Restriction fragment length polymorphism analysis of the kappa-casein locus in cattle

Effect of Protein Genotypes on Physicochemical Properties and Protein Functionality of Bovine Milk: A Review

Milk protein comprises caseins (CNs) and whey proteins, each of which has different genetic variants. Several studies have reported the frequencies of these genetic variants and the effects of variants on milk physicochemical properties and functionality. For example, the C variant and the BC haplotype of αS1-casein (αS1-CN), β-casein (β-CN) B and A1 variants, and κ-casein (κ-CN) B variant, are favourable for rennet coagulation, as well as the B variant of β-lactoglobulin (β-lg). κ-CN is reported to be the only protein influencing acid gel formation, with the AA variant contributing to a firmer acid curd. For heat stability, κ-CN B variant improves the heat resistance of milk at natural pH, and the order of heat stability between phenotypes is BB > AB > AA. The A2 variant of β-CN is more efficient in emulsion formation, but the emulsion stability is lower than the A1 and B variants. Foaming properties of milk with β-lg variant B are better than A, but the differences between β-CN A1 and A2 variants are controversial. Genetic variants of milk proteins also influence milk yield, composition, quality and processability; thus, study of such relationships offers guidance for the selection of targeted genetic variants.

Allele and Genotype Frequencies of the Κappa-Casein (CSN3) Locus in Macedonian Holstein-Friesian Cattle

The bovine kappa-casein (κ-CN) is a phospho-protein with 169 amino acids encoded by the CSN3 gene. The two most common gene variants in the HF breed are CSN3*A and CSN3*B while CSN3*E has been found with lower frequency. The aim of this study was to optimize a laboratory method for genotyping of these three alleles as well as to determine their genotype and allele frequencies in the HF cattle population in the Republic of North Macedonia. Genomic DNA was extracted from full blood from 250 cows. The target DNA sequence was amplified with newly designed pair of primers and the products were subjected to enzymatic restriction with HindIII and HaeIII endonucleases. Genotype determination was achieved in all animals. The primers successfully amplified a fragment of 458 bp and the digestion of this fragment with both endonucleases enabled differentiation of five different genotypes with the following observed frequencies: AA (0.39), AB (0.29), BB (0.16), AE (0.10), and BE (0.06). The estimated allele frequencies were: CSN3*A (0.584), CSN3*B (0.336) and CSN3*E (0.08). The observed genotype frequencies differed significantly (P<0.01) from those that would be expected under HW equilibrium, while the fixation index (F=0.17) indicated moderate heterozygosity deficiency. Nevertheless, the CSN3*B allele was present with relatively high frequency which should be used to positively select for its carriers, since increasing its frequency could help to improve the rheological properties of the milk intended for cheese production.

Invited review: milk protein polymorphisms in cattle: effect on animal breeding and human nutrition

The 6 main milk proteins in cattle are encoded by highly polymorphic genes characterized by several nonsynonymous and synonymous mutations, with up to 47 protein variants identified. Such an extensive variation was used for linkage analysis with the description of the casein cluster more than 30 yr ago and has been applied to animal breeding for several years. Casein haplotype effects on productive traits have been investigated considering information on the whole casein complex. Moreover, mutations within the noncoding sequences have been shown to affect the specific protein expression and, as a consequence, milk composition and cheesemaking. Milk protein variants are also a useful tool for breed characterization, diversity, and phylogenetic studies. In addition, they are involved in various aspects of human nutrition. First, the occurrence of alleles associated with a reduced content of different caseins might be exploited for the production of milk with particular nutritional qualities; that is, hypoallergenic milk. On the other hand, the frequency of these alleles can be decreased by selection of sires using simple DNA tests, thereby increasing the casein content in milk used for cheesemaking. Furthermore, the biological activity of peptides released from milk protein digestion can be affected by amino acid exchanges or deletions resulting from gene mutations. Finally, the gene-culture coevolution between cattle milk protein genes and human lactase genes, which has been recently highlighted, is impressive proof of the nonrandom occurrence of milk protein genetic variation over the centuries.

Genotyping of bovine kappa-casein (kappa-CNA, kappa-CNB, kappa-CNC, kappa-CNE) following DNA sequence amplification and direct sequencing of kappa-CNE PCR product

Genomic DNA isolated from blood and semen of dairy cattle with known kappa-casein (kappa-CN) genotypes was subjected to Southern blot hybridization and polymerase chain reaction (PCR) using up to 14 restriction endonucleases. kappa-casein genotypes AA, AB and BB were identified using Hin dIII and Hin fI while genotypes with kappa-CNC and kappa-CNE were misidentified. Direct sequencing of the PCR product (kappa-CN EE) showed a substitution of guanine (kappa-CNA,B) by adenine (kappa-CNE) which creates a HaeIII restriction site. Therefore using PCR followed by Hin dIII or HinfI and Hae III digest allows discrimination between kappa-casein A, B and E directly at the DNA level.

SSCP analysis at the bovine CSN3 locus discriminates six alleles corresponding to known protein variants (A, B, C, E, F, G) and three new DNA polymorphisms (H, I, A1)

A high resolution SSCP protocol was developed for simultaneous discrimination of the known CSN3 alleles A, B, C, E, F and G. Furthermore, three new DNA polymorphisms were identified in different Bos taurus and Bos indicus breeds or crosses. Mendelian segregation was shown for two of these polymorphisms (named CSN3*H and 1), and the third (named CSN3*A1) was found in unrelated animals, thus indicating the presence of three additional alleles at the bovine CSN3 locus. DNA sequencing revealed single mutations that led to a Thr/Ile substitution in amino acid position 135 for CSN3*H and to a Ser/Ala substitution in position 104 of the deduced amino acid sequence of CSN3*1 (GenBank accession numbers AF105260 and AF121023) compared to CSN3*A. In CSN3*A1, a silent mutation in the third codon position of Pro150 was found (GenBank accession number AF092513).

Kappa-casein polymorphisms in Indian dairy cattle and buffalo: a new genetic variant in buffalo

We screened 57 Sahiwal cattle (Bos indicus) and 53 Murrah, 19 Nili-Ravi and 11 Egyptian buffaloes (Bubalus bubalis) to detect the polymorphisms at kappa-casein (CSN3) gene using the polymerase chain reaction (PCR). CSN3 A and B alleles were identified by PCR-RFLP using the restriction enzymes that detect the underlying nucleotide changes at codon 136 (Taql) and at codon 148 (HindIII or HinfI) in cattle. The frequency of CSN3 B allele in the Sahiwal cattle was estimated as 0.16 with no homozygous BB animal. Using the same set of primers as used in the Sahiwal cattle, a part of exon IV of buffalo CSN3 gene was amplified, but restriction enzyme analysis using HindIII/HinfI and TaqI did not reveal any polymorphism. However, DNA sequencing of the amplified fragment (GenBank Acc. No. U96662) revealed one polymorphism at codon 135 (ThrACC -->I1eATC) in buffalo; the frequencies of 135 Thr/Ile alleles were estimated as 0.88 and 0.12, respectively.

Molecular genetics as a diagnostic tool in farm animals

In this review, the importance of molecular genetics for diagnostic applications in animal production and breeding is underlined. Recently, several new techniques and methods based on gene technology have been developed, such as the polymerase chain reaction, fluorescence in situ hybridization, and the use of microsatellite polymorphism. The examples include detection of favourable alleles of genes coding for milk proteins, recognition of negative recessive alleles in hereditary syndromes, the use of microsatellite variants for breeding purposes and parentage control, and application of specific DNA-probes for identification of Y-chromosome-bearing spermatozoa and the sex of embryos. It is to be understood that this list is not complete and more applications will undoubtedly show up in the future. For this review, the authors have mainly selected areas where they themselves or their co-workers have gained experience.

Structure of the rabbit kappa-casein encoding gene: expression of the cloned gene in the mammary gland of transgenic mice

The rabbit kappa-casein (kappa-Cas) encoding gene has been isolated as a series of overlapping DNA fragments cloned from a rabbit genomic library constructed in bacteriophage lambda EMBL3. The clones harboured the 7.5-kb gene flanked by about 2.1 kb upstream and 9 kb downstream sequences. The cloned gene is the most frequently occurring of two kappa-Cas alleles identified in New Zealand rabbits. Comparison of the corresponding domains in rabbit and bovine kappa-Cas shows that both genes comprise 5 exons and that the exon/intron boundary positions are conserved whereas the introns have diverged considerably. The first three introns are shorter in the rabbit, the second intron showing the greatest difference between the two species: 1.35 kb instead of 5.8 kb in the bovine gene. Repetitive sequence motives reminiscent of the rabbit C type repeat and the complementary inverted C type repeat were identified in the fourth and first introns, respectively. Transgenic mice were produced by microinjecting into mouse oocytes an isolated genomic DNA fragment which contained the entire kappa-Cas coding region, together with 2.1-kb 5' and 4.0-kb 3' flanking region. Expression of transgene rabbit kappa-Cas mRNA could be detected in the mammary gland of lactating transgenic mice and the production of rabbit kappa-Cas was detected in milk using species-specific antibodies. The cloned gene is thus functional.

A microsatellite within the bovine kappa-casein gene reveals a polymorphism correlating strongly with polymorphisms previously described at the protein as well as the DNA level

The polymorphism of a (TA)n(CA)n repeat microsatellite present in the third intron of the bovine kappa-casein gene (CASK) has been investigated. The existence of six alleles differing only in the number of dinucleotide repeats has been established. A total of 330 animals belonging to nine different pure bred Bos taurus French breeds or to a cross-bred Bos taurus x Bos indicus population (Créole) were genotyped. The distribution of the microsatellite alleles was examined and clear breed differences were noted. Genotyping of animals by isoelectric focusing (IEF) or restriction fragment length polymorphism (RFLP) (TaqI) was performed, in order to examine the relationship of the microsatellite polymorphism to other previously described CASK polymorphisms, at the protein and DNA levels. Strong correlation was seen, indicating that evolution of the various polymorphisms was not independent, and nine CASK haplotypes were observed.

Kappa-casein polymorphisms among cattle breeds and bison herds

We identified the HindIII restriction site polymorphism of kappa-casein in cattle reported by Pinder et al. (Animal Genetics 22, 11, 1991) and found an additional polymorphism (RsaI) in cattle and bison. The HindIII and RsaI restriction sites were mapped and three haplotypes (alleles) were identified. Preliminary screening of 39 cattle and 71 bison revealed one allele restricted to cattle, one restricted to bison, and one shared by the species. No fixed allelic differences were observed among cattle breeds or among bison herds or subspecies.

Chromosome substitution effects associated with kappa-casein and beta-lactoglobulin in Holstein cattle

Allelic variants of kappa-casein and beta-lactoglobulin were used to estimate chromosome substitution effects on transmitting abilities for yield traits among sons of two Holstein sires. Sire 1 was a heterozygote for both loci, whereas sire 2 was a heterozygote for beta-lactoglobulin only. Transmitting abilities for fat percentage and the exchange of protein and fat (protein yield minus fat yield) were influenced by kappa-casein genotype among offspring of sire 1. The B allele of kappa-casein was associated with a decrease in fat percentage, whereas fat yield was not affected; the result was 4.5 kg more transmitting ability for protein than for fat. Favorable chromosome substitution effects on transmitting abilities for fat percentage, protein yield, and the exchange of protein and fat were also observed for the A allele of beta-lactoglobulin among offspring of sire 1; there were consistent but not significant estimates for sire 2. These results suggest that different estimates could be obtained from offspring of different parents, perhaps from linkage disequilibrium between families. The chromosome substitution effects appeared to be in the direction opposite to the average correlation of milk fat and protein content; marker-assisted selection for increased yield of protein would result in decreased fat yield.

Long range restriction analysis of the bovine casein genes

Pulsed field gel electrophoresis (PFGE) was used to analyse the organization of the bovine alpha s1, alpha s2, beta and kappa casein genes. High molecular weight DNA was prepared from fibroblasts and lymphocytes embedded in agarose and was digested with the restriction endonucleases Clal, Sall, Smal, Xhol. The digestion products were separated by PFGE, transfered to nitrocellulose filters and hybridized to probes corresponding to the cDNAs of the four bovine casein genes. The casein genes were demonstrated to be physically linked within a region of 300 kb, represented by two adjacent Xhol fragments in fibroblasts and by a single fragment in lymphocytes. A restriction map of the casein locus was derived and the order of the genes was shown to be kappa, alpha s2, beta, alpha s1.