Mutations away from splice site recognition sequences might cis-modulate alternative splicing of goat alpha s1-casein transcripts. Structural organization of the relevant gene

Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats (Capra hircus), with an Important Role of CSN1S2 for Milk Yield

This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype.

A novel allelic donkey β-lactogobulin I protein isoform generated by a non-AUG translation initiation codon is associated with a nonsynonymous SNP

β-Lactoglobulin I (β-LG I) is one of the most important whey proteins in donkey milk. However, to our knowledge, there has been no study focusing on the full nucleotide sequences of this gene (BLG I). Current investigation of donkey BLG I gene is very limited with only 2 variants (A and B) characterized so far at the protein level. Recently, a new β-LG I variant, with a significantly higher mass (+1,915 Da) than known variants has been detected. In this study, we report the whole nucleotide sequence of the BLG I gene from 2 donkeys, whose milk samples are characterized by the β-LG I SDS-PAGE band with a normal electrophoretic mobility (18,514.25 Da, β-LG I B1 form) the first, and by the presence of a unique β-LG I band with a higher electrophoretic mobility (20,428.5 Da, β-LG I D form) the latter. A high genetic variability was found all over the 2 sequenced BLG I alleles. In particular, 16 polymorphic sites were found in introns, one in the 5' flanking region, 3 SNPs in the 5' untranslated region and one SNP in the coding region (g.458G > A) located at the 40th nucleotide of exon 2 and responsible for the AA substitutions p.Asp28 > Asn in the mature protein. Two SNPs (g.920-922CAC > TGT and g.1871G/A) were genotyped in 93 donkeys of 2 Italian breeds (60 Ragusana and 33 Amiatina, respectively) and the overall frequencies of g.920-922CAC and g.1871A were 0.3065 and 0.043, respectively. Only the rare allele g.1871A was observed to be associated with the slower migrating β-LG I. Considering this genetic diversity and those found in the database, it was possible to deduce at least 5 different alleles (BLG I A, B, B1, C, D) responsible for 4 potential β-LG I translations. Among these alleles, B1 and D are those characterized in the present research, with the D allele of real novel identification. Haplotype data analysis suggests an evolutionary pathway of donkey BLG I gene and a possible phylogenetic map is proposed. Analyses of mRNA secondary structure showed relevant changes in the structures, as consequence of the g.1871G > A polymorphism, that might be responsible for the recognition of an alternative initiation site providing an additional signal peptide. The extension of 19 AA sequence to the mature protein, corresponding to the canonical signal peptide with an additional alanine residue, is sufficient to provide the observed molecular weight of the slower migrating β-LG I encoded by the BLG I D allele.

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.

Capture Sequencing to Explore and Map Rare Casein Variants in Goats

Genetic variations in the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats (CSN1S1^∗C1), Bezoar ibex (CSN1S1^∗J), and Alpine ibex (CSN1S1^∗K), for beta and kappa caseins in Alpine ibex (CSN2^∗F and CSN3^∗X), and for alpha S2 casein in all domesticated and wild goats (CSN1S2^∗H), in Nubian and Desert goats (CSN1S2^∗I), or in Nubian ibex only (CSN1S2^∗J and CSN1S2^∗K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants.

Association Analysis between SPP1, POFUT1 and PRLR Gene Variation and Milk Yield, Composition and Coagulation Traits in Sarda Sheep

Many studies focus on the identification of genomic regions that undergo selective processes, where evidence of selection is revealed and positional candidate genes are identified. The aim of the research was to evaluate the association between positional candidate genes, namely secreted phosphoprotein 1 (SPP1, sheep chromosome Ovis aries OAR6, 36.651-36.658 Mb), protein O-fucosyltransferase 1 (POFUT1, OAR13, 61.006-61.027 Mb) and prolactin receptor (PRLR, OAR16, 38.969-39.028 Mb) with milk yield, composition and coagulation traits. Eight single nucleotide polymorphisms (SNPs) mapping to the three genes were genotyped in 380 Sarda dairy sheep. Statistical analysis revealed an association between SNP rs161844011 at SPP1 (chromosome position Oar_v3 OAR6:36651870, gene region exon 7) and somatic cell score, while POFUT1 SNP rs424501869 (OAR13:61007495, intron 1) was associated with curd firmness both 45 and 60 min after rennet addition (p = 0.015 and p = 0.007, respectively). SNP rs400874750 at PRLR gene (OAR16:39004070, intron 2) had a significant association with lactose content (p = 0.020), somatic cell score (p = 0.038), rennet coagulation time (p = 0.018) and curd firming time (p = 0.047). The outcome of this research confirmed predictions based on genomic studies, producing new information regarding the SPP1, POFUT1 and PRLR genes, which may be useful for future breeding schemes.

Alternative splicing events expand molecular diversity of camel CSN1S2 increasing its ability to generate potentially bioactive peptides

In a previous study on camel milk from Kazakhstan, we reported the occurrence of two unknown proteins (UP1 and UP2) with different levels of phosphorylation. Here we show that UP1 and UP2 are isoforms of camel αs2-CN (αs2-CNsv1 and αs2-CNsv2, respectively) arising from alternative splicing events. First described as a 178 amino-acids long protein carrying eight phosphate groups, the major camel αs2-CN isoform (called here αs2-CN) has a molecular mass of 21,906 Da. αs2-CNsv1, a rather frequent (35%) isoform displaying a higher molecular mass (+1,033 Da), is present at four phosphorylation levels (8P to 11P). Using cDNA-sequencing, αs2-CNsv1 was shown to be a variant arising from the splicing-in of an in-frame 27-nucleotide sequence encoding the nonapeptide ENSKKTVDM, for which the presence at the genome level was confirmed. αs2-CNsv2, which appeared to be present at 8P to 12P, was shown to include an additional decapeptide (VKAYQIIPNL) revealed by LC-MS/MS, encoded by a 3'-extension of exon 16. Since milk proteins represent a reservoir of biologically active peptides, the molecular diversity generated by differential splicing might increase its content. To evaluate this possibility, we searched for bioactive peptides encrypted in the different camel αs2-CN isoforms, using an in silico approach. Several peptides, putatively released from the C-terminal part of camel αs2-CN isoforms after in silico digestion by proteases from the digestive tract, were predicted to display anti-bacterial and antihypertensive activities.

Effect of αS1-casein genotype on phenolic compounds and antioxidant activity in goat milk yogurt fortified with Rhus coriaria leaf powder

The aim of this work was to evaluate the phenolic compounds and antioxidant activity of goat milk yogurt characterized by different α_S1-casein genotypes and fortified with Rhus coriaria leaf powder. The α_S1-casein genotype was determined by isoelectric focusing, total phenol content was determined by the Folin-Ciocalteu method, phenolic compounds were identified and quantified by HPLC-UV analysis, and antioxidant activity was measured using 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid and ferric-reducing antioxidant power. The statistical analysis showed a significant effect of the studied factors. Comparing different genotypes it emerged that yogurt from goats with weak alleles at CSN1S1 loci (FF) showed the lowest phenolic compounds and therefore a lower antioxidant activity compared with yogurt from goats with strong alleles at CSN1S1 loci (AA, BB, AB). Rhus coriaria-fortified yogurt showed a significant increase in total phenolic compounds and antioxidant activity in comparison with plain yogurt. The FF-fortified yogurt presented the lowest total phenol content and antioxidant activity. This could be due to a greater capacity of proteins and peptides in this yogurt to form stable complexes with phenols. The different total phenol content detected in R. coriaria-fortified yogurt indicates that the α_S1-casein genotype influenced the amount of added phenols that are bound to the caseins and, therefore, the part that remains free and that affects the biological capacity of the final product.

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content

The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.

Revisión: E1 polimorfismo del gen de la caseina αs1 caprina y su efecto sobre la producción, la composición y las propiedades tecnológicas de la leche y sobre la fabricación y la maduración del queso

The caprine α s1-casein gene displays a high degree of polymorphism, with eight different protein variants described up to date. The rate of synthesis of the mature protein is closely linked to the caprine αs1-casein genotype. There are three variants which are associated to high αs1-casein content in milk (A, B, and C), one to an intermediate content (E), three to a low content (D, F, and G) and one to a null content (O). During the last few years studies of goat milk protein polymorphism have gained renewed interest, as the ocurrence of certain milk protein genetic variants is correlated with the composititon of milk and also with some milk processing parameters. For instance, analyses of the physicochemical properties of milk from goats homozy gous for the three main α s1-casein alleles (A, E, F) confirm the effects of the genotypes on the percentage of casein and fat, and shows significant effects on the diameter of the micelles and their calcium content. These characteristics seem to be associated with enhanced clotting of goat milk, cheese curd firmness, curd syneresis and overall cheese yield. The caprine αs1-casein gene constitutes a very attractive model for studying the regulation of the expression of the corresponding protein, and might also become a very powerful tool in improving the technolog ical properties of goat milk.

Molecular Characterization of the Llamas (Lama glama) Casein Cluster Genes Transcripts (CSN1S1, CSN2, CSN1S2, CSN3) and Regulatory Regions

In the present paper, we report for the first time the characterization of llama (Lama glama) caseins at transcriptomic and genetic level. A total of 288 casein clones transcripts were analysed from two lactating llamas. The most represented mRNA populations were those correctly assembled (85.07%) and they encoded for mature proteins of 215, 217, 187 and 162 amino acids respectively for the CSN1S1, CSN2, CSN1S2 and CSN3 genes. The exonic subdivision evidenced a structure made of 21, 9, 17 and 6 exons for the αs1-, β-, αs2- and κ-casein genes respectively. Exon skipping and duplication events were evidenced. Two variants A and B were identified in the αs1-casein gene as result of the alternative out-splicing of the exon 18. An additional exon coding for a novel esapeptide was found to be cryptic in the κ-casein gene, whereas one extra exon was found in the αs2-casein gene by the comparison with the Camelus dromedaries sequence. A total of 28 putative phosphorylated motifs highlighted a complex heterogeneity and a potential variable degree of post-translational modifications. Ninety-six polymorphic sites were found through the comparison of the lama casein cDNAs with the homologous camel sequences, whereas the first description and characterization of the 5'- and 3'-regulatory regions allowed to identify the main putative consensus sequences involved in the casein genes expression, thus opening the way to new investigations -so far- never achieved in this species.

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.

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.

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.

Comparison between Holstein Cow’s Milk and Japanese-Saanen Goat’s Milk in Fatty Acid Composition, Lipid Digestibility and Protein Profile

The fatty acid composition, the lipid digestibility and protein profile of Japanese-Saanen goat's milk were characterized. Caprine milk contained substantial quantities of C(4:0) to C(10:0) fatty acids as compared with Holstein cow's milk. The lipids of the former showed significantly higher digestibility in vitro by porcine lipase than those of the latter (P<0.05). As determined by SDS-PAGE, the respective contents of alpha(s1)-casein, one of the major allergens, were 3.9% and 33.7% in caprine and bovine milk.

Identification of an intronic regulatory mutation at the buffalo αS1-casein gene that triggers the skipping of exon 6

The characterization of casein polymorphism is an essential step in order to understand the genetic basis of milk quality in dairy ruminants. In this work, we report the identification of a regulatory mutation at the buffalo αs1-casein (CSN1S1) gene that alters the normal processing of the primary transcript. Sequencing of CSN1S1 cDNA from individuals harbouring this new variant revealed that its most distinctive feature is the loss of exon 6 that encodes eight amino acids between positions 35-42 of mature protein. In an effort to map the causal mutation, we sequenced a genomic region spanning exons 5-7 of the buffalo CSN1S1 gene. This experiment allowed us to establish that exon 6-skipping is produced by a G to C substitution at the first position of intron 6 that inactivates the donor splice site. This mutation can be typed by PCR-RFLP by using either TaaI or Bpu10I diagnostic restriction enzymes, and it has a frequency of 0.18 in Romanian buffaloes. This exon skipping phenomenon is the first one described in buffalo CSN1S1 locus.

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.

Genetic polymorphism at the CSN1S1 gene in Girgentana dairy goat breed

The aim of this work was to evaluate the variability of the αs1-casein locus in the endangered Girgentana dairy goat breed in order to define genetic improvement and a conservation program for this breed. The study was performed on 200 dairy goats by means of different PCR protocols. The most frequent alleles were A (0.590) and F (0.290) followed by B (0.065) and N (0.047). CSN1S1 E allele was identified with a very low frequency (0.008). The most common genotype was AF (0.365) followed by AA (0.340). The high frequency of the strong genotypes is associated with the production of milk with high fat and protein content and with optimal technological properties. In Girgentana goat breed, the CSN1S1 genotype information could be utilised in selection strategies for milk protein content and milk yield, in order to select genetic lines for the production of ‘drinking milk’ using weak and null genotypes, and for niche products using strong genotypes.

The occurrence of genetic polymorphism and related non-allelic proteins increases the compositional complexity of goat α((s1)) -CN

A genetic survey on three autochthonous goat breeds reared in Italy was carried out by a proteomic approach. This methodology, further to providing the phenotypic frequency of identified α(s1) genetic variants, allowed to determine (i) the additional constitutive presence of a non-allelic 'α(s1) -casein (CN) F like' protein in goat 'strong' α(s1) variants; (ii) an α(s1) -CN B(2) like protein, expressed at very low quantitative level, in goat 'weak' α(s1) -CN variants, and, as main focus; (iii) the occurrence of a new α(s1) -CN D(1) variant characterised by the lack of α(s1) (f59-69) sequence otherwise encoded by exon 9 in goat α(s1) B(2) reference. The same exon skipping event had been identified since 1990, as responsible of the 'weak quantitative class' of α(s1) -CN D variant (0.6 g/L), while the new α(s1) -CN D(1,) has been 'quantitatively' classified as an 'intermediate' variant, since 1.8 g/L per allele was assessed in the milk.

Genetic testing for phenotype-causing variants in sheep and goats

This review gives an overview on ovine and caprine defects/disorders, disease predispositions, production traits and coat colours for which causal gene variants are known. Most phenotypes are inherited autosomal-recessive or dominant and in the majority are caused by single nucleotide substitutions or deletions. Causative sequence variants mainly were identified by sequencing candidate genes in the past, and recently also by whole genome analysis using the ovine 50k SNP chip. While PCR-fragment length polymorphism analyses were developed for the majority of causative sequence variants, other low- to medium-throughput PCR-based methods as PCR-single strand conformation analysis and allele-specific PCR were also established frequently. For processing large sample numbers, high-throughput methods as MALDI-ToF MS or real-time PCR are available for some gene variants. Further progress in development of ovine and caprine genome sequences and SNP chips will be beneficial for the discovery of additional causative variants in these two species.

Evolution of major milk proteins in Mus musculus and Mus spretus mouse species: a genoproteomic analysis

Background

Due to their high level of genotypic and phenotypic variability, Mus spretus strains were introduced in laboratories to investigate the genetic determinism of complex phenotypes including quantitative trait loci. Mus spretus diverged from Mus musculus around 2.5 million years ago and exhibits on average a single nucleotide polymorphism (SNP) in every 100 base pairs when compared with any of the classical laboratory strains. A genoproteomic approach was used to assess polymorphism of the major milk proteins between SEG/Pas and C57BL/6J, two inbred strains of mice representative of Mus spretus and Mus musculus species, respectively.

Results

The milk protein concentration was dramatically reduced in the SEG/Pas strain by comparison with the C57BL/6J strain (34 ± 9 g/L vs. 125 ± 12 g/L, respectively). Nine major proteins were identified in both milks using RP-HPLC, bi-dimensional electrophoresis and MALDI-Tof mass spectrometry. Two caseins (β and α_s1) and the whey acidic protein (WAP), showed distinct chromatographic and electrophoresis behaviours. These differences were partly explained by the occurrence of amino acid substitutions and splicing variants revealed by cDNA sequencing. A total of 34 SNPs were identified in the coding and 3'untranslated regions of the SEG/Pas Csn1s1 (11), Csn2 (7) and Wap (8) genes. In addition, a 3 nucleotide deletion leading to the loss of a serine residue at position 93 was found in the SEG/Pas Wap gene.

Conclusion

SNP frequencies found in three milk protein-encoding genes between Mus spretus and Mus musculus is twice the values previously reported at the whole genome level. However, the protein structure and post-translational modifications seem not to be affected by SNPs characterized in our study. Splicing mechanisms (cryptic splice site usage, exon skipping, error-prone junction sequence), already identified in casein genes from other species, likely explain the existence of multiple α_s1-casein isoforms both in SEG/Pas and C57BL/6J strains. Finally, we propose a possible mechanism by which the hallmark tandem duplication of a 18-nt exon (14 copies) may have occurred in the mouse genome.

The CSN1S1 N and F alleles identified by PCR-SSCP and their associations with milk yield and composition in Chinese dairy goats

A method was depicted to identify null allele CSN1S1 N and low allele CSN1S1 F of the CSN1S1 gene of goat using PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism). First, primer A was designed to amplify the exon 9 of CSN1S1 gene which produced three genotypes AA, AB, and BB. Among these three genotypes, only AA and AB individuals had a cytosine deletion at exon 9 after DNA sequencing, which cannot be used to identify the N and F alleles. Therefore, primer B was used to amplify intron 14 of CSN1S1 of described AA and AB individuals. Genotypes FF, FN and NN were detected within AA individuals and genotypes FO and NO were detected in the above AB individuals. The frequencies of F and N alleles in 708 samples from Xinong Saanen (XS) and Guanzhong (GZ) dairy goat breeds were 0.1139, 0.0927, and 0.2376, 0.1193, respectively. In 268 XS samples, the individuals with NN genotype contained a significant lower protein content than that of other genotypes (P<0.01). Individuals of FF genotype had significant higher milk yield than that of NO genotype in the first milk lactation of 202 XS individuals (P<0.05). Therefore, the variability at CSN1S1 locus contains enough genetic diversity to be potentially useful in improving the quality and production of milk in Chinese dairy goat breeds.

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.

Short communication: molecular genetic characterization of ovine alpha(S1)-casein allele H caused by alternative splicing

Sequencing of ovine CSN1S1*H cDNA showed an absence of exon 8 in comparison with GenBank sequences; the absence was confirmed by protein sequencing. We demonstrated that this allelic aberration is the result of a deletion of 4 nucleotides, the last 3 of exon 8 and the first 1 of intron 8, which are replaced by an insertion of 13 nucleotides in the DNA sequence. The insertion is a precise duplication of a part of the adjacent intronic sequence of CSN1S1*C''. These sequence differences result in an inactivation of the splice donor sequence distal to exon 8, leading to upstream exon skipping during the serial splice reactions of the ovine CSN1S1*H pre-mRNA, and may affect the specific casein expression as well as protein characteristics.

Prevalence of alphas1-casein genotypes in American dairy goats

Widespread genotyping of US dairy goat breeds for casein variants has not been reported, even though the genetic data could be of use in selective breeding programs. For instance, variability in the content of protein and solids in goat milk is attributed to allelic differences in the goat alpha(s1)-casein gene. Concentrations of alpha(s1)-casein in goat milk are positively correlated with milk components and coagulation properties. The alleles A and B are designated as strong alleles, resulting in the greatest amount of alpha(s1)-casein in goat milk, whereas the E allele produces intermediate amounts and the weak allele F produces the least concentrations of alpha(s1)-casein in goat milk. Here we report on one of the first surveys of the distribution of alpha(s1)-casein genotypes in US dairy goats. The population surveyed, consisting of a total of 257 American dairy goats representing 7 main dairy breeds, contained a greater predominance of the weaker alleles, E and F, than the strong alleles, A and B. Allele distribution was related to breed, with Toggenburg, Alpine, Saanen, and Oberhasli containing the most E and F alleles and LaMancha, Nubian, and Nigerian Dwarf the fewest. Quantification of alpha(s1)-casein production by 2-dimensional gel electrophoresis demonstrated that F/F animals had the least amount of alpha(s1)-casein protein in their milk compared with all other genotypes. The results indicate that genetic improvement of dairy goats in the United States could be achieved if an alpha(s1)-casein breeding scheme were adopted.

Diet selection and milk production and composition in Girgentana goats with different alpha s1-casein genotype

In goats, alpha s1-casein polymorphism is related to different rates of protein synthesis. Two genetic variants, A and F, have been identified as strong and weak alleles based on a production of 3.5 and 0.45 g/l of alpha s1-casein per allele. The aim of the trial was to test whether goats can select their diet as a function of their genetic aptitude to produce milk at different casein levels and whether this selection can influence milk production or composition. Two groups of 8 animals, homozygous for strong (AA) or weak (FF) alleles were housed in individual pens. Using a manger subdivided into five separate containers, the goats were offered daily for 3 weeks: 1.5 kg of alfalfa pelleted hay, 0.7 kg of whole barley, 0.7 kg of whole maize, 0.7 kg of whole faba bean and 0.7 kg of pelleted sunflower cake. Total dry matter intake was similar between groups and resulted in nutrient inputs much higher than requirements. On average, goats selected 86% of maize plus barley and only 46% of faba bean plus sunflower. Indeed, AA goats selected less faba bean compared with FF goats (37.2 v. 56.7% of the available amount; P=0.01); during week 2 and week 3 they significantly increased maize selection (respectively for week 2 and week 3: 94.9 and 99.1% v. 85.3 and 87.3%) thus increasing the ratio between the high-energy feeds and the high-protein feeds (2.41 v. 1.81, P=0.023). As for true protein, the high soluble fraction (B1) and the indigestible fraction (C) were lower in the diet selected by AA goats (respectively in AA and FF groups: B1, 7.85 v. 9.23% CP, P<0.01; C, 6.07 v. 6.30% CP, P<0.001); these diet characteristics can be associated with lower losses of protein. Milk production, being similar in AA and FF groups when goats were fed with a mixed diet, significantly increased in AA group, when free-choice feeding was given (mean productions: 1198 v. 800 g/d, P<0.01). Casein content was higher in AA group than in FF group (2.70 v. 2.40%, P<0.01) whereas milk urea was higher in FF group (59.7 v. 48.8 mg/dl, P<0.01). In conclusion, when the animals were free to select their diet, their higher genetic aptitude to produce casein seemed to adjust their energy and protein dietary input in qualitative terms, thus leading to an increase in milk production and a decrease in milk urea. These results seem to demonstrate that interactions probably occurred between genetic polymorphism at the alpha s1-casein locus, diet selection and the efficiency of nutrient transformation into milk.

Focusing on casein gene cluster and protein profile in Garganica goat milk

A survey was carried out in eight goat dairy farms, a total of 71 individual Garganica goat milk samples were collected for genomic DNA extraction. Casein alleles and haplotype frequencies of Garganica population were estimated. Individual milks were also analysed for chemical composition, rheological properties, and protein profile. The strong A* allele of CSN1S1 was predominant in the population investigated, the weak allele F of CSN1S1 showed a relatively high frequency and the null alleles N and 01 were first observed in this breed. At CSN1S2 locus the strong A* allele was the most frequent, followed by the F allele and the null allele. The strong A* allele was predominant at CSN2 locus, and relatively high incidence of null allele 0 was observed. CSN3 locus was monomorphic for B* allele. The exact test of sample differentiation based on haplotype frequencies discriminate the farms into two groups characterized by the highest frequency of strong (S-CSN1S1) or weak (W-CSN1S1) alleles at CSN1S1. Protein and casein contents were higher in the group characterized by strong allele than in the group with weak allele at CSN1S1. The 2D electrophoresis technique was performed to screen goat casein variability at the protein level and to evaluate global casein genotype (alphas1, alphas2, beta and kappa-CN). Gels displayed the protein profile associated with casein genotype, and demonstrated differences in the protein expression deriving from interactions between loci. The variability of goat casein loci in Garganica goat breed could be exploited to differentiate the population on the basis of milk utilization and could represent a strategy to preserve the genotype of this autochthonous breed.

Effect of alphas1-casein ( CSN1S1) genotype on milk CSN1S1 content in Malagueña and Murciano-Granadina goats

There is substantial evidence showing that the polymorphism of the goat alphas1-casein (CSN1S1) gene has a major effect on milk protein, casein and fat content as well as on cheese yield. However, its influence on the synthesis rate of CSN1S1 has been less studied, with measurements only available in French breeds. In this article, we have measured milk CSN1S1 content in 89 Malagueña and 138 Murciano-Granadina goats with 305 and 460 phenotypic registers, respectively. In the Malagueña breed, average values of CSN1S1 content estimated for BB, BF, EE and FF genotypes were 6.94+/-0.38, 5.36+/-0.22, 4.58+/-0.13 and 3.98+/-0.27 g/l, respectively, being all significantly different (P<0.05). Conversely, in the Murciano-Granadina breed only the BB genotype (8.50+/-0.60 g/l) was significantly associated with increased levels of CSN1S1 (P<0.05), whereas BF (6.56+/-0.82 g/l), EE (6.39+/-0.60 g/l) and EF (6.91+/-0.76 g/l) genotypes displayed non-significant differences when compared with each other. Our results highlight the existence of breed-specific genetic and/or environmental factors modulating the impact of the CSN1S1 gene polymorphism on the synthesis rate of the corresponding protein.

A critical analysis of production-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig

Increasing productivity is one of the main objectives in animal production. Traditional breeding methods have led to increased gains in some traits but gains are not easily attainable in traits with low heritabilities. Exploiting the genetic variations underlying desired phenotypes is the goal of today's animal producers. Such positive genetic variants must, however, be known before possible application. Consequently, candidate genes of traits of interest have been searched for possible relationships with such traits or to explain reported quantitative trait loci (QTL) for such traits. DNA variants or polymorphisms have been identified in many such genes and their relationships with production traits determined. However, only a few genes have been evaluated, given the wealth of information on reported QTL for production traits, and in most cases genes are only partially investigated. This review presents available information on DNA variants for production traits and discusses steps that are required for effective utilization of this information for successful marker-assisted selection programs.

The primary structure of a low-Mr multiphosphorylated variant ofβ-casein in equine milk

Highly phosphorylated casein with a low molecular mass was isolated from Haflinger mare's milk by RP-HPLC. It accounts for 4.0% of the casein content. Its mass was determined by LC-ESI-MS before and after treatment by alkaline phosphatase. The molecular mass found for the apo-form (10,591 +/- 2 Da) is in agreement with its primary structure, which was established by ESI-MS/MS from tryptic peptides. It appeared that this short protein (94 amino acid residues) is an internally truncated form of the full-length equine beta-casein (226 residues). This low-Mr variant of equine beta-casein displays a large deletion (residues 50-181), due to a cryptic splice site usage occurring within exon 7 during the course of primary transcripts processing. The phosphorylation pattern of this equine beta-casein variant was investigated by LC-ESI-MS and 2-DE. Seven phosphorylation forms were identified with one to seven phosphate groups with pIs ranging between 4.67 and 4.01. The major isoforms carry five and six phosphate groups.

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.

Comparative analysis of gene sequence of goat CSN1S1 F and N alleles and characterization of CSN1S1 transcript variants in mammary gland

In this paper, we report the full characterization, at DNA and RNA level, of the defective goat CSN1S1 F and N alleles and an extensive comparison with the A allele counterpart. By utilizing genomic DNA as template, we amplified the whole CSN1S1 gene plus 1972/3 nucleotides of the 5' region plus 610 nucleotides of the 3' region of the goat CSN1S1 N and CSN1S1 F alleles. Comparison of sequences of the N, F and A CSN1S1 alleles showed a total of 118 polymorphic sites. In particular, both the N and the F alleles are characterized by a deletion of the cytosine at the 23rd nucleotide of the 9th exon. The resulting one-nucleotide frameshift determines a premature stop codon (TGA, nucleotides 17-19 of the 12th exon). On the basis of the information so far available, it seems reasonable to hypothesize that the CSN1S1 N allele might be originated by interallelic recombination events. Comparison of transcripts produced by the N and F alleles shows a remarkable variability in alternative splicing events which concern, even though with different percentage ratios, mainly the lack of the 9th exon, the deletion of the last 5 nucleotides of the 9th exon and the contemporary deletion of exons 10 and 11.

The goat alphas1-casein gene: gene structure and promoter analysis

The level of alphas1-casein in goat milk shows strong variations determined by at least 15 alleles associated with four different efficiencies of protein synthesis. The nucleotide sequence of the whole goat alphas1-casein-encoding gene (CSN1S1) plus 1973 nucleotides at the 5' flanking region and 610 nucleotides at the 3' flanking region was determined and aligned with its bovine counterpart. The gene is spread over 16.7 kb and consists of 19 exons varying in length from 24 bp (exons 5, 6, 7, 8, 10, 13 and 16) to 385 bp (exon 19) and 18 introns from 90 bp of intron 10 to 1685 bp of intron 2. Furthermore, highly conserved sequences, mainly located in the 5' flanking region, were found between this gene and other casein-encoding genes. Finally, seven interspersed repeated elements (10 in the bovine CSN1S1 gene) were also identified at four different locations of the sequenced region: 5' untranscribed region and introns 2, 8 and 11.