Milk protein variants are highly associated with milk performance traits in East Friesian Dairy and Lacaune sheep

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.

Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants

The RNA-Seq data provides new opportunities for the detection of transcriptome variants' single nucleotide polymorphisms (SNPs) in various species and tissues. Herein, milk samples from two sheep breeds and two cow breeds were utilized to characterize the genetic variation in the coding regions in three stages (before-peak (BP), peak (P), and after-peak (AP)) of the lactation process. In sheep breeds Assaf and Churra, 100,462 and 97,768, 65,996 and 62,161, and 78,656 and 39,245 variants were observed for BP, P, and AP lactation stages, respectively. The number of specific variants was 59,798 and 76,419, 11,483 and 49,210, and 104,033 and 320,817 in cow breeds Jersy and Kashmiri, respectively, for BP, P, and AP stages. Via the transcriptome analysis of variation in regions containing QTL for fat, protein percentages, and milk yield, we detected a number of pathways and genes harboring mutations that could influence milk production attributes. Many SNPs detected here can be regarded as appropriate markers for custom SNP arrays or genotyping platforms to conduct association analyses among commercial populations. The results of this study offer new insights into milk production genetic mechanisms in cow and sheep breeds, which can contribute to designing suitable breeding systems for optimal milk production.

Comparative Analysis of the Polymorphism of the Casein Genes in Camels Bred in Kazakhstan

Caseins play an important role in determining the technological properties and quantitative characteristics of camel milk. To date, only a few studies on the genetic polymorphism of casein genes have been reported in the camel populations of Kazakhstan. Therefore, this work aimed to identify the genetic polymorphism level of casein genes among camel populations of the Almaty region of Kazakhstan. The PCR-RFLP method was used for this purpose and the following genotypes were revealed as a result: CSN3 gene—CC, CT, TT, where the T allele predominated in all populations, with a frequency of 0.60; CSN2 gene—AA, AG, GG, with the predomination of A allele (0.64); and CSN1S1 gene—GG and GT, with the predomination of G allele (0.94). Statistical analysis was carried out using the POPGENE and GenAlEx software. The χ2 values were equal to 12.1 (CSN3), 8.6 (CSN2), and 14.5 (CSN1S1). As a result, three out of 53 animals were designated as the “core” of the population—animals with the desired genotypes: CC genotype for the CSN3 gene and AA genotype for the CSN2 gene. Such animals can be selected for further use with an increase in the number of livestock with high productivity rates.

Challenging Sustainable and Innovative Technologies in Cheese Production: A Review

It is well known that cheese yield and quality are affected by animal genetics, milk quality (chemical, physical, and microbiological), production technology, and the type of rennet and dairy cultures used in production. Major differences in the same type of cheese (i.e., hard cheese) are caused by the rennet and dairy cultures, which affect the ripening process. This review aims to explore current technological advancements in animal genetics, methods for the isolation and production of rennet and dairy cultures, along with possible applications of microencapsulation in rennet and dairy culture production, as well as the challenge posed to current dairy technologies by the preservation of biodiversity. Based on the reviewed scientific literature, it can be concluded that innovative approaches and the described techniques can significantly improve cheese production.

Single and combined effects of CSN1S1 and CSN2-casein genes on Awassi sheep milk quantity and quality

Background and Aim: Milk produced from Awassi sheep is of high nutritive value; its production is relatively low in Awassi sheep, so the genetic improvement programs targeted milk production and its components are of high importance, especially when using genes that have an important signal to milk traits. This study was aimed at assessing the influence of alpha S1 (CSN1S1) and beta-casein (CSN2) genes genotypes interaction on Awassi ewes milk productivity. Materials and Methods: A total number of 391 milk yield and its composition records (taken through five consecutive years, 2007-2011) of 167 ewes were utilized for this study. DNA samples were extracted from the ewe's blood samples, then the polymerase chain reaction products of alpha S1 (CSN1S1) and beta-casein (CSN2) genes were sequenced. The obtained sequences were analyzed; thereafter, the detected variants were tested for their possible association with milk traits. Results: The CSN1S1 and CSN2 variants allelic frequencies were 0.85 and 0.15, and 0.95 and 0.05, respectively. Lactose and solid not fat (SNF) % were associated with TC CSN1S1 genotypes. No association was found among CSN1S1 polymorphic genotypes with milk production, lactose, and SNF % were associated with TC CSN1S1 genotypes. Ewes of CSN2 AC genotype showed higher milk production traits, while no association was found between milk composition traits and CNS2 genotypes. Nevertheless, CSN1S1∗CSN2 interaction showed the highest SNF, fat percentages, and milk production. Conclusion: The substantial interaction effects between CSN1S1×CSN2 genes were significantly affected the amount of milk, fat, and SNF% produced. The detected variants should be included in the breeding programs of Awassi sheep that are designed for improving their milk quantity and quality.

Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds

This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.

Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits

Different studies have shown that polymorphisms in the sequence of genes coding for the milk proteins and milk fatty acids are associated with milk composition traits as well as with cheese-making traits. However, the lack of coincident results across sheep populations has prevented the use of this information in sheep breeding programs. The main objective of this study was to exploit the information derived from a total of 175 whole genome resequencing (WGR) datasets from 43 domestic sheep breeds and three wild sheep to evaluate the genetic diversity of 24 candidate genes for milk composition and identify genetic variants with a potential phenotypic effect. The functional annotation of the identified variants highlighted five single nucleotide polymorphisms (SNPs) predicted to have a high impact on the protein function and 42 missense SNPs with a putative deleterious effect. When comparing the allelic frequencies at these 47 polymorphisms with relevant functional effects between the genomes of Assaf and Churra sheep breeds, two missense deleterious variants were identified as potential markers associated to the milk composition differences found between the Churra and Assaf: XDH:92215727C>T and LALBA:137390760T>C. Future research is required to confirm the effect of the potential functionally relevant variants identified in the present study on milk composition and cheese-making traits.

Effect and Interaction of β-Lactoglobulin, Kappa Casein, and Prolactin Genes on Milk Production and Composition of Awassi Sheep

Simple Summary

Beta-lactoglobulin (β-LG), prolactin (PRL), and Kappa casein (CSN3) all contribute to the determination of milk production and composition, but have not been assessed in local Awassi sheep. Therefore, our aim was to analyze the contribution of these genes in milk production and composition traits in commercial Awassi ewe population by genotyping and sequencing these genes. Our results showed the prevalence of the different variations (alleles) of the tested genes in the Awassi population, and no association among β-LG and CSN3 polymorphic genotypes and milk production, or PRL and fat%. Also, all 3 genes help determine the milk production potential of Awassi ewes and help assess milk components, and thus can be used in breeding programs to select for milk potential.

Abstract

A participatory animal-breeding program was applied to 9 commercial Awassi sheep flocks in Jordan. This study aimed to assess the influence of Beta-lactoglobulin (β-LG), Prolactin (PRL), and Kappa casein (CSN3) genes, genotypes and their interaction on milk production and composition traits of 167 genotyped Awassi ewes via Polymerase Chain Reaction (PCR) followed by sequencing. Allele frequencies for the two variants were 0.42 and 0.58 for β-LG, 0.82 and 0.18 for PRL, and 0.92 and 0.08 for CSN3. No association was found among β-LG and CSN3 polymorphic genotypes with milk production traits. However, ewes with PRL AA genotype showed higher milk production, β-LG AB was associated with lowest fat%, high solid not fat (SNF)%, protein%, and lactose%. β-LG BB was associated with highest milk density. PRL, β-LG, and CSN3 polymorphic genotypes were differentially associated with milk production and component traits. Furthermore, β-LG × PRL interaction showed the highest milk production and fat%; β-LG × PRL recorded the highest SNF%, protein%, lactose%, and milk density, while the PRL × CSN3 had the highest fat% and SNF%. The enhancing effects of these gene interactions can be incorporated in Awassi breeding programs to improve milk production and composition.

Bioactive peptides from milk: animal determinants and their implications in human health

Milk is an important protein source in human diets, providing around 32 g protein/l (for bovine milk, which constitutes some 85% of global consumption). The most abundant milk proteins are α-lactalbumin, β-lactoglobulin, αs-casein, β-casein, and κ-casein. Besides their nutritional value, milk proteins play a crucial role in the processing properties of milk, such as solubility, water bonding, heat stability, renneting and foaming, among others. In addition, and most importantly for this review, these proteins are the main source of bioactive components in milk. Due to the wide range of proposed beneficial effects on human health, milk proteins are considered as potential ingredients for the production of health-promoting functional foods. However, most of the evidence for bioactive effects comes from in vitro studies, and there is a need for further research to fully evaluate the true potential of milk-derived bioactive factors. Animal genetics and animal nutrition play an important role in the relative proportions of milk proteins and could be used to manipulate the concentration of specific bioactive peptides in milk from ruminants. Unfortunately, only a few studies in the literature have focused on changes in milk bioactive peptides associated to animal genetics and animal nutrition. The knowledge described in the present review may set the basis for further research and for the development of new dairy products with healthy and beneficial properties for humans.

Variant discovery in the sheep milk transcriptome using RNA sequencing

BACKGROUND

The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportunities for the detection of transcriptome variants (SNPs and short indels) in different tissues and species. In this study, we used RNA-Seq on Milk Sheep Somatic Cells (MSCs) with the goal of characterizing the genetic variation within the coding regions of the milk transcriptome in Churra and Assaf sheep, two common dairy sheep breeds farmed in Spain.

RESULTS

A total of 216,637 variants were detected in the MSCs transcriptome of the eight ewes analyzed. Among them, a total of 57,795 variants were detected in the regions harboring Quantitative Trait Loci (QTL) for milk yield, protein percentage and fat percentage, of which 21.44% were novel variants. Among the total variants detected, 561 (2.52%) and 1,649 (7.42%) were predicted to produce high or moderate impact changes in the corresponding transcriptional unit, respectively. In the functional enrichment analysis of the genes positioned within selected QTL regions harboring novel relevant functional variants (high and moderate impact), the KEGG pathway with the highest enrichment was "protein processing in endoplasmic reticulum". Additionally, a total of 504 and 1,063 variants were identified in the genes encoding principal milk proteins and molecules involved in the lipid metabolism, respectively. Of these variants, 20 mutations were found to have putative relevant effects on the encoded proteins.

CONCLUSIONS

We present herein the first transcriptomic approach aimed at identifying genetic variants of the genes expressed in the lactating mammary gland of sheep. Through the transcriptome analysis of variability within regions harboring QTL for milk yield, protein percentage and fat percentage, we have found several pathways and genes that harbor mutations that could affect dairy production traits. Moreover, remarkable variants were also found in candidate genes coding for major milk proteins and proteins related to milk fat metabolism. Several of the SNPs found in this study could be included as suitable markers in genotyping platforms or custom SNP arrays to perform association analyses in commercial populations and apply genomic selection protocols in the dairy production industry.

The effect of non-standard heat treatment of sheep's milk on physico-chemical properties, sensory characteristics, and the bacterial viability of classical and probiotic yogurt

Classical and probiotic set yogurt were made using non-standard heat treatment of sheep's milk at 60°C/5min. Physico-chemical properties, sensory characteristics, and the viability of bacteria that originated from cultures in classical and probiotic yogurt were analysed during 21days of storage at 4°C. For the production of yogurt, a standard yogurt culture and a probiotic strain Lactobacillus rhamnosus GG were used. At the end of storage time of the classical and probiotic yogurt the totals of non-denatured whey proteins were 92.31 and 91.03%. The viability of yogurt culture bacteria and Lactobacillus rhamnosus GG were higher than 10⁶cfu/g. The total sensory score (maximum - 20) was 18.49 for the classical and 18.53 for the probiotic. In nutritional and functional terms it is possible to produce classical and probiotic sheep's milk yogurt by using a non-standard temperature of heat treatment with a shelf life of 21days.

Variations at regulatory regions of the milk protein genes are associated with milk traits and coagulation properties in the Sarda sheep

Regulatory variation at the ovine casein genes could have important effects on the composition and coagulation properties of milk. Herewith, we have partially resequenced the promoters and the 3'-UTR of the four casein genes in 25 Sarda sheep. Alignment of these sequences allowed us to identify a total of 29 SNPs. This level of polymorphism (one SNP every 250 bp) is remarkably high if compared with SNP densities estimated in human genic regions (approximately one SNP per bp). The 29 SNPs identified in our resequencing experiment, plus three previously reported SNPs mapping to the lactalbumin, alpha (LALBA) and β-lactoglobulin (BLG, also known as progestagen-associated endometrial protein, PAEP) genes, were genotyped with a multiplex TaqMan Open Array Real-Time PCR assay in 760 Sarda sheep with records for milk composition and coagulation properties. Association analysis revealed the existence of significant associations of CSN1S2 and CSN3 genotypes with milk protein and casein contents. Moreover, genotypes at CSN1S1 were significantly associated with rennet coagulation time, curd firming time and curd firmness, whereas CSN2 was associated with curd firming time. These results suggest that SNPs mapping to the promoters and 3'-UTRs of ovine casein genes may exert regulatory effects on gene expression and that they could be used for improving sheep milk quality and technological traits at the population level through marker assisted selection.

The effect of long term under- and over-feeding on the expression of six major milk protein genes in the mammary tissue of sheep

Milk protein synthesis in the mammary gland involves expression of six major milk protein genes whose nutritional regulation remains poorly defined. In this study, the effect of long term under- and over-feeding on the expression of αs1-casein: CSN1S1, αs2-casein: CSN1S2, β-casein: CSN2, κ-casein: CSN3, α-lactalbumin: LALBA and β-lactoglobulin: BLG gene in sheep mammary tissue (MT) was examined. Twenty-four lactating dairy sheep, at 90-98 d in milk, were divided into three groups and fed the same ration, for 60 d, in quantities which met 70% (underfeeding), 100% (control) and 130% (overfeeding) of their energy and crude protein requirements. The results showed a significant reduction on mRNA of CSN1S1, CSN1S2, CSN2 and BLG gene in the MT of underfed sheep compared with the overfed ones and a significant reduction in CSN3 and LALBA gene expression compared with the respective control animals. Significant positive correlations were observed between the mRNA levels of milk proteins' genes with the milk protein yield and milk yield respectively. In conclusion, the feeding level and consequently the nutrients availability, affected the milk protein yield and milk volume by altering the CSN1S1, CSN1S2, CSN2, CSN3, LALBA and BLG gene expression involved in their metabolic pathways.