Investigation of coat colour affecting genes in several sheep breeds

Economic values for production and functional traits in Valle del Belice dairy sheep using profit functions

Abstract A deterministic static model was used to estimate the economic values (EV) of production (MY, milk yield; BW, birth weight; and ADG, average daily gain) and functional traits (ASR, adult survival rate; LSR, lamb survival rate; FE, fertility; PR, prolificacy; and LW ewe , mature weight of ewe) in Valle del Belice dairy sheep. In this study, values for the biological parameters and the production traits used in the model were taken from real data, by surveying 15 Valle del Belice farmers and reflected the production circumstances of pasture based dairy production systems. In this system feed cost accounted for 95% of total variable costs, whereas fixed costs were low and reflected tr…

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)

Phenotypic and genetic analysis of udder health using SCC in Valle del Belice dairy sheep

Intramammary infections (IMI) are a complex of inflammatory diseases which are defined as an inflammation of the mammary gland resulting from the introduction and multiplication of pathogenic micro-organisms.

Polymorphisms of β-defensin genes in Valle del Belice dairy sheep

The aim of this work was to study β-defensin 1 (SBD1) and β-defensin 2 (SBD2) genes in Valle del Belice dairy sheep in order to identify polymorphisms that can be utilized as markers of the analyzed genes, and search for the functional effects and roles of the identified polymorphisms (variation of the amino acid sequence of the protein and stability of mRNA molecule). The study was conducted on 300 randomly selected animals belonging to four flocks. A total of seven SNPs were identified, two in SBD1 and five in SBD2. The two SNPs identified in SBD2 coding region, at position 1659 and position 1667, were non-synonymous, leading to amino acid changes in the protein product. Nevertheless, the…

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…

Genetic diversity and phylogenetic relationships among four breeds reared in Sicily using β-lactoglobulin promoter region polymorphisms

The aim of this work was to analyze the genetic diversity and the phylogenetic relationships among the Valle del Belice (VDB) breed and the other sheep breeds considered as ancestors, using -lactoglobulin (BLG) promoter region polymorphisms. The BLG promoter region of 50 randomly chosen animals from the four breeds (VDB n=20; Comisana (COM) n=10; Pinzirita (PIN) n=10; Sarda (SAR) n=10) were sequenced and aligned, and results showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. The number of polymorphic sites identified showed high variability within breeds. Nucleotide (π) and haplotype (Hd) diversity were estimated with DnaSP software, whereas PHASE software w…

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

Effect of somatic cell count on longevity in dairy ewes using survival analysis

Test-Day Model Heritabilities for somatic cvell score and production traits in primiparous Valle del Belice sheep

A repeatability test-day animal model was used to investigate heritabilities of somatic cell score (SCS) and milk production traits in Valle del Belice sheep. The heritability estimate for SCS falls within the range reported in literature (0.14±0.03), while estimates for milk production and composition traits were below those obtained by others, 0.12±0.03, 0.09±0.02, 0.14±0.03, 0.14±0.03, and 0.12±0.03, respectively, for milk yield, fat %, fat yield, protein %, and protein yield. Flock-test-day had a substantial effect on milk production traits but not on SCS. These results provide the basic parameters required for discussion of selection strategies and objectives in Valle del Belice sheep.

Effect of somatic cell count level on functional longevity in Valle del Belice dairy sheep assessed using survival analysis.

The objectives of this study were to evaluate the effect of somatic cell count (SCC) on functional longevity and to estimate the heritability of functional longevity using survival analysis in Valle del Belice dairy sheep. A total of 4,880 lactations of 2,190 ewes from 11 flocks were used. In this study, SCC was considered as an indication of subclinical mastitis. In case of clinical cases, identified by the technicians at milking time, test-day weights and milk samples of those ewes were not considered. Somatic cells were analyzed as counts, without any transformation, and were grouped in 3 classes based on the observed SCC maximum (mxSCC). The mxSCC classes, expressed as 103 cells/mL, wer…

Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures

Genome-wide association studies (GWASes) have become a powerful tool for identifying genomic regions associated with important traits in livestock. Milk production traits in dairy sheep are measured at different time points during their life span. Using phenotypic data generated from longitudinal traits could improve the power of association studies but until now have received less attention in GWASes as a methodology and has not been implemented. The aim of this study was to carry out a GWAS for milk production traits in Valle del Belice sheep using repeated measures. After quality control, 469 ewes and 37 228 SNPs were retained for the analysis, and phenotypic data included 5586 test-day …

Genetic selection for reduced Somatic Cell Counts in sheep milk: A review

Mastitis is an inflammation of the udder, mainly caused by bacteria, and leads to economic loss, due to discarded milk, reduced milk production, reduced milk quality and increased health costs in both dairy sheep and cattle. Selecting for increased genetic resistance to mastitis can be done directly or indirectly, with the indirect selection corresponding to a prediction of the bacteriological status of the udder based on traits related to the infection. The most frequently used indirect method is currently milk somatic cell count (SCC) or somatic cell score (SCS). This review reports the state of the art relating to the genetic basis of mastitis resistance in sheep and explores the opportu…

Influenza del pastazzo di limone sulle caratteristiche qualitative e quantitative del latte di pecora

Relationship between Beta Lactoglobulin and Subclinical Mastitis in Dairy Sheep

processo civile

Estimation of genetic and phenotypic parameters for bacteriological status of the udder,somatic cell score,and milk yield in dairy sheep using a threshold animal model

Abstract The objective of this study was to estimate the genetic parameters for infection status (INF), as indicator of mastitis, SCS (i.e., log-transformed SCC), and milk yield (MY), by using a Gibbs sampling algorithm. The data comprised 17,843 test-day records of 2040 ewes. The pedigree file included 2948 animals. A bivariate variance component analysis was performed using the TM software. Fixed effects considered in the analysis were litter size, parity, flock by test-day interaction, year by season of lambing interaction, and stage of lactation; whereas the animal, and the permanent environmental effect within and across lactations were considered as random as well as the error. Flat p…

Receiver-operating characteristic curves for somatic cell scores and California mastitis test in Valle del Belice dairy sheep.

Using receiver-operating characteristic (ROC) curve methodology this study was designed to assess the diagnostic effectiveness of somatic cell count (SCC) and the California mastitis test (CMT) in Valle del Belice sheep, and to propose and evaluate threshold values for those tests that would optimally discriminate between healthy and infected udders. Milk samples (n = 1357) were collected from 684 sheep in four flocks. The prevalence of infection, as determined by positive bacterial culture was 0.36, 87.7% of which were minor and 12.3% major pathogens. Of the culture negative samples, 83.7% had an SCC < 500,000/mL and 97.4% had <1,000,000 cells/mL. When the associations between SC score (SC…

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)

A Comparative Analysis of Copy Number Variation of the Sheep and Goat Genomes

Recent studies have shown that copy number variants (CNVs) are important sources of variability of mammalian genomes. We applied a cross species array comparative genome hybridization (aCGH) experiment using as reference the cattle genome to investigate, for the first time, variability in the sheep and goat genomes derived from copy number variation and identified 431 and 358 CNVs, respectively. A comparison of these results to those obtained in other mammals for similar experiments is reported. The identified CNVs could be important in determining phenotypic and production differences between and within breeds. Further studies will be carried out to evaluate the identified CNVs from both f…

Genetic parameters for early lamb survival and growth in Scottish Blackface sheep1

The objectives of this study were 1) to estimate the heritability of lamb survival and growth in the Scottish Blackface breed; 2) to examine the relationship between lamb survival and live BW; and 3) to investigate the possibility of using lamb survival in a breeding program for this breed. The data used for the analyses contained information about survival and live BW at different ages on 4,459 animals. The records were collected from 1988 to 2003 in a Scottish Blackface flock. Live BW was recorded every 4 wk from birth to 24 wk. Survival was defined either by perinatal or postnatal mortality (up to weaning at 12 wk), or as cumulative survival to 1, 4, 8, and 12 wk. The pedigree file compr…

Relationship between beta lactoglobulin and subclinical mastitis in Valle del Belice sheep breed

The objective of the following research was to determine the effect of LGB genotypes on subclinical mastitis in Valle del Belice dairy sheep. Ewes were classified as affected or not by subclinical mastitis within a lactation based on i) a positive culture in one of the test-days and ii) more than 750,000 somatic cells. Generalized linear mixed models were fitted to assess the significance of LGB genotypes on MTB and MTC. The LGB genotypes significantly affected MTB (p=0.0387), and showed a tendency on MTC (p=0.1104). Least square means showed that in the analysis for MTB, individuals with genotypes BB and AB had a higher frequency of subclinical mastitis. Moreover, the least square differen…

Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping

The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of six years (2006-2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities, and repeatability within and across lactations were estimated, fitting parity, litter size, season of lambing, and fortnights in milk, as fixed; and additive genetic, permanent environment within and across …

Relazioni tra esame batteriologico, cellule somatiche e California mastitis test in latte ovino

Genetic parameters for early lamb survival and growth in Scottish Blackface sheep.

Effects of different simplified milk recording methods on genetic evaluation with Test-Day animal model

The aims of the present study were to compare estimated breeding values (EBV) for milk yield using different testing schemes with a test-day animal model and to evaluate the effect of different testing schemes on the ranking of top sheep. Alternative recording schemes that use less information than that currently obtained with a monthly test-day schedule were employed to estimate breeding values. A random regression animal mixed model that used a spline function of days in milk was fitted. EBVs obtained with alternative recording schemes showed different degrees of Spearman correlation with EBVs obtained using the monthly recording scheme. These correlations ranged from 0.77 to 0.92. A redu…

Phenotypic and genetic analysis of udder health using SCC in Valle del Belice dairy sheep

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)

Study of polymorphisms in the promoter region of ovine β-lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other sheep breeds considered as ancestors

The aim of this work was to sequence the promoter region of b-lactoglobulin (BLG) gene in four sheep breeds, in order to identify polymorphisms, infer and analyze haplotypes, and phylogenetic relationship among the Valle del Belice breed and the other three breeds considered as ancestors. Sequencing analysis and alignment of the obtained sequences showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. A total of 22 haplotypes found in ‘‘best’’ reconstruction were inferred considering the 37 polymorphic sites identified. Haplotypes were used for the reconstruction of a phylogenetic tree using the Neighbor-Joining algorithm. The number of polymorphisms identified s…

Short communication: casein haplotype variability in sicilian dairy goat breeds.

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgenta…

Stima delle componenti della (co)varianza per il contenuto in cellule somatiche (CCS) in pecore di razza Valle del Belice

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

Authors’ original file for figure 3

Casein haplotype variability in Sicilian dairy goat breeds

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgenta…

Indici economici per l’allevamento caprino in Sicilia

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)

Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Summary Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north–south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sa…

Lactation curves in Valle del Belice sheep using random regression models

Time-to-event analysis of mastitis at first-lactation in Valle del Belice ewes

A time-to-event study for mastitis at first-lactation in Valle del Belice ewes was conducted, using survival analysis with an animal model. The goals were to evaluate the effect of lambing season and level of milk production on the time from lambing to the day when a ewe experienced a test-day with a recorded SCC greater than or equal to 750,000 cells/ml, and to estimate, for this trait, its heritability and the percentage of variation explained by the flock-year of lambing effect. A dataset with 2468 first-lactation records, collected from 1998 to 2003 in Valle del Belice ewes allocated in 17 flocks, was used. The Cox model used included lambing season and total milk yield adjusted for lac…

Genetic analysis of early lamb survival in extensively reared lambs

In sheep production, lamb survival is an important economic trait (Conington et al., 2004). Therefore, this trait has been studied by many scientists, especially in countries with an extensive husbandry system. In the United Kingdom, the number of lambs dying before weaning has been estimated ranging from 5 to 40% (Eales et al., 1983).

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,…

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

In goats, classical genetic studies reported a large number of alleles at the &lt;i&gt;Agouti&lt;/i&gt; locus with effects on coat color and pattern distribution. From these early studies, the dominant &lt;i&gt;A&lt;/i&gt;&lt;sup&gt;Wt&lt;/sup&gt; (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat &lt;i&gt;ASIP&lt;/i&gt; 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

Genetic parameters for somatic cell score according to udder infection status in Valle del Belice dairy sheep

GeneticParameters for Milk Somatic Cell Score and Relationships with Production Traits in Primparous Dairy Sheep

A total of 13,066 first-lactation test-day records of 2,277 Valle del Belice ewes from 17 flocks were used to estimate genetic parameters for somatic cell scores (SCS) and milk production traits, using a repeatability test-day animal model. Heritability estimates were low and ranged from 0.09 to 0.14 for milk, fat, and protein yields, and contents. For SCS, the heritability of 0.14 was relatively high. The repeatabilities were moderate and ranged from 0.29 to 0.47 for milk production traits. The repeatability for SCS was 0.36. Flock-test-day explained a large proportion of the variation for milk production traits, but it did not have a big effect on SCS. The genetic correlations of fat and …

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…