Casein Haplotype Structure in Five Italian Goat Breeds

Relation between αS1-casein, genotype, and quality traits of milk from Swedish dairy goats

Locally produced food is becoming popular among Swedish consumers. One product that has increased in popularity is artisan-manufactured goat cheese, and although the dairy goat industry in Sweden is small-scale, production is gradually increasing. In goats, the CSN1S1 gene regulates expression of the protein α_S1-casein (α_S1-CN), which has been found to be important for cheese yield. Over the years, breeding animals have been imported to Sweden from Norway. Historically, a high frequency of the Norwegian goat population carried a polymorphism at the CSN1S1 gene. This polymorphism, called the Norwegian null allele (D), leads to zero or significantly reduced expression of α_S1-CN. Using milk samples from 75 goats, this study investigated associations between expression of α_S1-CN and genotype at the CSN1S1 gene on milk quality traits from Swedish Landrace goats. Milk samples were grouped according to relative level of α_S1-CN (low: 0-6.9% of total protein; medium-high: 7-25% of total protein) and genotype (DD, DG, DA/AG/AA). While the D allele leads to extremely low expression of α_S1-CN, the G allele is low expressing and the A allele is highly expressing for this protein. Principal component analysis was used to explore the total variation in milk quality traits. To evaluate the effect of different allele groups on milk quality attributes, 1-way ANOVA and Tukey pairwise comparison tests were used. The majority (72%) of all goat milk samples investigated showed relative α_S1-CN content of 0% to 6.82% of total protein. The frequency of individuals homozygous for the Norwegian null allele (DD) was 59% in the population of sampled goats, and only 15% carried at least one A allele. A low relative concentration of α_S1-CN was associated with lower total protein, higher pH, and higher relative concentration of β-casein and levels of free fatty acids. Milk from goats homozygous for the null allele (DD) showed a similar pattern as milk with low relative concentration of α_S1-CN, but total protein was only numerically lower, and somatic cell count and α_S2-CN were higher than for the other genotypes. The associations between levels of α_S1-CN and the investigated genotype at the CSN1S1 gene indicate a need for a national breeding program for Swedish dairy goats.

A New AS-PCR Method to Detect CSN201 Allele, Genotyping at Ca-Sensitive Caseins Loci and Milk Traits Association Studies in Autochthonous Lazio Goats

Calcium-sensitive caseins are the main protein component of milk. In the goat, they are encoded by three genes (CSN1S1, CSN2, and CSN1S2) located on chromosome 6. A high number of alleles has been discovered for these genes in the goat species, responsible for changes in the milk’s qualitative and quantitative characteristics. This study aimed to develop an Allele-Specific PCR (AS-PCR), which allowed us to unequivocally detect goat carriers of the CSN201 allele. Subsequently, the calcium-sensitive casein loci genotype was investigated in three native goat breeds of the Lazio Region (Bianca Monticellana, Capestrina, and Ciociara Grigia). No individuals were carriers of the CSN1S101, CSN1S1E, CSN201, CSN1S2D, and CSN1S20 alleles, while a high frequency of the alleles CSN1S1F and CSN1S1A*,B* was observed. Association analyses between the different genotypes at the CSN1S1 locus and some milk traits, namely the fat and protein yielded and the fat, protein, solids-not-fat, and casein percentages without an effect on the milk yield, were observed.

Review: Genetic and protein variants of milk caseins in goats

The milk casein genes in goats, are highly polymorphic genes with numerous synonymous and non-synonymous mutations. So far, 20 protein variants have been reported in goats for alpha-S1-casein, eight for beta-casein, 14 for alpha-S2-casein, and 24 for kappa-casein. This review provides a comprehensive overview on identified milk casein protein variants in goat and non-coding DNA sequence variants with some affecting the expression of the casein genes. The high frequency of some casein protein variants in different goat breeds and geographical regions might reflect specific breeding goals with respect to milk processing characteristics, properties for human nutrition and health, or adaptation to the environment. Because protein names, alongside the discovery of protein variants, go through a historical process, we linked old protein names with new ones that reveal more genetic variability. The haplotypes across the cluster of the four genetically linked casein genes are recommended as a valuable genetic tool for discrimination between breeds, managing genetic diversity within and between goat populations, and breeding strategies. The enormous variation in the casein proteins and genes is crucial for producing milk and dairy products with different properties for human health and nutrition, and for genetic improvement depending on local breeding goals.

The Effect of Alpha s1 Genotype on Some Physiological and Chemical Milk Characteristics in Garganica Goat

In the present study individual milk samples were collected from 80 Garganica goats and the population was genotyped for CSN1S1. Seven different alleles were observed with the A allele found as predominant, followed by the F and B allele, and 14 different genotypes were observed. A proteomic approach was used to classify the individual milk on the basis of protein abundance: four levels of αs1-casein (CN) expression were identified as high (HAS-1), intermediate (IAS-1), low (LAS-1), and null (NAS-1). The present paper aimed to investigate the influence of the level of expression of αs1-casein fraction in milk on proteolytic activities, chemical composition, and renneting properties of individual Garganica goat milk. Results from the present study evidenced that the level of expression of αs1-casein fraction in Garganica goat milk affected chemical composition, curd firmness, and indigenous proteolytic enzymes. In particular, fat, protein, and casein content were higher in HAS-1 and IAS-1 compared to LAS-1 and NAS-1. The SCC decreased passing from the HAS-1 to the NAS-1 and the curd firmness displayed the highest value in HAS-1. The activity of plasmin (PL) was higher in HAS-1 and IAS-1 groups compared to the LAS-1 and NAS-1; whereas, PL plasminogen-derived (PG) activity was the highest in NAS-1 group. On the contrary, the activity of elastase was the highest in LAS-1, intermediate in the IAS-1 group, and the lowest in HAS-1 and NAS-1 groups. Present data demonstrated that the level of synthesis of αs1-CN reflects the efficiency of the mammary gland in the activation of the cellular mechanisms and influences the proteolytic activity in milk, especially the PL-PG system.

Post translational modifications of milk proteins in geographically diverse goat breeds

Goat milk is a source of nutrition in difficult areas and has lesser allerginicity than cow milk. It is leading in the area for nutraceutical formulation and drug development using goat mammary gland as a bioreactor. Post translational modifications of a protein regulate protein function, biological activity, stabilization and interactions. The protein variants of goat milk from 10 breeds were studied for the post translational modifications by combining highly sensitive 2DE and Q-Exactive LC-MS/MS. Here we observed high levels of post translational modifications in 201 peptides of 120 goat milk proteins. The phosphosites observed for CSN2, CSN1S1, CSN1S2, CSN3 were 11P, 13P, 17P and 6P, respectively in 105 casein phosphopeptides. Whey proteins BLG and LALBA showed 19 and 4 phosphosites respectively. Post translational modification was observed in 45 low abundant non-casein milk proteins mainly associated with signal transduction, immune system, developmental biology and metabolism pathways. P_asp is reported for the first time in 47 sites. The rare conserved peptide sequence of (SSSEE) was observed in αS1 and αS2 casein. The functional roles of identified phosphopeptides included anti-microbial, DPP-IV inhibitory, anti-inflammatory and ACE inhibitory. This is first report from tropics, investigating post translational modifications in casein and non-casein goat milk proteins and studies their interactions.

A highly selective two-way purification method using liquid chromatography for isolating αS2-casein from goat milk of five different breeds

The main challenges in the purification of α_S2-casein are due to the low quantity in milk and high homology with other casein subunits, i.e., α_S1-casein, β-casein, and κ-casein. To overcome these challenges, the aim of this study was to develop a two-step purification to isolate native α_S2-casein in goat milk from five different breeds; British Alpine, Jamnapari, Saanen, Shami, and Toggenburg. The first step of the purification was executed by anion-exchange chromatography under optimal elution conditions followed by size exclusion chromatography. Tryptic peptides from in-gel digestion of purified α_S2-casein were sequenced and analyzed by LC-ESI-MS/MS. From 1.05 g of whole casein, the highest yield of α_S2-casein (6.7 mg/mL) was obtained from Jamnapari and the lowest yield (2.2 mg/mL) was from Saanen. A single band of pure α_S2-casein was observed on SDS-PAGE for all breeds. The α_S2-casein showed coverage percentage of amino acid sequence from 76.68 to 92.83%. The two-step purification process developed herein was successfully applied for isolating native α_S2-casein from goat milk with high purity, which will allow for future in vitro studies to be conducted on this protein.

Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats

Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats.

Effects of Breed and Stage of Lactation on Milk Fatty Acid Composition of Italian Goat Breeds

Fatty acid (FA) profile plays an important role on human health and on sensory quality of dairy products. There is few information about breed influence on milk FA profile of local goat breeds. This study aimed to characterize and compare the milk FA profile of 5 local endangered goat breeds (Garganica, Girgentana, Jonica, Maltese, and Mediterranean Red) and a cosmopolitan breed (Saanen) reared in the same farm during a complete lactation. A total of 252 milk samples were collected monthly from 42 goats (7 goats per breed) and analyzed for gross composition and FA profile. Individual FA was determined using gas-chromatography. Data were analyzed using a mixed model with repeated measures with breed and week of lactation as fixed effects. Results showed that the FA profile was significantly affected by week of lactation and only few FA by breed effect (p < 0.05). Overall, the main differences were found between Saanen and local breeds. This study contributed to the characterization of goat milk FA profile, and it may be of interest for the valorization of milk from local goat breeds which seem to have a healthier profile than milk of the cosmopolitan breed.

Casein haplotype diversity in seven dairy goat breeds

Selection, drift, gene flow and breeding have extensively shaped the genomic variability of domestic animals. In goat species, several mutations identified within the casein genes have been shown to affect the level of gene expression of milk production traits. The four casein genes - CSN1S1, CSN2, CSN1S2 and CSN3 - are organized in a cluster of 250 kb located in chromosome 6, and due to tight linkage, their genetic variability is well depicted by haplotypes which are transmitted to the progeny. Thirty single nucleotide polymorphisms (SNPs) located within the casein gene cluster were used to characterize the haplotype variability of six southern Italian goat breeds (Girgentana, Maltese, Rossa Mediterranea, Argentata dell'Etna, Messinese, Capra dell'Aspromonte). A representative sample of the Norwegian dairy goat breed (Norsk melkegeit) has been used as an out-group to obtain a weighted measure of genetic diversity in the metapopulation. A total of 54 haplotypes were detected among the seven breeds: 26, 9, 8 and 11 haplotypes were found at CSN1S1, CSN2, CSN1S2 and CSN3 respectively. The number of haplotypes per breed was 14 (Norwegian), 26 (Messinese), 27 (Rossa Mediterranea and Girgentana) and 31 (Maltese, Argentata dell'Etna and Capra dell'Aspromonte). The Maltese breed showed the highest number of private haplotypes, whereas the Norwegian goat recorded the highest number of shared haplotypes. The linkage disequilibrium analysis showed higher levels of association for the SNP pairs within casein loci than SNP pairs between casein loci, likely reflecting low levels of intra-genic recombination. The highest linkage disequilibrium values were found in CSN1S1 and CSN2 genes in all the breeds, except for Argentata dell'Etna and Rossa Mediterranea. The resolution of the haplotype diversity at the casein cluster can be exploited both for selective and conservative plans.

Genomic analysis of the origins of extant casein variation in goats

The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.

Autochthonous dairy goat breeds showed better milk quality than Saanen under the same environmental conditions

Studies on goat milk have mainly focused on cosmopolitan breeds and very limited information is available on local breeds, which is important for biodiversity preservation and local cheese production. The aim of this study was to evaluate the breed effect on milk yield, composition and somatic cell score (SCS) of five local Italian goat breeds (Garganica, Girgentana, Jonica, Maltese and Mediterranean Red) compared with a cosmopolitan specialized dairy breed (Saanen). A total of 60 goats (10 per breed) from an experimental farm were enrolled in the study. Milk yield, composition and SCS were recorded and analyzed every 2 weeks during the entire lactation. Data were analyzed using a mixed model with repeated measures. Saanen yielded between 0.27 and 0.62 kg day-1 more milk than the local breeds. Among local breeds, Maltese and Jonica were the most productive, with an average of 1.28 and 1.25 kg day-1, respectively, while Mediterranean Red, Garganica and Girgentana produced ≤1 kg day-1. Saanen had the highest SCS (6.81) and the lowest fat content (3.26 %). In relation to protein, Garganica showed the greatest content (3.71 %), and Saanen had a similar content to other local breeds (3.42 %) except for Maltese, which was lower (3.11 %). Saanen and Garganica had the lowest lactose percentage (4.28 % and 4.26 %, respectively). All breeds followed a similar pattern across lactation: SCS and fat and protein content peaked at the end of the lactation, whereas lactose percentage was highest at the beginning of the lactation. Differences between Saanen and the local breeds for milk yield, composition and SCS were consistent across lactation. In conclusion, local breeds produced less milk but with lower SCS and greater fat and lactose content than the Saanen cosmopolitan breed, suggesting a better milk quality.

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log₁₀(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log₁₀(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.

Caprine and ovine Greek dairy products: The official German method generates false-positive results due to κ-casein gene polymorphism

Caseins are widely used for species identification of dairy products. Isoelectric focusing (IEF) of para-κ-casein peptide is used as the official German method for the differentiation between caprine (isoform A) and ovine (isoform B) dairy products, based on their different isoelectric points. The discrimination between Greek goat and ewe dairy products using IEF has, however, been shown to be problematic because of the existence of the ewe isoform in milk from Greek indigenous dairy goats. This could be due to nucleotide polymorphisms within the goat κ-casein gene of Greek indigenous breeds, which alter the isoelectric point of the para-κ-casein peptide and lead to false positive results. Previous DNA analysis of the goat κ-casein gene has shown high levels of polymorphism; however, no such information is available for Greek indigenous dairy goats. Therefore, 87 indigenous dairy goats were sequenced at exon IV of κ-casein gene. In total, 9 polymorphic sites were detected. Three nonsynonymous point mutations were identified, which change the isoelectric point of the goat para-κ-casein peptide so that it appears identical to that of the ewe peptide. Ten composite genotypes were reconstructed and 6 of them included the problematic point mutations. For the verification of genetic results, IEF was carried out. Both goat and ewe patterns appeared in the problematic genotypes. The frequency of these genotypes could be characterized as moderate (0.23) to high (0.60) within Greek indigenous breeds. However, this is not an issue restricted to Greece, as such genotypes have been detected in various non-Greek goat breeds. In conclusion, IEF based on the official German method is certainly inappropriate for ovine and caprine discrimination concerning Greek dairy goat products, and consequently a new method should be established.

Population genetic structure and milk production traits in Girgentana goat breed

The aim of this work was to evaluate the genetic status of the Girgentana goat, an endangered breed from Sicily (Italy), using microsatellite markers. Furthermore, as the main purpose of the Girgentana breed is milk production, quantitative milk traits were investigated, including fatty acid profile. Molecular data from CSN1S1, CSN2, CSN1S2, and CSN3 casein genes were also used to infer haplotypes. A total of 264 individuals were collected. Samples of Maltese (n = 41) and Derivata di Siria (n = 33) goat breeds were also used to understand the genetic relationship among breeds. Test-day records for milk production were collected to determine daily milk yield, fat, protein, casein, lactose, and somatic cell count. Individual milk samples were also collected for fatty acid extraction. Wright’s statistics, gene flow, Nei genetic distance, factorial correspondence analysis, and Bayesian assignment test showed the existence of genetic variability and differentiation among breeds. The AMOVA results indicated that 89.96% of the total variance was partitioned within populations. The Girgentana breed appears to have a subdivided population, and has not experienced a recent bottleneck. A high variability in milk yield was observed. Mean morning milk yield was 1448 ± 404 g, with 4.30 ± 0.87% and 3.72 ± 0.44% of fat and protein percentages, respectively. The average somatic cell count found in Girgentana goat milk was higher than the threshold of 1 500 000 cells/mL advised in Europe for fresh milk. Gross milk and fatty acid composition were similar to that reported in the literature for other local goat breeds.

Cloning and comparative analysis of gene structure in promoter site of alpha-s1 casein gene in Naeinian goat and sheep

The 5' end or alpha-S1 casein promoter has a significant role in milk protein gene expression. The understanding of the translation process of alpha-S1 casein mutants will provide us an opportunity to make the best selection in livestock providing more proteins in milk. Blood samples were taken from three hundred of Naeinian goats and sheep, and DNA extraction was done using modified salting out method. Polymerase chain reactions (PCR) were carried out using a specific primer pairs for amplification a fragment of 1133 bp from part of 5'-UTR and exon 1 of alpha s1 casein gene. The AluI and HinfI restriction enzyme treatment of all samples provided the same homozygous AA genotype in both species. Subsequently, one sample of each species was selected and cloned, and the final sequences were analyzed by BioEdit, CLC genomic, Mega4 and DNASIS MAX software. Several polymorphisms are recognized between Naeinian goat and sheep that are presented on motif sites. In this research, the interested location, including exon I and a part of 5', was analyzed, and genetic element comparisons were done between Naeinian goat and sheep. The number and location of probable binding sites can have a crucial role as a result of antagonistic and synergistic effects on gene regulation activities.

Effects of CSN1S2 Genotypes on Economic Traits in Chinese Dairy Goats

The aim of this study was to investigate allele frequencies at the CSN1S2 locus in two Chinese dairy goat breeds and the effects of its variation on dairy goat economic traits. Seven hundred and eight goats from Xinong Saanen (XS, n = 268) and Guanzhong (GZ, N = 440) breeds were selected. The milk samples of 268 XS goats were collected during the middle of lactation, body size parameters (708 goats) and daily milk yield (202 goats) were registered. The RFLP (restriction fragment length polymorphism) and SSCP (single strand conformation polymorphism) were used to detect the polymorphisms in CSN1S2. The Hardy-Weinberg (HW) equilibrium and the associations between body size, milk yield and composition and the genotypes were calculated. The results revealed that only A and F CSN1S2 alleles were found in the two Chinese dairy goat breeds. Allelic frequencies of A and F were 0.795, 0.205 and 0.739, 0.261 in Xinong Saanen and Guanzhong population respectively. Xinong Saanen breed was in Hardy-Weinberg equilibrium, while Guanzhong breed deviated from Hardy-Weinberg equilibrium (p<0.05). The association of polymorphism with economic traits indicated that the goats with FF genotype have higher milk fat and total solid concentration than those with AA and AF genotypes (p<0.05).

Goat casein genotypes are associated with milk production traits in the Sarda breed

The aim of the current work was to analyze, in the Sarda breed goat, genetic polymorphism within the casein genes and to assess their influence on milk traits. Genetic variants at the CSN1S1, CSN2, CSN1S2 and CSN3 gene loci were investigated using PCR-based methods, cloning and sequencing. Strong alleles prevailed at the CSN1S1 gene locus and defective alleles also were revealed. Null alleles were evidenced at each calcium-sensitive gene locus. At the CSN3 gene locus, we observed a prevalence of the CSN3 A and B alleles; the occurrence of rare alleles such as CSN3 B'', C, C', D, E and M; and the CSN3 S allele (GenBank KF644565) described here for the first time in Capra hircus. Statistical analysis showed that all genes, except CSN3, significantly influenced milk traits. The CSN1S1 BB and AB genotypes were associated with the highest percentages of protein (4.41 and 4.40 respectively) and fat (5.26 and 5.34 respectively) (P < 0.001). A relevant finding was that CSN2 and CSN1S2 genotypes affected milk protein content and yield. The polymorphism of the CSN2 gene affected milk protein percentage with the highest values recorded in the CSN2 AA goats (4.35, at P < 0.001). The CSN1S2 AC goats provided the highest fat (51.02 g/day) and protein (41.42 g/day) (P < 0.01) production. This information can be incorporated into selection schemes for the Sarda breed goat.

Newly identified mutations at the CSN1S1 gene in Ethiopian goats affect casein content and coagulation properties of their milk

Very high casein content and good coagulation properties previously observed in some Ethiopian goat breeds led to investigating the αs1-casein (CSN1S1) gene in these breeds. Selected regions of the CSN1S1 gene were sequenced in 115 goats from 5 breeds (2 indigenous: Arsi-Bale and Somali, 1 exotic: Boer, and 2 crossbreeds: Boer × Arsi-Bale and Boer × Somali). The DNA analysis resulted in 35 new mutations: 3 in exons, 3 in the 5' untranslated region (UTR), and 29 in the introns. The mutations in exons that resulted in an amino acid shift were then picked to evaluate their influence on individual casein content (αs1-, αs2-, β-, and κ-CN), micellar size, and coagulation properties in the milk from the 5 goat breeds. A mutation at nucleotide 10657 (exon 10) involved a transversion: CAG→CCG, resulting in an amino acid exchange Gln77→Pro77. This mutation was associated with the indigenous breeds only. Two new mutations, at nucleotide 6072 (exon 4) and 12165 (exon 12), revealed synonymous transitions: GTC→GTT in Val15 and AGA→AGG in Arg100 of the mature protein. Transitions G→A and C→T at nucleotides 1374 and 1866, respectively, occurred in the 5' UTR, whereas the third mutation involved a transversion T→G at nucleotide location 1592. The goats were grouped into homozygote new (CC), homozygote reference (AA), and heterozygote (CA) based on the nucleotide that involved the transversion. The content of αs1-CN (15.32g/kg) in milk samples of goats homozygous (CC) for this newly identified mutation, Gln77→Pro77 was significantly higher than in milks of heterozygous (CA; 9.05g/kg) and reference (AA; 7.61g/kg) genotype animals. The αs2-, β-, and κ-CN contents showed a similar pattern. Milk from goats with a homozygous new mutation had significantly lower micellar size. Milk from both homozygote and heterozygote new-mutation goats had significantly shorter coagulation rate and stronger gel than the reference genotype. Except the transversion, the sequence corresponded to allele A and presumably derived from it. Therefore, this allele is denoted by A3. All goats from the reference genotype (AA) were homozygous for the allele at nucleotide position 1374 and 1866, whereas all mutations in the 5' UTR existed in a heterozygous form in both heterozygous (CA) and the new mutation (CC) genotype. The newly identified mutation (CC) detected in some of the goat breeds is, therefore, important in selection for genetic improvement and high-quality milk for the emerging goat cheese-producing industries. The finding will also benefit farmers raising these goat breeds due to the increased selling price of goats. Further studies should investigate the effect of this amino acid exchange on the secondary and tertiary structure of the αs1-CN molecule and on the susceptibility of peptide hydrolysis by digestive enzymes.

Influence of fresh forage-based diets and αs₁-casein (CSN1S1) genotype on nutrient intake and productive, metabolic, and hormonal responses in milking goats

Polymorphism at the αS1-casein locus (CSN1S1) in goats influences several milk production traits. Milk from goats carrying strong alleles, which are associated with high αS1-casein (αS1-CN) synthesis, has higher fat and casein contents, longer coagulation time and higher curd firmness than milk from goats with weak alleles linked to low αS1-CN content. Nutrition also affects these milk properties; therefore, it is important to better understand the interaction between dietary characteristics and the CSN1S1 genotype in goats. This study aimed to investigate the effect of fresh forage based diet or energy supplement on feeding behavior, milk production, and metabolic and hormonal parameters of Girgentana goats with different genotypes at CSN1S1 loci. From a group of goats genotyped by PCR at the DNA level, 12 were selected because they had the same genotype for αS2-CN, β-CN, and κ-CN but a different genotype for αS1-CN: 6 were homozygous for strong alleles at the CSN1S1 loci (AA) and 6 were heterozygous for a weak allele (AF). Goats of each genotype were allocated to 3 subgroups and fed 3 diets ad libitum in a 3×3 Latin square design. The diets were sulla (Hedysarum coronarium L.) fresh forage, sulla fresh forage plus 800 g/d of barley meal (SFB), and mixed hay plus 800 g/d of barley meal (MHB). Diet had a stronger effect than CSN1S1 genotype. The SFB diet led to the highest energy intake, dry matter (DM) digestibility, and milk yield. The fresh forage diets (SFF and SFB) increased DM and crude protein (CP) intake, CP digestibility, and milk CN compared with the MHB diet. The diets supplemented with energy (SFB, MHB) reduced milk fat and urea, improved CP utilization for casein synthesis, and limited body fat mobilization, in accordance with a lower level of nonesterified fatty acids and higher levels of glucose and IGF-1. With regard to CSN1S1 genotype, AA goats showed higher CP digestibility and lower free thyroxine hormone and cholesterol levels than AF goats. Significant diet × genotype interactions indicated how AA goats, compared with AF goats, showed higher DM digestibility and milk yield when fed the SFB diet, which had more energy. A reduction in free triiodothyronine hormone occurred in AF goats fed the MHB diet, whereas no differences were observed in AA goats. These results demonstrate how goats with a higher capacity for αS1-CN synthesis exhibit more efficient energy and protein utilization, evident at the digestive level, and better productive responses to high-nutrition diets.

Effect of CSN1S1 gene polymorphism and stage of lactation on milk yield and composition of extensively reared goats

The effect of CSN1S1 genotype and lactation stage on milk yield and composition were investigated in 80 extensively reared goats. Milk yield was recorded in early, mid and late lactation and individual milk samples were collected to determine: fat, protein, lactose and casein content, pH, freezing point, somatic cell count (SCC) and total microbic mesophilic count (TMC). Relative casein composition and amino acid profile were quantified by HPLC. Fatty acid profile was measured by gas-chromatography. Genotype did not affect milk yield, while this trait was significantly affected by lactation stage (P < 0·01). CSN1S1 BB goats produced significantly higher protein and casein percentages (P < 0·05). αs1-casein (CN) was significantly higher in BB and AB goats than AF and BF, showing intermediate values in AA goats (P < 0·01). The protein percentage and the αs1 and αs2-CN fractions were not affected by lactation stage, while the casein content and the β and κ-CN significantly increased throughout lactation (P < 0·01). C4 : 0 and C6 : 0 were not affected by genotype, while C8 : 0 and C10 : 0 were higher in the AA goats than BB; most of the long chain FA were higher in BB than AA goats. MUFA and PUFA increased in late lactation. In addition, BB goats showed higher essential amino acids, resulting in an optimal composition from the nutritional point of view, when compared with AA goats. The increase of MUFA, PUFA, essential and cis-FA in late lactation indicate that the lipid composition of goat's milk, with the progress of lactation, tends to improve its nutritional value.

Additive and dominance effects of the α(s1)-casein locus on milk yield and composition traits in dairy goats

The objective of this study was to evaluate the effects of the CSN1S1 locus polymorphism on 305-d records of milk, fat, protein, lactose and total solids yields, fat, protein, lactose and total solids contents in Mexican dairy goats. A total of 514 lactation records belonging to Alpine (n=60), Saanen (n=105) and Toggenburg (n=74) goats, born from 2003 to 2006 in three herds were used. Discrimination between alleles E, F, N, A* (CSN1S1 A, G, H, I, O1 and O2) and B* (CSN1S1 B1, B2, B3, B4, C and L) were made by amplification of fragments of the gene CSN1S1 and digestion with the restriction endonuclease XmnI. In order to estimate additive and dominance effects, data sets including (1) all genotypes, and (2) only homozygote genotypes, were analysed using linear mixed models. The allele A*, had significant additive effects for protein content (0·21±0·07%; P=0·002) and total solids content (0·66±0·23%; P=0·005) when compared with allele F. An unfavourable additive effect of allele A* on milk yield was found in the Alpine breed (-81·4±40·2; P=0·046) when compared with allele F. Favourable dominance effects were found for some genotypes (P<0·05) for milk yield (A*N and B*N), fat yield (A*N and B*E), protein yield (A*N and B*E), lactose yield (A*N) and total solids yield (A*N). Also, unfavourable dominance effects were found (P<0·05) for protein content (A*B* and A*N) and total solids content (A*B*, A*N, and A*F). Allele A* was the only one with a positive effect for protein content. Significant allele-year interaction effects were also observed. The presence of significant dominance effects, estimated between specific pairs of alleles, challenged the purely additive nature of the genetic effect at the CSN1S1 locus. Implications from use of CSN1S1 effects in goat breeding programmes are presented.

Identification of the CSN1S1 allele in Indian goats by the PCR-RFLP method

The allelic distributions of the CSN1S1 (αs1-casein) in the Indian goats are quite different from European goat breeds. Majority of Indian goat breeds and non-descript goats carry A, B, E and F alleles at αs1-casein locus, as found by analysing both DNA and protein levels. However, A and B alleles, known to be associated with better casein yield, were observed in the highest proportion in all the Indian goat breeds. Gene frequency and breed heterozygosity were computed for the CSN1S1 gene. The gene frequency of allele A in Indian goats varies from 0.68 to 1.00 and allele B varies from 0.098 to 0.23. Allele F was observed in Beetal, Marwari, Chegu and non-descript goats of MP (Local MP) in less than 1% of population. The expected heterozygosity (He) varied from 0.141 to 0.506 over the population. The Beetal breed showed the highest gene diversity (0.506) followed by Jamunapari (0.395), Chegu (0.383) and Jakhrana (0.381) breeds. Therefore, the variability at CSN1S1 locus can be utilised for conservation as well as for genetic improvement of Indian goat breeds for increasing both the quality and quantity of milk production.

Characterization of casein gene complex and genetic diversity analysis in Indian goats

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

Toward milk speciation through the monitoring of casein proteotypic peptides

The possibility of detecting extraneous milk in singles species cheese-milk has been explored. A mass spectrometry (MS)-based procedure has been developed to detect 'signature peptides', corresponding to the predefined subset of 'proteotypic peptides', as matchless analytical surrogates of the parent caseins. Tryptic digests of skimmed milk samples from four species were analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Amongst the candidate signature peptides that are able to differentiate milks from the four species, the alpha(s1)-casein (CN) f8-22 peptide was selected as a convenient marker for bovine, ovine and water buffalo milk while the f4-22 peptide was selected as a marker for the two caprine alpha(s1)-CN A and B variants, which differ by a Pro(16) (B)->Leu(16) (A) substitution. MALDI analysis of the digest allowed the detection of alpha(s1)-CN f8-22 and caprine alpha(s1)-CN f4-22. The accurate evaluation of caprine milk in a quaternary mixture required the development of a liquid chromatography/electrospray ionization (LC/ESI)-MS procedure. Five synthetic signature peptide analogues, which differed from their natural counterparts by a single amino acid substitution, were used as internal standards to quantify the alpha(s1)-CN, which was chosen as a reference milk protein, from the different species. The limits of detection were 0.5% (1% for caprine) for either the MALDI or the LC/ESI-MS method. The isotopic-label-free quantification of isoform- or variant-specific signature peptides has disclosed a convenient approach for targeting proteins in complex mixtures.

Effect of CSN1S1 genotype and its interaction with diet energy level on milk production and quality in Girgentana goats fed ad libitum

A study was carried out to evaluate how the energy level of the diet can affect milk production and quality in Girgentana lactating goats in relation to polymorphism at the αs1-casein (CSN1S1) genotype locus. Twenty-seven goats, homogeneous for milk production (1·5±0·3 kg/d), days of lactation (90±10 d) and body weight (35·8±5·5 kg) were selected on the basis of their CSN1S1 genotype, as follows: nine goats homozygous for strong (AA) alleles, nine goats homozygous for weak alleles (FF) and nine goats heterozygous (AF). The goats were used in a 3×3 factorial arrangement of treatments, with three genotypes (AA, FF, AF) and three diets at different energy levels (100%, 65% and 30% of hay inclusion). The experiment consisted of three simultaneous 3×3 Latin squares for the three genotypes, with one square for each level of hay inclusion in the diet. All the animals were housed in individual pens. Each experimental period lasted 23 d and consisted of 15 d for adaptation and 8 d for data and sample collection, during which the goats received the scheduled diet ad libitum. The animals were fed three different diets designed to have the same crude protein content (about 15%) but different energy levels: a pelleted alfalfa hay (H100) and two feeds including 65% (H65) and 30% (H30) of alfalfa hay (respectively 1099, 1386 and 1590 kcal NE for lactation/kg DM). All the diets were ground and pelleted (6 mm diameter). AA goats were more productive than AF and FF goats (respectively: 1419v. 1145 and 1014 g/d;P=0·002). Indeed the interaction energy level×genotype was significant (P=0·018): in fact AA goats showed their milk increase only when fed with concentrates. Differences in protein and in casein levels between the three genotypes were in line with results expected from the different allele contribution to αs1-casein synthesis. Milk urea levels were significantly lower in AA goats compared with AF and FF genotypes (respectively 32·7v. 40·4 and 40·4 mg/dl;P=0·049) and significantly lower when goats were fed with 65H and 30H diets than with 100H diet (respectively 37·4 and 34·3v. 41·7 mg/dl;P<0·001). Indeed, a significant interaction genotype×diet (P=0·043) occurred for milk urea, which was significantly lower in AA goats but only when fed with concentrates (65H and 30H). Blood concentrations of energy indicators (glucose, non-esterified fatty acids and beta-hydroxybutyric acid) were not influenced by genotype. The results confirm that strong alleles are associated with a greater efficiency of feed utilization and seem to show that a high energy level of the diet can further improve this efficiency.

Divergence at the casein haplotypes in dairy and meat goat breeds

Casein genes have been proved to have an influence on milk properties, and are in addition appropriate for phylogeny studies. A large number of casein polymorphisms exist in goats, making their analysis quite complex. The four casein loci were analyzed by molecular techniques for genetic polymorphism detection in the two dairy goat breeds Bunte Deutsche Edelziege (BDE; n=96), Weiße Deutsche Edelziege (WDE; n=91), and the meat goat breed Buren (n=75). Of the 35 analyzed alleles, 18 were found in BDE, and 17 in Buren goats and WDE. In addition, a new allele was identified at the CSN1S1 locus in the BDE, showing a frequency of 0·05. This variant, named CSN1S1*A′, is characterized by a t→c transversion in intron 9. Linkage disequilibrium was found at the casein haplotype in all three breeds. A total of 30 haplotypes showed frequencies higher than 0·01. In the Buren breed only one haplotype showed a frequency higher than 0·1. The ancestral haplotype B-A-A-B (in the order: CSN1S1-CSN2-CSN1S2-CSN3) occurred in all three breeds, showing a very high frequency (>0·8) in the Buren.