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Milk protein genes are associated with milk yield and composition in dairy animals. The present study aimed to identify milk protein genes (CSN1S1, CSN2, CSN3, and BLG) genetic variants and their association with milk yield in Sahiwal cattle and Nili-Ravi buffaloes. One hundred animals from each species were selected to collect blood samples and milk production records. Primers were designed for these milk protein genes for PCR amplification. Sequencing of resultant PCR products revealed a higher number of SNPs (13 vs. 7, 5 vs. 1, and 6 vs. 2) in Sahiwal as compared to Nili-Ravi animals in CSN1S1, CSN2, and CSN3 genes, respectively. However, a single SNP was observed in BLG gene of both species. Association analysis revealed that one SNP in BLG gene of Nili-Ravi was associated (p < 0.05) with 305-day milk yield. Two SNPs at CSN1S1 gene in Sahiwal were associated with dry-period. Similarly, one SNP at CSN1S1 and two SNPs at CSN3 gene showed significant association (p < 0.05) with average calving-interval in Sahiwal while two SNPs in CSN1S1 gene were associated (p < 0.05) with this trait in Nili-Ravi. These SNPs could be helpful as candidate variants for marker-assisted selection in cattle and buffaloes for improvement of lactation performance.

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Milk is a primary protein source that has always played a role in mammalian health. Despite the intensification of research projects on dromedary and the knowledge of the genetic diversity at the casein loci, the genetic structure of the Tunisian camel population still needs exploration. This study sought to determine the genetic diversity of 3 casein gene variants in 5 Tunisian camel ecotypes: c.150G>T at CSN1S1 (αS1-casein), g.2126A>G at CSN2 (ß-casein), and g.1029T>C at CSN3 (κ-casein). The obtained results were compared with data published on Sudanese and Nigerian camels to establish the level of differentiation within and between populations. A total of 159 blood samples were collected from 5 Tunisian camel ecotypes and the extracted DNA was genotyped by PCR-RFLP. A streamlined genotyping protocol was also developed for CSN3. Results indicated that allele T was quite rare (0.06) at CSN1S1 for all ecotypes. Minor allele frequency was found for G (0.462) in CSN2 except for Ardhaoui Medenine ecotype who deviated from the average CSN2 allele frequency of the total population. Allele C showed minor allele frequency of 0.384 in CSN3. Among the Tunisian population, GAT (0.343) was the most represented haplotype in all ecotypes except for Ardhaoui Medenine, where GGC (0.322) was the most frequent one. Significant differences in heterozygosity and local inbreeding were observed across the Tunisian, Sudanese, and Nigerian populations, although the global fixation index indicated that only 2.2% of the genetic variance is related to ecotype differences. Instead, phylogenetic analysis revealed a closer link between the Tunisian and Sudanese populations through a clade subdivision with 3 main branches among the ecotypes. This study represents the first attempt to understand casein gene variability in Tunisian camels; with further study, milk traits and genetic differentiation among populations can be associated with the history of camel domestication.

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We aimed to determine whether casein variants that are currently segregating in ovine populations existed before the domestication of sheep or, to the contrary, if their emergence is much more recent. To this end, we have retrieved whole-genome sequences from Iranian and domestic sheep from Africa, Europe, South and East Asia and West Asia. Population structure analysis based on 55,352,935 SNPs revealed a clear separation between Iranian mouflons and domestic sheep. Moreover, we also observed a strong genetic differentiation between Iranian mouflons sampled in geographic areas close to Tehran and Tabriz. Based on sequence data, hundreds of SNPs mapping to the casein αS1 (CSN1S1, 248 SNPs), casein αS2 (CSN1S2, 268 SNPs), casein ß (CSN2, 146 SNPs) and casein κ (CSN3, 112 SNPs) genes were identified. Approximately 25-63.02% of the casein variation was shared between Iranian mouflons and domestic sheep, and the four domestic sheep populations also shared 44.2-57.4% of the casein polymorphic sites. These findings suggest that an important fraction of the casein variation present in domestic sheep was already segregating in the mouflon prior to its domestication. Genomic studies performed in horses and dogs are consistent with this view, suggesting that much of the diversity that we currently detect in domestic animals comes from standing variation already segregating in their wild ancestors.

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BACKGROUND: In this study, we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats. To achieve these two goals, we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points, i.e. 78 d (T1, early lactation), 216 d (T2, late lactation) and 285 d (T3, dry period) after parturition. Moreover, we have performed a genome-wide association study (GWAS) for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats. RESULTS: The expression profiles of the mammary gland in the early (T1) and late (T2) lactation were quite similar (42 differentially expressed genes), while strong transcriptomic differences (more than one thousand differentially expressed genes) were observed between the lactating (T1/T2) and non-lactating (T3) mammary glands. A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids, cholesterol, triglycerides and steroids as well as with glycerophospholipid metabolism, adipocytokine signaling, lipid binding, regulation of ion transmembrane transport, calcium ion binding, metalloendopeptidase activity and complement and coagulation cascades. With regard to the second goal of the study, the performance of the GWAS allowed us to detect 24 quantitative trait loci (QTLs), including three genome-wide significant associations: QTL1 (chromosome 2, 130.72-131.01 Mb) for lactose percentage, QTL6 (chromosome 6, 78.90-93.48 Mb) for protein percentage and QTL17 (chromosome 17, 11.20 Mb) for both protein and dry matter percentages. Interestingly, QTL6 shows positional coincidence with the casein genes, which encode 80% of milk proteins. CONCLUSIONS: The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein, lipid and carbohydrate metabolism, calcium homeostasis, cell death and tissue remodeling, as well as immunity. We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.

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This research paper addresses the hypothesis that comparative genomics can give a new insight into the functionality of casein genes with respect to the casein micelle. Comparative genomics is a rapidly emerging field in computational biology whereby two or more genomes are compared in order to obtain a global view on genomes as well as assigning previously unknown functions for genes. Casein genes are among the most rapidly evolving mammalian genes, with the gene products mainly grouped into four types (αs1-, αs2-, ß- and κ-casein). Functionally, casein genes are central to the casein micelle, the exact structure of which is still a subject of intense debate. Moreover, and adding to this complexity, some mammals lack some of the casein genes, although casein micelles have been observed in their milk. This observation has prompted an investigation into the distribution of casein genes across a host of mammalian species. It was apparent from this study that casein gene sequences are very diverse from each other and we confirmed that many mammalian species lack one or more of the casein genes. The genes encoding ß- and κ-caseins are present in most mammals whereas α-casein encoding genes are less represented. This suggests different mechanisms for casein micelle formation in different species as well as the functions that are assigned to each individual casein.

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Genes encoding casein proteins are important candidates for milk composition traits in mammals. In the case of the domestic horse, our knowledge of casein genes is limited mainly to coding sequence variants. This study involved screening for polymorphism in 5'-flanking regions of four genes encoding equine caseins (CSN1S1, CSN1S2, CSN2, and CSN3) and making a preliminary assessment of their effect on the gene expression (on the mRNA and protein levels) and milk composition traits in selected horse breeds. Altogether, 23 polymorphisms (21 described previously SNPs and two novel InDels) were found in the studied sequences, the majority of which are common in various horse breeds. Statistical analysis revealed that some are putatively associated with gene expression or milk composition - for example, the c.-2047_-2048insAT polymorphism (CSN1S1) turns out to be related to the total milk protein content in Polish Primitive Horse (p < 0.05), whereas c.-2105C>G SNP (CSN2) is related to beta-casein relative mRNA level and milk lactose concentration in the Polish Coldblood Horse breed (p < 0.05). We have also found significant effects of horse breed and lactation time-point on gene expression and mare's milk composition. Our study indicates that the 5'-regulatory regions of genes encoding casein proteins are interesting targets for functional studies of their expression and the composition traits of mare's milk.

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For several decades, the regulation of casein gene expression by the lactogenic hormones, prolactin and glucocorticoids, has provided an excellent model system in which to study how steroid and peptide hormones regulate gene expression. Early studies of casein gene regulation defined conserved sequence elements in the 5' flanking region of these genes, including one of which was identified as a γ-interferon activation sequence (GAS). Although this site was thought to interact with a mammary gland-specific factor, purification and cloning of this factor by Bernd Groner and his colleagues revealed it was instead a new member of the signal transducers and activators of transcription family, Stat5, which was expressed in many tissues. The exquisite tissue-specific expression of the casein genes was subsequently shown to depend not on a single transcription factor but on composite response elements that interacted with a number of ubiquitous transcription factors in response to the combinatorial effects of peptide and steroid hormone signaling. More recent studies have defined cooperative effects of prolactin and glucocorticoids as well as antagonistic effects of progesterone on the chromatin structure of both the casein gene proximal promoter region as well as a distal enhancer. Local chromatin modifications as well as long-range interactions facilitated by DNA looping are required for the hormonal regulation of ß-casein gene expression. The casein genes are part of a large gene cluster, and the chromatin landscape of the entire cluster is regulated in a tissue-specific and developmental manner. Finally, newly discovered large non coding RNAs, such as the pregnancy-induced non coding RNA (PINC) may play an important role in the epigenetic regulation of mammary gland differentiation.