Genetic structure of the casein gene cluster in the Tunisian native goat breed

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.

Haplotype structure of MSTN, IGF1, and BMP2 genes in Tunisian goats (Capra hircus) and their association with morphometric traits

The aim of the present study was to evaluate variability and haplotype structure of twenty-eight single nucleotide polymorphisms (SNPs) at myostatin (MSTN), insulin-like growth factor 1 (IGF1), and bone morphogenetic protein 2 (BMP2) genes. Association between the polymorphic SNPs and morphometric traits was performed on a population of 263 Tunisian goats. The SNPs analyzed were all polymorphic (except one), and the three genes had different haplotype structures. Significant association of SNPs at MSTN with head length was highlighted in the Tunisian goats. The variability at IGF1 gene was associated with body length, ear length, tail length, and chest depth. For BMP2, significant association was revealed with chest depth. Significant association was also detected between linkage disequilibrium (LD) block 2 at IGF1 with body length. These findings might play a potential role in gene-assisted programs.

Small ruminants milk from Tunisian oasis: physicochemical characteristics, mineral contents, and microbiological quality

Characteristics and quality aspects of milk from native ovine Queue Fine de l'Ouest (QFO) and the exotic D'man (DMN) breeds were investigated and compared with those of two subgroups of the local goat population Arbi and Serti. A total of 418 individual milk samples were collected from multiparous lactating animals reared in the continental oasis region of Tunisia. Samples were analyzed for physical parameters (pH, density, and acidity), chemical composition (dry matter, fat, protein, lactose, casein, ash, and casein/protein ratio), mineral concentrations (Ca, P, Na, K, and Ca/P) and microbiological features (total mesophilic aerobic bacteria (TMAB), total coliforms count (TCC), lactic acid bacteria (LAB), sulphite-reducing Clostridium (CSR), yeast and molds (Y/M), Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), and Salmonella) according to standard methods. The values obtained for physicochemical, mineral, and microbial parameters revealed noticeable differences in the milk of the four studied breeds. On the whole milk samples, the mean value of pH, density, and acidity in milk collected from sheep breeds appeared higher than in milk collected from goat subgroups. As for milk composition, results showed a remarkable disparity between studied breeds and clear superiority of sheep breeds compared to goat's subgroups in all chemical contents being studied (dry matter, fat, protein, lactose, casein, and ash). The differences are more important, especially for dry matter, fat, protein, and casein content, whereas casein/protein ratio distinguished goat's genotypes, and the highest one was obtained for Serti Subgroup. When comparing sheep versus goat's milk for macro-minerals, the current study indicated lower K and higher concentrations of Ca, P, and Na. The milk of QFO sheep, the richest in casein and protein, was expressed with significantly higher levels of calcium and phosphorus compared to the DMN sheep breed and the two goat subgroups. The microbiological examination evidenced that the milk of both species complies with standard criteria required by the Tunisian legislation on the hygiene of milk and dairy products. The microbial quality of ewe milk was higher than goat milk, based on LAB and Y/M, while goats produced milk with better quality referring to TMAB and TCC counts. No significant differences were found for Staphylococcus aureus and Escherichia coli between examined breeds. Got results highlighted the complete absence of the two dangerous pathogens Salmonella and CSR in all investigated samples of small ruminants' milk.

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.

Variability of the caprine whey protein genes and their association with milk yield, composition and renneting properties in the Sarda breed. 1. The LALBA gene

The 5' flanking region and 3' UTR of the caprine LALBA gene were analysed by SSCP and sequencing. A total of nine SNPs were detected: three in the promoter region, two were synonymous coding SNPs at exon-1, and four SNPs were in exon-4, within the 3'UTR. The nucleotide changes located in the promoter region (c.-358T>C, c.-163G>A, c.-121T>G) were genotyped by SSCP in 263 Sarda goats to evaluate their possible effect on milk yield, composition and renneting properties. We observed an effect of the three SNPs on milk yield and lactose content. Genotypes TT and CT at c.-358T>C (P A (P C and c.-121T>G were part of transcription factors binding sites, potentially involved in modulating the LALBA gene expression. The LALBA genotype affected renneting properties (P < 0.001), as heterozygotes c.-358CT and c.-163GA were characterised by delayed rennet coagulation time and curd firming time and the lowest value of curd firmness. The present investigation increases the panel of SNPs and adds new information about the effects of the caprine LALBA gene polymorphism.

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.