A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products

Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set …

Analisi dei geni ASIP e MC1R in razze caprine con diversa colorazione del mantello

Sequence characterization of the melanocortin 1 receptor (MC1R) gene in sheep with different coat colour and identification of the putative e allele at the ovine Extension locus

Abstract Sequence of the melanocortin 1 receptor (MC1R) gene (the Extension locus) was obtained from a panel of 73 animals belonging to 9 Italian sheep breeds or populations (Appenninica, Bergamasca, Comisana, Cornigliese-like, Delle Langhe, Massese, Merinizzata Italiana, Sarda and Valle del Belice) with different coat colours. Evaluation of the identified polymorphisms on this phenotype was reported with in silico predictions and comparative approaches within and across breeds and across species. Five novel single nucleotide polymorphisms (SNPs), organized in three haplotypes, were detected. Another haplotype, including the two missense mutations already described for the ED allele, was id…

Additional file 11 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 11:PANTHER categories significantly overrepresented in goat CNVRs. PANTHER annotation has been obtained for the whole cattle genome. (DOC 101 KB)

Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: association with red and black coat colour phenotypes but with unexpected evidences

Abstract Background Agouti and Extension loci control the relative amount of eumelanin and pheomelanin production in melanocytes that, in turn, affects pigmentation of skin and hair. The Extension locus encodes the melanocortin 1 receptor (MC1R) whose permanent activation, caused by functional mutations, results in black coat colour, whereas other inactivating mutations cause red coat colour in different mammals. Results The whole coding region of the MC1R gene was sequenced in goats of six different breeds showing different coat colours (Girgentana, white cream with usually small red spots in the face; Maltese, white with black cheeks and ears; Derivata di Siria, solid red; Murciano-Granad…

Copy number variation and missense mutations in the caprine agouti signaling protein (ASIP) gene are present in goat breeds with different coat colour

Analysis of the melanocortin receptor 1 (MC1R) gene in Sicilian goat breeds

AbstractMammalian coat colour is mainly determined by the distribution of two different types of melanins: pheomelanin (red/yellow pigments) and eumelanin (black pigments). Their synthesis is regulated by the melanocortin 1 receptor (MC1R/Extension locus) that binds the α-melanocyte-stimulating hormone (α-MSH) and the agouti signalling protein (ASIP, coded by the Agouti locus). In mammals, several studies have reported that loss-of-function mutations in MC1R lead to red/yellow pigmentation, while gain-of-function mutations lead to black/dark colours. Mutations at the Agouti locus exert, in general, epistatic interactions on the Extension locus. In goats, classical genetic studies have indic…

Mutations of the MC1R gene in Sicilian goat breeds, relationships with coat colours and perspectives for their use in breed traceability systems of goat products

A new system for animal products traceability and authentication: Use of DNA analysis of natural tracers and example of application to dry cured hams

A few DNA based approaches have been developed to trace animal products from the farm to the consumer “fork”. These approaches make use of the animal DNA that can be recovered during all steps of t...

Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.

In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val1…

Additional file 10 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 10:Gene ontology (GO) categories significantly overrepresented in goat CNVRs at different False Discovery Rate (FDR) levels. GO categories were Molecular function, Biological process, and Cellular component. (DOC 118 KB)

Additional file 5 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 5:Tables reporting the P values for the overlapping between goat and cattle CNVRs and among the four CNVR datasets available in cattle. Table S1 reports the results obtained comparing the goat CNVRs with the cattle CNVRs. Table S2 reports the results obtained comparing the different cattle datasets. (DOC 110 KB)

Additional file 15 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 3

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 6 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 6:Primers and PCR conditions used to validate goat CNVRs. The table includes the goat CNVRs number, the corresponding bovine chromosome, gene symbol, amplified gene fragment data (including Ensembl number), sequence of the PCR primers, length of the amnplified fragment and PCR conditions. (DOC 38 KB)

An initial comparative map of copy number variations in the goat (Capra hircus) genome

Abstract Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi,…

Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes

Massese is an Italian dairy sheep breed characterized by animals with black skin and horns and black or apparent grey hairs. Owing to the presence of these two coat colour types, this breed can be considered an interesting model to evaluate the effects of coat colour gene polymorphisms on this phenotypic trait. Two main loci have been already shown to affect coat colour in sheep: Agouti and Extension coding for the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes, respectively. The Agouti locus is affected by a large duplication including the ASIP gene that may determine the Agouti white and tan allele (A(Wt)). Other disrupting or partially inactivating mutations ha…

Copy Number Variation and Missense Mutations of the Agouti Signaling Protein (<i>ASIP)</i> Gene in Goat Breeds with Different Coat Colors

In goats, classical genetic studies reported a large number of alleles at the <i>Agouti</i> locus with effects on coat color and pattern distribution. From these early studies, the dominant <i>A</i><sup>Wt</sup> (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat <i>ASIP</i> gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-ri…

Identification of SNPs and copy number variation in goat MC1R and ASIP genes: an association study with coat colour in a few Mediterranean goat breeds

A first comparative map of copy number variations in the sheep genome.

article i nfo We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle a…

Additional file 8 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 8:Gene Ontology (GO) annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using GO for Biological process, Cellular component, and Molecular function. (XLS 108 KB)

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 12 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 12:List of goat CNVRs with human orthologous genes. EntrezGene ID and gene name are reported for human orthologous genes. The file includes genes already mapped in goat and genes for which mutations in human cause or are associated with human genetic diseases (data have been retrieved from OMIM database, May 2010). (XLS 60 KB)

Additional file 16 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 4

Additional file 3 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 3:Extension of CNVRs in the different chromosomes. Proportion of the CNVRs identified in goat compared to the dimension of the bovine chromosomes. (XLS 14 KB)

Additional file 14 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 2

Additional file 7 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 7:Semiquantitative fluorescent multiplex-PCR (SQF-PCR) results obtained for different goats. The averaged SQF-PCR ratio normalized against the reference Camosciata delle Alpi goat is reported for the goats of the aCGH panel and for additional goats (additional panel) for the validated CNVs. (XLS 20 KB)

Additional file 9 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 9:PANTHER annotation of genes included in goat CNVRs. Ensembl cattle transcripts located in goat CNVRs have been annotated using PANTHER. (XLS 102 KB)

Additional file 4 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 4:List of cattle CNVRs reported in four other experiments[49–52]and overlapping with goat CNVRs. CNVRs identified in cattle have been merged from the four reported experiments [49–52]. Progressive CNVR number has been assigned using the complete list. CNVRs are indicated with nucleotide positions (begin and end) on the Btau_4.0 version. Information reported for the four different experiments includes the progressive number and in parenthesis the chromosome number and the nucleotide positions (start and end). The goat CNVRs are reported. (XLS 128 KB)

Additional file 1 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 1:List of CNVs identified in the analysed goats. The Excel file reports the chromosome, the nucleotides position of the CNV start and end (referred to the Btau_4.0 genome assembly), the size of the CNV in bp, the number of valid probes in the CNV (additional probes are included in CNV considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNV), log2 mean of the probes in the CNV (see Methods), the type of CNV (gain/loss), the goat sample (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen; numbers after the breed symbols indicate the different animals used in the aCGH experiment), and t…

Additional file 17 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 5

Additional file 13 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Authors’ original file for figure 1

Additional file 2 of An initial comparative map of copy number variations in the goat (Capra hircus) genome

Additional file 2:List of CNVRs obtained by merging overlapping CNVs across animals. The Excel file reports the progressive CNVR number, the chromosome, the nucleotides position of the CNVR start and end (referred to the Btau_4.0 genome assembly), the size of the CNVR in bp, the number of valid probes in the CNVR (additional probes are included in CNVR considering the position between two contiguous regions without 0.175 log2 value; see Methods for the definition of CNVR), the type of CNVR (gain/loss), the frequency of CNVR in the analysed goat panel, the goat breed (C = Camosciata delle Alpi; G = Girgentana; MG = Murciano-Granadina; S = Saanaen), and the goat subject (numbers after the bre…