spotted and non-spotted groups of cattle showed significant differences in their haplotype distribution (P = 0.001), which was further supported by the analysis of molecular variance (amova) of two genotyped SNPs in an enlarged sample of cattle. Variability in the MITF gene clearly explained the differences between spotted and non-spotted phenotypes but, at the same time, it is evident that this gene is not the only genetic factor determining piebaldism in Italian Holstein and Italian Simmental cattle breeds.

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Available from: Emilio Scotti, Dec 11, 2014
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    • "is in complete LD with the QTL as illustrated in Fig. 1. (A haplotype refers to the combination of alleles observed on a chromosome at neighboring polymorphisms.) Use of haplotypes has been analyzed in the field of genome wide association study, recently [4] [5] [6]. "
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    ABSTRACT: Recently, genome wide DNA markers have been used in breeding value estimation of livestock species. The computational technique is known as genomic selection. Typically, a large number of marker effects are estimated from a small number of animals, which presents an under-determined problem. In this paper, we propose sparse marker selection methods using haplotypes for both breeding value estimation and QTL mapping. By applying a two-stage regression strategy, markers are selected in the first stage, then in the second stage the selected markers are fitted in a range of models including linear, kernel and semi-parametric models. The estimation accuracy of breeding values is measured by the correlation coefficient, as well as the regression coefficient, between the true breeding values and the estimated breeding values by the models. We show that the estimation accuracy by using sparse markers, as low as 5000 or 500 dimensions, is comparable to that obtained from genome wide markers of about 230,000 dimensions of DNA haplotypes. The selected sparse markers can also be used for QTL mapping. In this paper we use protein yield to demonstrate the methods, and show that loci of large effects confirm published QTL.
    Mathematical biosciences 02/2013; 243(1). DOI:10.1016/j.mbs.2013.01.009 · 1.30 Impact Factor
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    • "The Mitf (Microphthalmia-associated transcription factor) gene encodes a transcription factor of Tyr family genes with important roles in pigmentation. MITF seems to be primarily associated with loss of pigmentation and patterning, i.e., white spotting in both dogs and cattle [5]–[7] as opposed to hyperpigmentation, which in the Silky was recently shown that the higher expression of Mitf is a downstream effect of increased EDN3 expression [8]. Higher expression of Mitf, which is associated with hyperpigmentation, was observed in Silky Fowl [9]. "
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