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* Dipartimento di Scienze Biomediche e Biotecnologie, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università degli Studi di Milano, Via Trentacoste 2, 20134 Milano, Italy
1 Corresponding author: anna.caroli{at}unimi.it
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONSACKNOWLEDGEMENTSREFERENCES |
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S1-casein (CSN1S1), ß-casein (CSN2), S2-casein (CSN1S2), and 
-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.
Key Words: casein genotype • goat • proteome • variability
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONSACKNOWLEDGEMENTSREFERENCES |
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S1-CN, ß- CN, and S2-CN, are coded by CSN1S1, CSN2, and CSN1S2 genes, respectively, whereas -CN, which plays an essential role in the casein micelle stabilization (Alexander et al., 1988), is coded by the CSN3 gene. Initial investigations into goat casein polymorphisms were carried out by Boulanger et al. (1984) with research on CSN1S1. Until now, 16 alleles associated with different rates of protein synthesis have been identified. On the basis of the milk content of S1-CN, the CSN1S1 variants can be grouped into 4 classes: strong alleles (A, B1, B2, B3, B4, C, H, L, and M), producing almost 3.5 g/L of S1-CN each; intermediate alleles (E and I; 1.1 g/L); weak alleles (F and G; 0.45 g/L); and null alleles (01, 02, and N) apparently producing no S1-casein (reviewed by Grosclaude and Martin, 1997; Rando et al., 2000; Chessa et al., 2003a; Ramunno et al., 2005). The evolutionary pathway of goat CSN1S1, first proposed by Grosclaude et al. (1994), was slightly modified by Grosclaude and Martin (1997) and Chianese et al. (1997). The B1 allele was considered ancestral, and 2 divergent lineages were suggested, one leading to the A, G, 01, 02, I, and H variants (lineage A), and the other leading to B2, B3, B4, L, F, C, and E variants (lineage B). Later, Bevilacqua et al. (2002), including the M allele in the phylogeny, focused on the intragenic recombination event possibly responsible for this new variant, which could be placed in both lineages (A and B) arising from the putative ancestral allele. A similar event was also proposed for the origin of CSN1S1*N (Ramunno et al., 2005). More recently, variation has been described at the other casein genes. For the CSN2 gene, 3 variants were found to be associated with a normal ß-CN content: A, B (Mahé and Grosclaude, 1993), and C (Neveu et al., 2002). The C variant was found to be predominant in Italian goat breeds (Chessa et al., 2005). Furthermore, 2 null CSN2 alleles were identified, both characterized by mutations responsible for premature stop codons in exon 7 (Ramunno et al., 1995; Persuy et al., 1999). The 2 null alleles were named respectively as CSN2*0 'and CSN2*0 by Neveu et al. (2002). More recently an SspI PCR-RFLP, detecting a silent CSN2 allele, was described and named CSN2*A1 (Cosenza et al., 2005).
The alignment among the mature ß-CN sequence of different species suggests that CSN2*A is the ancestral allele in comparison with CSN2*C (Chessa et al., 2005). In fact, the presence of alanine at position 177 of the mature protein coded by goat CSN2*A has been found also in other ruminant species, whereas CSN2*C codes for valine at the same amino acid position.
At least 7 alleles have been identified at CSN1S2, associated with 3 synthesis levels. The A, B (Boulanger et al., 1984), C (Bouniol et al., 1994), E (Lagonigro et al., 2001), and F (Ramunno et al., 2001a) alleles were associated with a normal S2-CN synthesis level, whereas D and 0 were associated with lower and null synthesis levels, respectively (Ramunno et al., 2001a,b). An evolutionary pathway has been proposed (Sacchi et al., 2005) starting from the A variant and leading independently to the B, C, F alleles, each characterized by a different amino acid substitution with respect both to CSN1S2*A and to the bovine (Swissprot Accession number P02663) and ovine (P04654) sequences. Thus, CSN1S2*A may be considered the ancestral variant. Moreover, if goat CSN1S2*A, B, and C (P33049), and goat CSN1S2*E (CAC21704) sequences are compared, it can be postulated that CSN1S2*E variant derives from CSN1S2*C, because the 2 alleles share an Ile, instead of Lys, at position 167 of the mature protein (Lagonigro et al., 2001; Sacchi et al., 2005).
A total of 15 polymorphic sites were identified in domestic goat allowing the identification of 16 CSN3 alleles corresponding to 13 -CN variants, and 3 synonymous mutations. Prinzenberg et al. (2005) proposed a new nomenclature for the alleles, and their subdivision in 2 groups, on the basis of the different isoelectric point, which allows identifying 2 different patterns by isoelectrofocusing (IEF), named as AIEF (isoelectric point = 5.29) and BIEF (isoelectric point = 5.66). A phylogeny for CSN3 was proposed by Yahyaoui et al. (2003), Jann et al. (2004), and Prinzenberg et al. (2005). Apart from the conflicting nomenclature, the 3 papers agree that CSN3*A appeared later in the evolutionary pathway, and that 2 different lineages occurred. The phylogeny is complex, most probably resulting from different intragenic recombination events, similarly to CSN1S1.
Furthermore, goat casein genes are closely linked in a complex including in the order CSN1S1, CSN2, CSN1S2, and CSN3 (Ferretti et al., 1990; Threadgill and Womack, 1990). The entire casein gene complex spans about 250 kb on chromosome 6 (Hayes et al., 1993; Popescu et al., 1996). The 2 first genes of the casein complex, CSN1S1 and CSN2, are only 12 kb apart and convergently transcribed (Leroux and Martin, 1996). Due to the tight linkage among casein genes, the variability of the whole haplotype has to be accounted for when analyzing the goat caseins for biodiversity studies or breeding strategies. A previous work followed this research approach (Sacchi et al., 2005). However, CSN2 was not considered in the casein haplotype analysis in that study, because a typing test for CSN2*C allele was not yet available.
This paper aimed to focus on the goat casein complex variability, by including CSN2 in the haplotype analysis of 3 Lombardy local breeds, Orobica, Verzasca, and Frisa, which were compared with a sample of the Camosciata, a more widely distributed breed. A new CSN2 variant was also identified and characterized.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONSACKNOWLEDGEMENTSREFERENCES |
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. The nomenclature proposed by Prinzenberg et al. (2005) was used for CSN3 in the upcoming discussion of the results obtained.
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The Genepop program (Raymond and Rousset, 1995) was used for the evaluation of allele frequencies and deviations from Hardy-Weinberg equilibrium. The casein haplotype frequencies were estimated by the EH program (Xie and Ott, 1993). For EH computation, alleles with frequencies lower than 0.05 were ignored. Allele and haplotype frequencies of the 3 local breeds were compared with a sample of the Camosciata breed reared in different flocks of Northern Italy, analyzed by Budelli et al. (2005).
The structure of the whole casein complex was analyzed in silico at the protein and DNA levels. A multivariate analysis was performed by the average method of the CLUSTER procedure (SAS Institute, 1990) on the amino acid exchange or deletion classed as 1 (presence of the ancestral amino acid or amino acid sequence) or 0 (absence of the ancestral amino acid or amino acid sequence). Thirteen haplotypes showing a frequency higher than 0.05 were included in the cluster analysis. A phylogeny model was suggested for the whole casein complex.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONSACKNOWLEDGEMENTSREFERENCES |
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). Direct sequencing of the PCR products allowed the characterization of the new pattern, resulting from a transversion TCT TAT responsible for the amino acid exchange Ser166 Tyr166 in the mature protein. The transversion occurs in the codon 124 of exon 7 and involves nucleotide 8,215 of the reference CSN2 sequence (GenBank Acc. No. AJ011018). The amino acid exchange deduced from the nucleotide sequence in the new variant involved 2 apolar amino acids, and was not detectable by standard protein screening techniques such IEF, in which it shared the same migration pattern with CSN2*A and C. Typing at the DNA level or by a higher resolution protein approach was therefore necessary to correctly identify the genetic variation of goat ß-casein.
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Most probably, CSN2*E derived from CSN2*A, because its translated sequence corresponds to the CSN2*A allele (GenBank Acc. No. AJ011018) except for the substitution described. In fact, both CSN2*A and CSN2*E share the same codon (GCA, Ala177), different from CSN2*C (GTA, Val177). Moreover, the alignment among the mature ß-CN sequences of different species shown by Chessa et al. (2005) suggests that CSN2*A is the ancestral allele compared with CSN2*E because Ser166 occurs in other ruminants.
Allele Frequencies at Each Casein Gene
Table 2 shows the allele frequencies at the casein loci in the 3 local breeds, compared with the more widely distributed Camosciata (Budelli et al., 2005). The genotype frequencies as well as the genotype combinations at the 4 loci are available online at http://jds.fass.org.
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In the local breeds, the greatest number of alleles was found at CSN1S1 (from 4 to 5), even if a greater variability occurred at the same locus in the Camosciata, in which 7 alleles were detected. In Verzasca and Orobica (particularly), a rather unbalanced distribution was found for CSN1S1 alleles. Only 2 variants (F and E) occurred at a frequency higher than 0.05 in Verzasca, whereas Orobica was almost monomorphic for CSN1S1*F. In the 3 Lombardy breeds, CSN1S1*B was a rare variant, unlike the Camosciata. In the Frisa, the null CSN1S1*01 allele had a rather high frequency (0.11). The faint and null variants (F, 01, N) showed a cumulative frequency of 0.98 in Orobica, 0.76 in Verzasca, 0.66 in Frisa, compared with 0.25 in Camosciata.
At CSN2, C was the predominant allele, ranging from 0.66 in Camosciata to 0.99 in Orobica, and confirming previous results in Italian breeds (Chessa et al., 2005). No CSN2*0 'null allele was found, confirming its exclusive presence in Southern Italian goat breeds (Rando et al., 2000; Chessa et al., 2005).
The novel CSN2*E allele seems to be breed specific, because it was found only in Frisa in this study, and should also be absent in Camosciata, Saanen, Jonica, Garganica, Maltese, and Cilentana breeds (Budelli et al., 2005; Chessa et al., 2005) because the same PCR-SSCP method was used for CSN2 typing.
The greatest number of alleles at CSN1S2 occurred in Frisa, in decreasing frequency order: F, A, B, E, C, whereas 4 alleles were found in Camosciata and Verzasca (A > F > C > B). Orobica was almost monomorphic for CSN1S2*F, with the A allele occurring at a very low frequency (0.01).
In the Frisa, a high frequency was found for CSN1S2*B (0.11), which was associated with CSN1S1*01 as already demonstrated (Grosclaude et al., 1987). Interestingly, CSN1S2*B is characterized by an amino acid exchange leading to a further Lys residue in the protein variant compared with the other CSN1S2 alleles associated with a normal S2-content (Bouniol, 1993). Because goat milk is particularly rich in the essential amino acid lysine (Salvadori Del Prato, 1998), an adaptive mechanism might be responsible for the casein complex structure occurring in Frisa breed. In fact, the lack of S1-casein and its essential amino acids might be balanced by a genetic variant in the casein complex providing a larger amount of Lys, such as CSN1S2*B, to increase the individual fitness. However, the association between CSN1S1*01 and CSN1S2*B was not found in Orobica, in which CSN1S2*B did not occur. Two of the 3 Orobica goats carrying CSN1S1*01 were informative for CSN1S1-CSN1S2 linkage phase, revealing association between CSN1S1*01 and CSN1S2*F in this breed. The adaptive mechanism possibly involving CSN1S1 and CSN1S2 should be further investigated.
Only 2 CSN3 alleles (A and B) were found in Verzasca and Camosciata with rather similar frequencies. The CSN3*B allele was predominant in all 4 breeds, with frequency ranging from 0.55 (Orobica) to 0.72 (Verzasca). Two additional alleles, C and D, occurred in Frisa and Orobica. In the Orobica, the low genetic variation shown at the calcium-sensitive caseins seems to be balanced by a higher variation at -CN. The high frequency of CSN3*D (0.35) in the breed is particularly important. Among the 4 identified alleles, CSN3*D is the only one belonging to the BIEF group, according to the subdivision of CSN3 alleles suggested by Prinzenberg et al. (2005). The presence of CSN3*D in the casein haplotype modifies the electric charge of -casein and, consequently, the physicochemical properties of the casein micelle. The favorable effect of the BIEF variant on milk casein content (0.5 g/L more than AIEF variant) was recently observed by Chiatti et al. (2005). The high frequency of the CSN3*D allele in Orobica might be explained as an adaptive mechanism because in this breed, alleles associated with faint or null S1-casein content showed a high incidence (0.98). The high frequency of CSN3*D variant in the breed might balance the unfavorable CSN1S1 genetic effect on specific protein expression by increasing the milk content of casein fraction.
Haplotype Distribution
Haplotype frequencies at CSN1S1-CSN2-CSN1S2-CSN3 loci are reported in Table 3. A total of 26 haplotypes showed a frequency higher than 0.01 in at least 1 of the 4 breeds considered. We found 12, 3, 5, and 19 haplotypes with frequencies higher than 0.01 in Frisa, Orobica, Verzasca, and Camosciata, respectively. Only 13 haplotypes occurred at a frequency higher than 0.05 in at least one breed. High linkage disequilibrium was found in Frisa, Verzasca, and Camosciata, as indicated by the 
2 test for association performed by EH. Linkage disequilibrium was not tested in Orobica, because the observations used for the haplotype frequency evaluation were monomorphic at CSN1S1, CSN2, and CSN1S2.
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Among the 25 haplotypes carrying CSN3*A or CSN3*B, B-A-A-B may be considered the ancestral haplotype based on the evolutive hypotheses discussed in the introduction, which assume a parsimony evolution model at each casein gene. The results obtained in this study for CSN2*E are also in agreement with the parsimony model suggesting the origin of CSN2*E from CSN2*A. The assumption of B-A-A-B as the ancestral haplotype will be the basis for the following discussion.
The B-A-A-B haplotype had a high incidence in the Camosciata, whereas it was not found in the 3 local breeds. Four haplotypes carried an allele found only in a breed at a frequency higher than 0.05: 01-C-B-A, F-E-F-B, A-C-E-B in Frisa, and F-C-F-D in Orobica.
The amino acid exchanges and deletions in the casein variants affecting the 13 most common haplotypes are shown in Table 4. It is evident that Ala177, which characterizes CSN2*A, is usually associated with CSN1S1*B and CSN1S1*E, with an overall cumulative frequency of 0.19 compared with 0.01 for CSN2*C associated with the same CSN1S1 alleles (Table 3
). Alternatively, Val177, characterizing CSN2*C, is generally associated with CSN1S1*A and CSN1S1*F (overall cumulative frequency of 0.73 compared with 0.01 for CSN2*A associated with the same CSN1S1 alleles). However, the association CSN1S1*F-CSN2*C is related to breeds containing a very few number of haplotypes; i.e., Orobica and Verzasca, and needs to be confirmed in other goat populations.
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Figure 2 shows the tree obtained from the cluster analysis carried out on the thirteen haplotypes having a frequency higher than 0.05. For this analysis, amino acid exchanges or deletions at the different loci shown in Table 4 had been classified as a matrix of 0 or 1. As an example, the presence of Pro or Leu at position 16 of the CSN1S1 mature protein was coded as 1 or 0, whereas the occurrence or the deletion of the 59th-95th amino acid sequence at the same protein was classified as 1 or 0, respectively.
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, with CSN1S1*A) and B (left panel of Figure 2, with CSN1S1*B, E and F). The 2 clusters overlap for CSN2 locus. In fact, CSN2*C always occurred in the A cluster, whereas, in the B cluster, CSN2*A was associated with CSN1S1*B or CSN1S1*E, and CSN2*C was associated with CSN1S1*F. Some haplotypes representing exceptions to this trend were also found in the Camosciata (A-A-F-B, B-C-F-A, B-C-F-B, F-A-C-B) but were not included in the cluster analysis due to the low frequency (< 0.05) observed. The relationships among the other genes of the casein complex are less clear, possibly because of recombination events confounding the evolutive pathway.
A phylogeny model can be suggested for the whole haplotype starting from the ancestral CSN1S1*B-CSN2*A-CSN1S2*A-CSN3*B haplotype (Figure 3). The origin of E-A-A-B is self-explanatory, whereas the evolution of the other haplotypes is more complex. Two different pathways may be suggested, one leading to F-C-A-B and the other to A-C-A-B. It is most probably that a common B-C-A-B haplotype led to both pathways, although it was not found in the breeds considered. This fact might cause the overlapping between the 2 CSN1S1 lineages when considering CSN2 (Figure 2), and suggests that the CSN2*A to C exchange occurred before other mutations at CSN1S1 locus. Different recombination events involved CSN1S2 and CSN3 genes in the haplotype evolution.
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Most probably, the F-E-F-B and A-C-E-B haplotypes derived from further recombination events, on the basis of the supposed origin of CSN2*E and CSN1S2*E from CSN2*A and CSN1S2*C, respectively. Moreover, E-A-F-B might derive from recombinant events if CSN1S2*F originated from F-C-A-B, as suggested in the evolutive model. Although recombination among the casein genes is essential in explaining the haplotype variability, a strong linkage disequilibrium condition was found in the breeds, resulting in an unbalanced distribution of the haplotypes described before. The fact that only a few haplotypes occur with a high frequency in the breeds considered indicates that selection has strongly reduced the casein complex variability. A balance mechanism among the genetic variants in the casein micelles, as suggested by this study, might explain the high linkage disequilibrium found in Frisa, Camosciata, and Verzasca.
The results obtained in the current study can be partially compared with a previous investigation by Sacchi et al. (2005), in which CSN1S1-CSN2-CSN3 haplotype variability was analyzed in 5 Italian local breeds (Vallesana, Roccaverano, Jonica, Garganica, and Maltese). Among the 18 haplotypes considered, an evolutive pathway was proposed starting from the ancestral B-A-B haplotype, followed by B-F-B, which was suggested to give rise to the most common F-F-B. In the Camosciata, F-F-B haplotype had a lower frequency (0.07) than in the local breeds both analyzed by Sacchi et al. (2005) and in this study, whereas F-F-A was more common (0.10), as in the Vallesana. Interestingly, strong evidences of recombination events, not only among but also within the casein genes, were found for the 18 haplotypes taken into account by Sacchi et al. (2005).
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CONCLUSIONS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONSACKNOWLEDGEMENTSREFERENCES |
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At the CSN2 locus, the predominance of the C allele in Italian breeds was confirmed. Moreover, a new mutation was identified resulting in an amino acid exchange not detectable by standard protein screening techniques. The novel variant, named CSN2*E, was found in only one breed.
Adaptive mechanisms were suggested that could balance the effects of alleles at different loci. The CSN1S2*B and CSN3*D alleles, which were found prevalently associated with null and faint alleles at CSN1S1, lead to a higher content, respectively, in lysine and casein than other CSN1S2 and CSN3 variants.
Further studies should aim to explain how the goat casein complex evolution led to all the existing mutations. An answer to this problem might provide not only interesting elements from the point of view of the phylogenesis of the goat species, but also useful indications for the selection of the animals on the basis of functional and adaptive aspects concerning the whole casein complex.
An evolutive model has been suggested, starting from the haplotype CSN1S1*B-CSN2*A-CSN1S2*A-CSN3*B, and resulting in several protein variants that differently assemble the casein micelle. Both milk composition and technological properties can be strongly affected by the casein micelle structure, which is the result of "genome to proteome" relationships involving the goat caseins.
The proposed phylogeny was an attempt to explain goat casein cluster evolution on the basis of the subset of population, which was taken into account in the present paper. Alternative evolutionary pathways could be traced if considering further goat breeds, or fitting different phylogeny models; that is, not based on the parsimony assumption. Nevertheless, the proposed phylogeny pathway could be the basis for better understanding the biological mechanisms that differentiated the casein complex so deeply in the different goat populations because of natural and artificial selection.
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ACKNOWLEDGEMENTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONCONCLUSIONSACKNOWLEDGEMENTSREFERENCES |
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Received for publication October 30, 2005. Accepted for publication February 27, 2006.
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  A. M. Caroli, S. Chessa, and G. J. Erhardt Invited review: Milk protein polymorphisms in cattle: Effect on animal breeding and human nutrition J Dairy Sci, November 1, 2009; 92(11): 5335 - 5352. [Abstract] [Full Text] [PDF]
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S. Chessa, D. Rignanese, J. Kupper, G. Pagnacco, G. Erhardt, and A. Caroli Short Communication: The {beta}-Casein (CSN2) Silent Allele C1 Is Highly Spread in Goat Breeds J Dairy Sci, November 1, 2008; 91(11): 4433 - 4436. [Abstract] [Full Text] [PDF]
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Z. Sztankoova, J. Kysel'ova, T. Kott, and E. Kottova Technical Note: Detection of the C Allele of {beta}-Casein (CSN2) in Czech Dairy Goat Breeds Using LightCycler Analysis J Dairy Sci, October 1, 2008; 91(10): 4053 - 4057. [Abstract] [Full Text] [PDF]
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I. Gigli, D. O. Maizon, V. Riggio, M. T. Sardina, and B. Portolano Short Communication: Casein Haplotype Variability in Sicilian Dairy Goat Breeds J Dairy Sci, September 1, 2008; 91(9): 3687 - 3692. [Abstract] [Full Text] [PDF]
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