Casein haplotype structure in five Italian goat breeds

The aim of this work was to investigate the genetic structure of the casein gene cluster in 5 Italian goat breeds and to evaluate the haplotype variability within and among populations. A total of 430 goats from Vallesana, Roccaverano, Jonica, Garganica, and Maltese breeds were genotyped at alphas1-casein (CSN1S1), alphas2-casein, (CSN1S2), beta-casein (CSN2), and kappa-casein (CSN3) loci using several genomic techniques and milk protein analysis. Casein haplotype frequencies were estimated for each breed. Principal component analysis was carried out to highlight the relationship among breeds. Allele and haplotype distributions indicated considerable differences among breeds. The haplotype CSN1S1*F- CSN1S2*F-CSN3*D occurred in all breeds with frequencies >0.100 and was the most common haplotype in the Southern breeds. A high frequency of CSN1S1*0-CSN1S2*C-CSN3*A haplotype was found in Vallesana population (0.162). Principal component analysis clearly separated the Northern and Southern breeds by the first component. The variability of the caprine casein loci and variety of resulting haplotypes should be exploited in the future using specific breeding programs aiming to preserve biodiversity and to select goat genetic lines for specific protein production.     

Technical note: simultaneous identification of CSN1S2 A, B, C, and E alleles in goats by polymerase chain reaction-single strand conformation polymorphism

Most variability in goat caseins originates from the high number of genetic polymorphisms often affecting the specific protein expression, with strong effects on milk composition traits and technological properties. At least 7 alleles have been found in the goat α_S2-CN gene (CSN1S2). Five of them (CSN1S2*A, CSN1S2*B, CSN1S2*C, CSN1S2*E, and CSN1S2*F) are widespread in most breeds, whereas the other 2 (CSN1S2*D and CSN1S2*0) are rarer alleles. Four different PCR-RFLP tests are needed to detect all of these variants at the DNA level. The objective of this study was to develop and validate a rapid method for typing 4 of the 5 most-common goat CSN1S2 alleles by means of PCR-single strand conformation polymorphism (SSCP). The method was validated by analyzing 37 goat samples at the protein and DNA level, respectively, by milk isoelectrofocusing and PCR-RFLP methods already described. The genotypes obtained using the PCR-SSCP approach were in full agreement with those obtained by the validation analyses. The newly developed PCR-SSCP approach provides an accurate and inexpensive assay highly suitable for genotyping goat CSN1S2.     

Effects of the CSN1A(G) allele on the clotting time of cow milk and on the rheological properties of rennet-curd

The aim of this research was to study the effects of the CSN1A(G) allele on the main rennet coagulation properties of milk. The study was carried out on individual milk samples with low alphas1-casein obtained from 19 Italian Brown cows heterozygous for the CSN1A(G) allele (seventeen CSN1A BG and two CSN1A CG) from four herds in the province of Parma (Italy). Control cows (sixteen CSN1A BB and three CSN1A BC) giving milk with normal alphas1-casein levels were chosen from within the same herds in order to establish pairs of cows with identical environment and management conditions, and comparable lactation stages and numbers. Individual milk samples from single pairs of cows with somatic cell counts and lactose and chloride levels within the normal ranges were collected and analysed in parallel. Rennet coagulation properties of milk were analysed using Formagraph and Gel Tester. Milk from low alphas1-casein cows was characterized by lower casein content, lower titratable acidity and a higher proportion of kappa-casein in total casein. The clotting time of this milk was approximately 23% lower than that obtained with milk from normal alphas1-casein cows. Rennet curd from low alphas1-casein milk was obtained more rapidly and had a higher final firmness: curd-firming time was approximately 35% lower and curd firmness measured 30 min after rennet addition was approximately 27% higher compared with that for normal alphas1-casein milk. In addition, curd from low alphas1-casein milk had a higher resistance to compression. These results suggest that, although a role for the CSN2 locus cannot be definitely excluded, the CSN1A(G) allele can considerably affect the main rennet coagulation properties of milk.     

Effects of α s1-casein (CSN1S1) and κ-casein (CSN3) genotypes on milk coagulation properties in Murciano-Granadina goats

The effects of the caprine α s1-casein (CSN1S1) polymorphisms on milk quality and cheese yield have been widely studied in French and Italian goat breeds. Much less is known about the consequences of κ-casein (CSN3) genotype on the technological and coagulation properties of goat milk. In the current study, we have performed an association analysis between polymorphisms at the goat CSN1S1 and CSN3 genes and milk coagulation (rennet coagulation time, curdling rate and curd firmness) and technological (time to cutting of curd and cheese yield) properties. In this analysis, we have included 193 records from 74 Murciano-Granadina goats (with genotypes constituted by different combinations of alleles B, E and F of the gene CSN1S1 and alleles A and B of the gene CSN3) distributed in three herds, which were collected bimonthly during a whole lactation. Data analysis, using a linear mixed model for repeated observations, revealed significant associations between CSN1S1 genotypes and the rate of the curdling process. In this way, milk from EE goats had a significantly higher curdling rate than milk from BB individuals (P<0?·05). Contrary to previous experiments performed in French breeds, cheese yield was not significantly different in BB, EE and EF goats. Moreover, we have shown that CSN3 genotype has a significant effect on the rennet coagulation time (BB>AB, P<0?·05) but not on cheese yield. No interaction between the CSN1S1 and CSN3 genotypes was observed.     

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.     

Short communication: Genetic variability in the predicted microRNA target sites of caprine casein genes

The main goal of the current work was to identify single nucleotide polymorphisms (SNP) that might create or disrupt microRNA (miRNA) target sites in the caprine casein genes. The 3′ untranslated regions of the goat α_S1-, α_S2-, β-, and κ-casein genes (CSN1S1, CSN1S2, CSN2, and CSN3, respectively) were resequenced in 25 individuals of the Murciano-Granadina, Cashmere, Canarian, Saanen, and Sahelian breeds. Five SNP were identified through this strategy: c.*175C > T at CSN1S1; c.*109T > C, c.*139G > C, and c.*160T > C at CSN1S2; and c.*216C > T at CSN2. Analysis with the Patrocles Finder tool predicted that all of these SNP are located within regions complementary to the seed of diverse miRNA sequences. These in silico results suggest that polymorphism at miRNA target sites might have some effect on casein expression. We explored this issue by genotyping the c.*175C > T SNP (CSN1S1) in 85 Murciano-Granadina goats with records for milk CSN1S1 concentrations. This substitution destroys a putative target site for miR-101, a miRNA known to be expressed in the bovine mammary gland. Although TT goats had higher levels (6.25 g/L) of CSN1S1 than their CT (6.05 g/L) and CC (6.04 g/L) counterparts, these differences were not significant. Experimental confirmation of the miRNA target sites predicted in the current work and performance of additional association analyses in other goat populations will be an essential step to find out if polymorphic miRNA target sites constitute an important source of variation in casein expression.     

Short communication: predominance of beta-casein (CSN2) C allele in goat breeds reared in Italy

A protocol for the rapid and simultaneous genotyping of A, C, and 0 'CSN2 alleles in goat was developed by single strand conformational polymorphism polymerase chain reaction (SSCP-PCR) technique. Screening the CSN2 variability in 7 goat breeds reared in Italy validated the genotyping test. The SSCP-PCR technique was also suitable for monitoring CSN2 polymorphism. In particular, the discrimination between CSN2*A and CSN2*C is important because the 2 corresponding protein variants cannot be separated by standard typing techniques. The monitoring of CSN2 variability in the goat breeds indicates the predominance of the C allele. In most breeds, CSN2*C occurred with the highest frequency, except in Saanen where CSN2*A and CSN2*C showed similar frequencies. Variant CSN2*C occurred with a frequency of 0.68 (Camosciata), 0.70 (Jonica), 0.71 (Garganica), 0.82 (Maltese), 0.87 (Cilentana), and 0.97 (Orobica). The alignment among the mature CSN2 sequences of different species suggests that CSN2*A is the ancestral allele compared with CSN2*C. Interestingly, the CSN2*A goat variant showed higher frequencies in selected breeds (Saanen and Camosciata).     

Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.     

Focusing on the goat casein complex

The analysis of casein polymorphisms in goat species is rather difficult, because of a large number of mutations at each locus, and the tight linkage involving the 4 casein genes. Three goat breeds from Northern Italy, Orobica, Verzasca, and Frisa, were analyzed at the casein complex by milk isoelectrofocusing and analyses at the DNA level to identify the majority of all known polymorphisms. The casein gene structure of the 3 local breeds at α_S1-casein (CSN1S1), β-casein (CSN2), α_S2-casein (CSN1S2), and κ-casein (CSN3) was compared with that of Camosciata, a more widely distributed breed. A new allele was identified and characterized at CSN2 gene, which seemed to be specific to the Frisa breed. It was named CSN2*E, and was characterized by a transversion TCT → TAT responsible for the amino acid exchange Ser₁₆₆ → Tyr₁₆₆ in the mature protein. The casein haplotype structure is highly different among breeds. A total of 26 haplotypes showed a frequency higher than 0.01 in at least 1 of the 4 breeds considered, with 12, 3, 5, and 19 haplotypes in Frisa, Orobica, Verzasca, and Camosciata breeds, respectively. Only 13 haplotypes occurred at a frequency higher than 0.05 in at least 1 breed. With the molecular knowledge of each locus, the ancestral haplotype coding for CSN1S1*B, CSN2*A, CSN1S2*A, and CSN3*B protein variants can be postulated. A protein evolutionary model considering the whole casein haplotype is proposed.     

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 ≥0.01 and 27 with frequency ≥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, Girgentana and Messinese was ACAB (0.06, 0.23, and 0.10, respectively). According to the haplotype reconstruction, Argentata dell’Etna, Girgentana, and Messinese breeds presented the most favorable haplotype for cheese production, because the casein concentration in milk of these breeds might be greater than that in Derivata di Siria and Maltese breeds. Based on a cluster analysis, the breeds formed 2 main groups: Derivata di Siria, and Maltese in one group, and Argentata dell’Etna and Messinese in the other; the Girgentana breed was between these groups but closer to the latter.     

Goat milk allergenicity as a function of αs₁-casein genetic polymorphism

Cow milk allergy is the most frequent allergy in the first years of life. Milk from other mammalian species has been suggested as a possible nutritional alternative to cow milk, but in several cases, the clinical studies showed a high risk of cross-reactivity with cow milk. In the goat species, α_S1-casein (α_S1-CN), coded by the CSN1S1 gene, is characterized by extensive qualitative and quantitative polymorphisms. Some alleles are associated with null (i.e., CSN1S1*0₁) or reduced (i.e., CSN1S1*F) expression of the specific protein. The aim of this work was to obtain new information on goat milk and to evaluate its suitability for allergic subjects, depending on the genetic variation at α_s1-CN. Individual milk samples from 25 goats with different CSN1S1 genotypes were analyzed by sodium dodecyl sulfate PAGE and immunoblotting, using monoclonal antibodies specific for bovine α-CN and sera from children allergic to cow milk. A lower reaction was observed to 2 goat milk samples characterized by the CSN1S1* 0₁0₁ and 0₁F genotypes. Moreover, a fresh food skin prick test, carried out on 6 allergic children, showed the lack of positive reaction to the 0₁0₁ milk sample and only one weak reactivity to the 0₁F sample. The risk of cross-reactivity between cow and goat milk proteins suggests the need for caution before using goat milk for infant formulas. However, we hypothesize that it can be used successfully in the preparation of modified formulas for selected groups of allergic patients. The importance of taking the individual goat CN genetic variation into account in further experimental studies is evident from the results of the present work.     

Short communication: Polymorphism of casein cluster genes in Czech local goat breeds

The 4 casein loci were evaluated as haplotypes in 2 dairy goat breeds kept in the Czech Republic. Analysis of 41 White Shorthaired (WSH) trio families and 44 Brown Shorthaired (BSH) trio families revealed 14 and 20 haplotypes, respectively. Various genomic techniques were used to type the casein loci. Twenty-two different combinations of these alleles (casein haplotypes, in the order CSN1S1-CSN2-CSN1S2-CSN3) were found. Only 5 haplotypes in the WSH breed and 6 haplotypes in the BSH breed occurred at frequencies >0.05. For the WSH breed, the most common haplotype was FCFB (0.260), whereas for the BSH breed, the most common haplotype was FCFA (0.217). The information on the haplotype variability in both breeds could be used in breeding programs aimed at preserving biodiversity or selecting animals for specific protein production and cheesemaking.     

Caprine CSN1S1 haplotype effect on gene expression and milk composition measured by Fourier transform infrared spectroscopy

The Norwegian dairy goat population has a high frequency of a CSN1S1 (α_S1-casein) haplotype with negative effects on protein and fat content. It is characterized by a single point deletion in exon 12 of CSN1S1, leading to a truncated protein and hence a low content of α_S1-casein in the milk. This haplotype together with another haplotype with a deletion in exon 9 are called “weak” haplotypes. “Strong” haplotypes, on the other hand, have positive effects on important milk production traits. We show that expression of CSN1S1 in the mammary gland of lactating goats is significantly lower in animals with 2 weak haplotypes. Moreover, the effects of defective alleles were not detected in animals having 1 strong and 1 weak haplotype. Expression levels of other genes in the casein cluster were not affected by the CSN1S1 haplotypes investigated. Milk samples from goats with 2 weak haplotypes could be distinguished from the other milk samples using Fourier transform infrared (FTIR) spectroscopy and partial least squares discriminant analysis (PLS-DA). The PLS-DA components were related to spectra of pure caseins and whey proteins, hence FTIR has a potential for identifying milk samples with low α_S1-casein content and different protein composition. The results indicate that FTIR-based measurements can be incorporated into breeding plans, or for selection of milk samples with high casein content, which in turn may improve cheese-making properties of the milk.     

Caprine kappa-casein (CSN3) polymorphism: new developments in molecular knowledge

A high degree of polymorphism was recently found at the kappa-casein (CSN3) locus in the domesticated goat (Capra hircus). In the present study, 2 new patterns previously identified by PCR-single-strand conformation polymorphism analysis (SSCP) were characterized. The allele provisionally named "X" (GenBank Accession no. AY350425) differs from CSN3*C (AF485341) by a (silent) A-->G substitution at position 509 of the goat CSN3 reference sequence (X60763). As this newly identified sequence changes the amino acid sequence, and the already known CSN3*C allele (AF485341) has an additional silent mutation, we proposed a change in nomenclature to reflect these changes, indicating the silent mutation with the prime symbol (i.e.,'). The CSN3*M allele (provisionally named "Y") results in a new protein variant, differing by 2 nonsynonymous mutations from the CSN3*F allele. The new variant is characterized by a G-->A transition at nucleotide position 384, resulting in the amino acid exchange Asp90-->Asn90, and a C-->T transition at position 550, resulting in a Val145-->Ala145 substitution. Thus, the number of alleles identified in the domesticated goat has increased to 16, of which 13 are protein variants and 3 are silent mutations, involving a total of 15 polymorphic sites in CSN3 exon 4. Data on the distribution of the main alleles in 7 goat breeds of Europe, West Africa, and the Near East show differences in the occurrence and frequency of the alleles between breeds and geographic origin with the highest number of alleles found in goat breeds from the Near East.     

Technical note: detection of the C allele of beta-casein (CSN2) in Czech Dairy goat breeds using LightCycler analysis

A protocol was developed for rapid genotyping of A and C variants at the CSN2 locus in goat species (White Shorthaired and Brown Shorthaired goat) by PCR and LightCycler analysis. The LightCycler technique combines rapid and efficient in vitro amplification of DNA in glass capillaries, with melting curve analysis based on fluorescence resonance energy transfer, for the sensitive detection of point mutation. Analysis of the CSN2 variability in the 2 goat breeds reared in the Czech Republic validated the genotyping test. Monitoring of CSN2 variability in the goat breeds indicates the predominance of the C allele. In both breeds, CSN2*A and CSN2*C showed almost similar frequencies. Variant CSN2*C occurred with a frequency of 0.699 in White Shorthaired goats and 0.570 in Brown Short-haired goats.     

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.     

Additive and dominance effects of the αs1-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.     

Characterization of the casein gene complex in West African goats and description of a new alpha(s1)-casein polymorphism

The analysis of casein polymorphisms was carried out in West Africa goat populations: Red Sokoto (n = 57), West African Dwarf Nigeria (n = 27), West African Dwarf Cameroon (n = 39), and Borno (n = 37). The 4 casein genes α_s1 (CSN1S1), β (CSN2), α_s2 (CSN1S2), and κ (CSN3) were typed at the DNA level. No null alleles were found in any of the genes analyzed. A PCR single-strand conformation polymorphism method was implemented for the identification of CSN1S1*F allele simultaneously with A/0₁, B/E, N and the new allele. The allele differed from CSN1S1*B by a synonymous transversion TCG→TCT in the codon corresponding to Ser₆₆ of the mature protein. The new allele, named CSN1S1*B′, occurred at a high frequency in all the populations, ranging from 0.295 (West African Dwarf Cameroon) to 0.405 (Borno). A greater frequency was found for alleles associated with high α_s1-casein quantity, as has already been observed in the goat populations from the Mediterranean area. The intermediate E allele occurred only in the Red Sokoto and at a low frequency. The faint F allele occurred in 3 populations at frequencies lower than 0.03. Linkage disequilibrium occurred in all the populations, with highly significant differences in Borno, Red Sokoto, and West Africa Dwarf Nigeria, and significant differences in West Africa Dwarf Cameroon. Only 10 haplotypes showed frequencies ≥0.05 in at least 1 of the 4 populations considered, and the overall frequency was >0.1 only for 4 haplotypes: BAAB, B′ACA, ACAB, and BACA (in the order CSN1S1-CSN2-CSN1S2-CSN3). Haplotype BAAB, postulated as an ancestral haplotype in previous studies, was the most common haplotype in all breeds except Borno, where B′ACA was predominant. The results obtained are of considerable significance given that very little information exists on the subject for African goats. The high frequency of strong alleles in the calcium-sensitive caseins as well as the high linkage disequilibrium found among the casein genes in the African breeds analyzed may suggest that specific casein haplotypes have already been selected due to their advantages for nutrition. Haplotypes providing greater protein and casein content would increase the energy content of milk, thus resulting in more favorable growth and survival of young goats and humans consuming the milk.