Assaf Sheep Research Articles

Examining performance, milk, and meat in ruminants fed with macroalgae and microalgae: A meta-analysis perspective.

This meta-analysis consolidates various related studies to identify patterns in the impact of feeding algae on performance aspects, including milk fat, milk protein, and carcass yield in several ruminant species, such as cattle, sheep, and goats. The data were collected from 67 articles that examined factors such as the type of algae (macro- and microalgae), algal species, and animal breed. Barki sheep, Moghani sheep, and Zaraibi goats demonstrated an increased average daily gain (P < 0.05) when fed with both macro- and microalgae. Conversely, sheep such as Canadian Arcott and Ile-de-France showed adverse effects on the feed conversion ratio (FCR) (P < 0.05). Elevated FCR values were observed across castrated and young animals (P < 0.05). Algae extract notably increased the hot carcass weight (P < 0.001), particularly among Moghani sheep (P < 0.001). Raw algae significantly reduced the milk fat content (P < 0.001), particularly in cattle and sheep (P < 0.001). A decrease in milk fat was particularly noticeable in lactating females of Assaf sheep, Damascus goats, and Holstein cows (P < 0.001). Overall, algae inclusion tended to decrease the milk protein content (P < 0.05), leading to reduced milk production (P < 0.001) with cumulative algae feeding in Assaf sheep. However, conjugated linoleic acid (CLA; C18:2 c9,t11-CLA and C18:2 c12,t10-CLA) and docosahexaenoic acid (DHA; C22:6n-3) mostly increased in meat and milk from Holstein cow, Assaf sheep, Dorset sheep, and Ile-de-France sheep (P < 0.01). This meta-analysis highlights the necessity for additional research aimed at optimizing the sustainable use of algae in feed for ruminants, despite the demonstrated improvements in performance and the levels of CLA and DHA found in meat and milk.

Feeding Management of Small Ruminants as A Strategic Tool to Mitigate The Negative Impact of Climate Changes in Arid Regions of Egypt: A Case Study of Assaf Sheep

Feeding Management of Small Ruminants as A Strategic Tool to Mitigate The Negative Impact of Climate Changes in Arid Regions of Egypt: A Case Study of Assaf Sheep

Coadministration of ivermectin and abamectin affects milk pharmacokinetics of the antiparasitic clorsulon in Assaf sheep.

In veterinary field, drug exposure during milk production in dairy cattle is considered a major health problem which concerns dairy consumers. The induced expression of the ABC transporter G2 (ABCG2) in the mammary gland during lactation plays a significant role in the active secretion of many compounds into milk. The main objective of this study was to determine the involvement of ABCG2 in the secretion into milk of the antiparasitic clorsulon in sheep as well as the possible effect of the coadministration of model ABCG2 inhibitors such as macrocyclic lactones on this process. Cells transduced with the ovine variant of ABCG2 were used to carry out in vitro transepithelial transport assays in which we showed that clorsulon is a substrate of the ovine transporter. In addition, ivermectin and abamectin significantly inhibited clorsulon transport mediated by ovine ABCG2. In vivo interactions were studied in Assaf sheep after coadministration of clorsulon (in DMSO, 2 mg/kg, s.c.) with ivermectin (Ivomec®, 0.2 mg/kg, s.c.) or abamectin (in DMSO, 0.2 mg/kg, s.c.). After ivermectin and abamectin treatment, no relevant statistically significant differences in plasma levels of clorsulon were reported between the experimental groups since there were no differences in the area under the plasma concentration-curve (AUC) between clorsulon treatment alone and coadministration with macrocyclic lactones. With regard to milk, total amount of clorsulon, as percentage of dose excreted, did not show statistically significant differences when macrocyclic lactones were coadministered. However, the AUC for clorsulon significantly decreased (p < 0.05) after coadministration with ivermectin (15.15 ± 3.17 μg h/mL) and abamectin (15.30 ± 3.25 μg h/mL) compared to control group (20.73 ± 4.97 μg h/mL). Moreover, milk parameters such as half-life (T1/2) and mean residence time (MRT) were significantly lower (p < 0.05) after coadministration of macrocyclic lactones. This research shows that the milk pharmacokinetics of clorsulon is affected by the coadministration of ABCG2 inhibitors, reducing drug persistence in milk.

O-148 Effect of vaccination against biofilm-producing Staphylococci on milk production and individual and bulk tank somatic cell counts in Assaf sheep in Spain

O-148 Effect of vaccination against biofilm-producing Staphylococci on milk production and individual and bulk tank somatic cell counts in Assaf sheep in Spain

Low-density SNP panel for efficient imputation and genomic selection of milk production and technological traits in dairy sheep.

The present study aimed to ascertain how different strategies for leveraging genomic information enhance the accuracy of estimated breeding values for milk and cheese-making traits and to evaluate the implementation of a low-density (LowD) SNP chip designed explicitly for that aim. Thus, milk samples from a total of 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra) were collected and analyzed to determine 3 milk production and composition traits and 2 traits related to milk coagulation properties and cheese yield. The 2 studied populations were genotyped with a customized 50K Affymetrix SNP chip (Affymetrix Inc.) containing 55,627 SNP markers. The prediction accuracies were obtained using different multitrait methodologies, such as the BLUP model based on pedigree information, the genomic BLUP (GBLUP), and the BLUP at the SNP level (SNP-BLUP), which are based on genotypic data, and the single-step GBLUP (ssGBLUP), which combines both sources of information. All of these methods were analyzed by cross-validation, comparing predictions of the whole population with the test population sets. Additionally, we describe the design of a LowD SNP chip (3K) and its prediction accuracies through the different methods mentioned previously. Furthermore, the results obtained using the LowD SNP chip were compared with those based on the 50K SNP chip data sets. Finally, we conclude that implementing genomic selection through the ssGBLUP model in the current breeding programs would increase the accuracy of the estimated breeding values compared with the BLUP methodology in the Assaf (from 0.19 to 0.39) and Churra (from 0.27 to 0.44) dairy sheep populations. The LowD SNP chip is cost-effective and has proven to be an accurate tool for estimating genomic breeding values for milk and cheese-making traits, microsatellite imputation, and parentage verification. The results presented here suggest that the routine use of this LowD SNP chip could potentially increase the genetic gains of the breeding selection programs of the 2 Spanish dairy sheep breeds considered here.

No evidence of Rift Valley fever antibodies in veterinarians and sheep in Northern Palestine.

Background and Aim:Rift Valley fever virus (RVFV) is a vector-borne virus that causes RVF in humans and ruminants. The clinical symptoms in humans and animals are non-specific and often misdiagnosed, but abortions in ruminants and high mortality in young animals are characteristic. Since the initial outbreak in the Rift Valley area in Kenya, the disease has spread to most African countries and the Middle East. The presence and epidemiological status of RVFV in humans and animals in Palestine are unknown. This study aimed to investigate the presence and risk factors for RVF seroprevalence in veterinarians, as occupational hazard professionals, and sheep, as highly susceptible animals, in Northern Palestine.Materials and Methods:A cross-sectional study was conducted. Data and blood samples of 280 Assaf sheep and 100 veterinarians in close occupational contact with sheep were collected between August and September 2020 using an indirect enzyme-linked immunosorbent assay.Results:No evidence of RVF antibodies was found in any human or animal sample.Conclusion:Our results suggest that RVFV has not circulated in livestock in Northern Palestine, yet. Surveillance and response capabilities and cooperation with the nearby endemic regions are recommended. The distribution of competent vectors in Palestine, associated with global climate change and the role of wild animals, might be a possible route for RVF spreading to Palestine from neighboring countries.

Detection of candidate genes affecting milk production traits in sheep using whole-genome sequencing analysis.

BackgroundArtificial and natural selection for important economic traits and genetic adaptation of the populations to specific environments have led to the changes on the sheep genome. Recent advances in genome sequencing methods have made it possible to use comparative genomics tools to identify genes under selection for traits of economic interest in domestic animals.ObjectivesIn this study, we compared the genomes of Assaf and Awassi sheep breeds with those of the Cambridge, Romanov and British du cher sheep breeds to explore positive selection signatures for milk traits using nucleotide diversity (Pi) and FST statistical methods.MethodsGenome sequences from fourteen sheep with a mean sequence depth of 9.32X per sample were analysed, and a total of 23 million single nucleotide polymorphisms (SNPs) were called and applied for this study. Genomic clustering of breeds was identified using ADMIXTURE software. The FST and Pi values for each SNP were computed between population A (Assaf and Awassi) and population B (Cambridge, British du cher, and Romanov).ResultsThe results of the PCA grouped two classes for these five dairy sheep breeds. The selection signatures analysis displayed 735 and 515 genes from FST and nucleotide diversity (Pi) statistical methods, respectively. Among all these, 12 genes were shared between the two approaches. The most conspicuous genes were related to milk traits, including ST3GAL1 (the synthesis of oligosacáridos), CSN1S1 (milk protein), CSN2 (milk protein), OSBPL8 (fatty acid traits), SLC35A3 (milk fat and protein percentage), VPS13B (total milk production, fat yield, and protein yield), DPY19L1 (peak yield), CCDC152 (lactation persistency and somatic cell count), NT5DC1 (lactation persistency), P4HTM (test day protein), CYTH4 (FAT Production) and METRNL (somatic cell), U1 (milk traits), U6 (milk traits) and 5S_RRNA (milk traits).ConclusionsThe findings provide new insight into the genetic basis of sheep milk properties and can play a role in designing sheep breeding programs incorporating genomic information.

Effect of lipid supplementation on the endogenous synthesis of milk cis-9,trans-11 conjugated linoleic acid in dairy sheep and goats: A tracer assay with 13C-vaccenic acid

A major proportion of milk rumenic acid (RA; cis-9,trans-11 CLA) is synthesized through mammary Δ9-desaturation of vaccenic acid (VA; trans-11 18:1). Diet composition may determine the relative contribution of this endogenous synthesis to milk RA content, with effects that might differ between ruminant species. However, this hypothesis is mostly based on estimated values, proxies of stearoyl-CoA desaturase (SCD) activity, and indirect comparisons between publications in the literature. With the aim of providing new insights into this issue, in vivo Δ9-desaturation of 13C-labeled VA (measured via milk 13C-VA and -RA secretion) was directly compared in sheep and goats fed a diet without lipid supplementation or including 2% of linseed oil. Four Assaf sheep and 4 Murciano-Granadina goats were used in a replicated 2 × 2 crossover design to test the effects of the 2 dietary treatments during 2 consecutive 25-d periods. On d 22 of each period, 500 mg of 13C-VA were i.v. injected to each animal. Dairy performance, milk fatty acid profile, including isotope analysis, and mammary mRNA abundance of genes coding for SCD were examined on d 21 to 25 of each period. Supplementation with linseed oil improved milk fat concentration and increased the content of milk VA and RA. However, the isotopic tracer assay suggested no variation in the relative proportion of VA desaturated to milk RA, and the percentage of this CLA isomer deriving from SCD activity would remain constant regardless of dietary treatment. These results put into question a major effect of lipid supplementation on the endogenous synthesis of milk RA and support that mammary Δ9-desaturation capacity would not represent a limiting factor when designing feeding strategies to increase milk RA content. The lack of diet-induced effects was common to caprines and ovines, but inherent interspecies differences in mammary lipogenesis were found. Thus, the higher proportions of VA desaturation and endogenous synthesis of milk RA in sheep supported a greater SCD activity compared with goats, a finding that was not associated with the similar mRNA abundance of SCD1 in the 2 species. On the other hand, transfer efficiency of the isotopic tracer to milk was 37% higher in caprine than in ovine, suggesting a greater efficiency in mammary fatty acid uptake from plasma in caprine.

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.

Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed.

Simple SummaryMastitis causes economic loss due to discarded milk and reduced milk production and quality, increased medical care costs and somatic cell count (SCC) penalties. The use of genetic markers associated with the variability of this trait through marker-assisted selection (MAS) could help traditional methods. Our objectives were to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). Firstly, corrected phenotype estimates for somatic cell score (SCS) were calculated using 6173 records from 1894 multiparous Assaf ewes, and were used to select 192 extreme animals (low SCS group: n = 96; and high SCS group: n = 96) for the genome-wide association study (GWAS). Four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424), three of them totally linked, were found to be significant at the chromosome level (FDR 10%) in two different regions of OAR19 close to genes related to the immune system response. Validation studies of two SNPs (rs419096188 and rs424642424) by Kompetitive Allele-Specific PCR (KASP) genotyping in the total population (n = 1894) confirmed previous GWAS association results for the SCS trait. Finally, the SNP rs419096188 was also associated with lactose content trait.A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (n = 96) and bottom (n = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the NUP210 and close to the HDAC11 genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the ARPP21 gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (n = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content.

Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep.

Simple SummaryParentage misassignments directly affect genetic gain in traditional breeding programs. The use of genetic markers facilitates parentage verification. In sheep, microsatellite markers and single nucleotide polymorphism (SNP) markers have been proposed by the International Society of Animal Sciences (ISAG) for parentage testing. Since the implementation of genomic selection, the microsatellite information used for parental testing in previous generations is gradually being replaced by SNPs. However, parentage verifications should all be performed using the same technology. A strategy for transitioning from microsatellites to SNP markers, while avoiding extra genotyping costs, is the imputation of microsatellite alleles from SNP haplotypes. This study aims to identify the optimum approach, using a minimum number of SNPs to accurately impute microsatellite markers and developing a low-density SNP chip for parentage verification in the Assaf sheep breed. The imputation approach described here reached high accuracies using a low number of SNP markers, which supports the development of a low-density SNP chip that could avoid the problems of genotyping with both technologies, being a cost-effective method for parentage testing. This study will help sheep breeders to perform parentage verification when different genotyping platforms have been used across generations.Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r2), and allelic dosage (allelic r2), for all imputation scenarios tested (0.5–10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r2), and 0.75 (allelic r2), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations.

Genome-wide association studies for sperm traits in Assaf sheep breed

Sperm quality traits routinely collected by artificial insemination (AI) center for rams progeny test are related with the capacity to produce sperm doses for AI and, in more or less grade, with males' fertility. Low-quality ejaculates are unuseful to perform AI sperm doses, which suppose high economic loses for the AI center. Moreover, sperm quality traits have low heritability values which make traditional genetic selection little efficient to its improvement. In this work, a genome-wide association study (GWAS) was conducted by using sperm quality traits data and 50 K Affymetrix custom chip genotypes of 429 rams of Assaf breed from OVIGEN AI centre. Furthermore, 47 of these rams were also genotyped with the Illumina HD Ovine BeadChip, and therefore HD genotypes were imputed for all rams with phenotype data. Previous to the GWAS, a linear regression model was fitted including sperm traits as dependent variables; the flock of origin, date of sperm collection, and jump number as fixed effects; rams age at collection in months as covariate; and ram permanent effect as random. Pseudo-phenotypes obtained from this model were used as input for GWAS. Associations at the chromosome-wise level (FDR 10%) of 76 single-nucleotide polymorphisms (SNPs) in 4 chromosomes for ejaculate concentration (CON), 20 SNPs in 3 chromosomes for ejaculate volume (VOL), 32 SNPs in 1 chromosome for ejaculate number of spermatozoa (SPZ), and 23 SNPs for spermatozoa mass motility (MOT) in 17 chromosomes were found. Only SNPs associated with MOT overcame the genome-wide significance level. Some candidate genes for sperm traits variability were SLC9C1 (OAR1), TSN (OAR2), and FUT10 (OAR26) for MOT;. DOCK2, CPLANE1, SPEF2, and RAI14 (OAR16) for CON; SCAPER and PSMA4 (OAR18) for VOL; and PARM1 and LOC101110593 (OAR6) for SPZ. SNPs associated with sperm traits were not found to be correlated with milk production genetic variation; however, the high frequencies of some SNPs with negative effect over sperm traits found in animals at the top milk yield estimated breeding values (EBVs) ranking would allow to exert some selective presure to improve rams sperm performances. Effects and frequencies of some of the SNPs detected over sperm quality traits make these variants good candidates to be used in marker-assisted selection to improve sperm characteristics of Assaf rams and AI center efficiency to produce sperm doses.

A multiple-phenotype imputation procedure as a method for prediction of cheese-making efficiency in Spanish Assaf sheep.

Sheep milk is mainly intended to manufacture a wide variety of high-quality cheeses. The ovine cheese industry would benefit from an improvement, through genetic selection, of traits related to the milk coagulation properties (MCPs) and cheese yield-related traits, broadly denoted as "cheese-making traits." Considering that routine measurements of these traits needed for genetic selection are expensive and time-consuming, this study aimed to evaluate the accuracy of a cheese-making phenotype imputation method based on the information from official milk control records combined with the pH of the milk. For this study, we analyzed records of milk production traits, milk composition traits, and measurements of cheese-making traits available from a total of 1,145 dairy ewes of the Spanish Assaf sheep breed. Cheese-making traits included five related to the MCPs and two cheese yield-related traits. The milk and cheese-making phenotypes were adjusted for significant effects based on a general linear model. The adjusted phenotypes were used to define a multiple-phenotype imputation procedure for the cheese-making traits based on multivariate normality and Markov chain Monte Carlo sampling. Five of the seven cheese-making traits considered in this study achieved a prediction accuracy of 0.60 computed as the correlation between the adjusted phenotypes and the imputed phenotypes. Particularly the logarithm of curd-firming time since rennet addition (logK20) (0.68), which has been previously suggested as a potential candidate trait to improve the cheese ability in this breed, and the logarithm of the ratio between the rennet clotting time and the curd firmness at 60 min (logRCT/A60) (0.65), which has been defined by other studies as an indicator trait of milk coagulation efficiency. This study represents a first step toward the possible use of the phenotype imputation of cheese-making traits to develop a practical methodology for the dairy sheep industry to impute cheese-making traits only based on the analysis of a milk sample without the need of pedigree information. This information could be also used in future planning of specific breeding programs considering the importance of the cheese-making efficiency in dairy sheep and highlights the potential of phenotype imputation to leverage sample size on expensive, hard-to-measure phenotypes.

Determination of the Polymorphism of the Booroola Fecundity B, Callipyge and Calpastatin Genes in Assaf Sheep Breed by PCR-RFLP Method

Background: The development of local sheep breeds that have high fecundity levels, high meat content and high growth rates would help satisfy the Palestinian demand of meat and lower its price. It has been reported that mutant alleles of the genes Booroola fecundity (FecB), Callipyge (CLPG) and calpastatin (CAST) are associated with high litter size, larger muscular rumps and higher tenderness of meat after sheep slaughter, respectively. PCR-RFLPs methods have been established to facilitate the survey of sheep breeds for such mutants.Methods: In this study, 117 blood samples of the most common sheep breed in Palestine, Assaf, were collected from Bethlehem and Jenin districts. Genomic DNA was extracted and purified from the blood samples using the salting out method. The genotypic ratios and allelic frequencies of the FecB, CLPG and CAST genes were determined by PCR-RFLP method. Result: The results show that the mutant allele B of the FecB gene has a very low frequency among the screened sheep with 0.01 in Bethlehem and 0.07 in Jenin. Also, 94.4% of the tested sheep have the wildtype genotype AA for the CLPG gene with a frequency of 0.95 for allel A. Moreover, the desired heterzygous genotype MN for the CAST gene is 38.4% with an allelic frequency of 0.81 for the mutant allel M. These results would assist establishing sheep breeding programs with the appropriate parental genotypes to improve the livestock sector in the country.

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

Simple SummaryMost of the production of sheep’s milk is used in the manufacture of mature cheeses. The milk composition has a strong influence on the technological and organoleptic properties of dairy products. Several genetic polymorphisms have been related to variations of milk protein and milk fatty acid content. The use of whole genome resequencing (WGR) has encouraged the discovery of polymorphisms in the sheep genome. Exploiting information derived from a large number of sheep WGR datasets, this study aimed to evaluate the variability of 24 candidate genes involved in physiological pathways related to milk production. The genetic variants highlighted by this work have a potential influence on the function of the protein encoded by the candidate genes. The relevance of sheep milk composition on the cheese-making industry enhances the potential interest of the present study as the variants highlighted herein could be considered to increase the efficiency of breeding programs currently applied to dairy sheep populations. Further studies would be needed to understand the role of these genetic variants on milk production 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.

The Milk Microbiota of the Spanish Churra Sheep Breed: New Insights into the Complexity of the Milk Microbiome of Dairy Species.

Simple SummaryIn the last decade, the number of studies focused on the study of the microbiota of different tissues, organs, or physiological fluids has considerably increased. The milk of dairy species is an important and continuous source of commensal, mutualistic and potentially probiotic bacteria. Second-generation sequencing technologies have been applied to characterise the milk microbiota of dairy cows, whereas the study of the sheep milk microbiota is scarce. In the present study, we aimed to explore the bacterial diversity and composition of milk samples from the Churra sheep breed, a rustic autochthonous breed from the region of Castilla y León (Spain). Moreover, this study tries to clarify the complex bacterial composition of sheep milk comparing the results presented here with previous research on the milk microbiota of the Assaf sheep breed. This assessment has shown that the milk microbiota of ewes from one flock of the Assaf breed is more diverse than the milk microbiota reported here for two different flocks of Churra sheep. The study also provides a step into a better understanding of the link between the bacterial milk composition in these two sheep breeds and somatic cell count, an indicator trait of subclinical mastitis resistance in dairy sheep.Milk from healthy animals has classically been considered a sterile fluid. With the development of massively parallel sequencing and its application to the study of the microbiome of different body fluids, milk microbiota has been documented in several animal species. In this study, the main objective of this work was to access bacterial profiles of healthy milk samples using the next-generation sequencing of amplicons from the 16S rRNA gene to characterise the milk microbiome of the Churra breed. A total of 212 samples were collected from two Churra dairy farms with a different management system. The core milk microbiota in Churra ewes includes lesser genera (only two taxa: Staphylococcus and Escherichia/Shigella) than studies reported in other dairy species or even in a previous study in Assaf sheep milk. We found that diversity values in the two flocks of Churra breed were lower than the diversity of the milk microbiota in Assaf. The non-metric multidimensional scaling (NMDS) ordination using Bray-Curtis distance separates samples based on their microbiota composition. The information reported here might be used to understand the complex issue of milk microbiota composition.

Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

BackgroundIdentification of molecular characterization of genes underlying livestock productive traits may allow applying advanced biotechnology techniques to improve animal productivity. Growth hormone (GH) controls body growth rate, milk production, reproduction as well as carbohydrate, lipid, and protein metabolism. Therefore, the present study aims to investigate the genetic variations of growth hormone cDNA sequences between Assaf sheep (As_GH) and Boer goat (Bo_GH) that mainly used for genetic improvement in Egypt using bioinformatics analysis. Growth hormone cDNA was isolated from the pituitary gland tissue of Assaf sheep Boer goat and subcloned into pTZ57R/T cloning vector for sequencing. ResultsMolecular weight of As_GH cDNA was 665 bp and was 774 bp for Bo_GH cDNA. The complete coding sequences (CDS) of As_GH and Bo_GH were registered in the GenBank database under accession number (AC: MH128986 and AC: MG744290, respectively). High homology percentage was observed (99.5%) between AS_GH and Bo_GH protein sequences with one different amino acid in the As_GH protein sequence (Arg194). The protein sequence of As_GH has only one motif signature; Somatotropin_1 from 79 to 112 aa compared to Bo_GH protein sequences and GenBank database that had two motifs signature. The growth hormone cDNA sequence of Assaf sheep has a unique three single nucleotide polymorphisms (SNPs) (A637A638G639) that encodes for arginine (Arg194); this insertion mutation (AAG) was not found in the growth hormone cDNA sequences of Boer goat in the present study and GenBank database breeds. This mutation can be used to develop SNPs markers for Assaf sheep. ConclusionsGH sequence of Assaf and Boer goat is highly conserved and the homogeny in the codon region (99.5%). The Assaf sheep GH sequence has a unique three SNPs that may be used to develop SNPs markers for such breed. Further studies are needed to investigate the genetic variations of growth hormone gene in different sheep and goat breeds in Egypt and document the relationship between these variations and the productive performance of animals.

Gene Networks Driving Genetic Variation in Milk and Cheese-Making Traits of Spanish Assaf Sheep.

Most of the milk produced by sheep is used for the production of high-quality cheese. Consequently, traits related to milk coagulation properties and cheese yield are economically important to the Spanish dairy industry. The present study aims to identify candidate genes and their regulators related to 14 milk and cheese-making traits and to develop a low-density panel of markers that could be used to predict an individual’s genetic potential for cheese-making efficiency. In this study, we performed a combination of the classical genome-wide association study (GWAS) with a stepwise regression method and a pleiotropy analysis to determine the best combination of the variants located within the confidence intervals of the potential candidate genes that may explain the greatest genetic variance for milk and cheese-making traits. Two gene networks related to milk and cheese-making traits were created using the genomic relationship matrices built through a stepwise multiple regression approach. Several co-associated genes in these networks are involved in biological processes previously found to be associated with milk synthesis and cheese-making efficiency. The methodology applied in this study enabled the selection of a co-association network comprised of 374 variants located in the surrounding of genes showing a potential influence on milk synthesis and cheese-making efficiency.

Economic efficiency of Bulgarian dairy synthetic population and Assaf sheep breeds

Abstract. The economic efficiency of ewes from the Bulgarian dairy synthetic population (BDSP) and Assaf sheep breeds, reared in three production systems, e.g. grazing on pasture, stall-pasture rearing and stall rearing was studied. The results from the study showed that BDSP ewes in the stall-pasture rearing system had a relatively low milk yield for a specialised dairy sheep breed – 80L for the lactation period. In this system, without the subsidy, the profit and cost efficiency were negative, while with subsidy, minimum positive results were achieved. For BDSP ewes reared in a stall-pasture rearing system with stall feeding during the grazing period and grazing on improved pastures, the obtained milk yield was by 33% higher. The subsidy resulted in satisfactory profit and cost efficiency, while without the subsidy, the farm ended in loss. BDSP and Assaf ewes reared in stalls, demonstrated substantially higher milk yield and productivity. They realised a profit and good cost efficiency. The milk yield of BSDP sheep reared in stalls was 200L per lactation, and fertility – 140%. The Assaf breed in which a high level of selection and regulated reproduction cycle was achieved, had 250L milk per lactation and 140% fertility. The profit with subsidy was 128.85 BGN (1Lev=0.975€) and without the subsidy: 48.85 BGN, with relatively high cost efficiency. An introduction of traits for higher milk yield, polyestrus and fertility from Assaf into BSDP sheep is necessary.

Phenotypic and genetic parameter estimates of cheese-making traits and their relationships with milk production, composition and functional traits in Spanish Assaf sheep

Sheep milk is mostly used for the production of cheese. In this study, a commercial population of Spanish Assaf sheep was analyzed for six cheese-making traits: four related to milk-coagulation properties (MCPs) [rennet coagulation time (RCT), curd-firming time (K20), and curd firmness at minutes 30 and 60 (A30, A60)] and two related to cheese yield [individual laboratory cheese yield (ILCY) individual laboratory dried curd yield (ILDCY)]. Records for milk production traits were also available for this study. Restricted maximum likelihood (REML) analysis was used to estimate the genetic parameters and variance components, whereas bivariate models were used to calculate the phenotypic and genetic correlations among the traits considered in this work. Of the 1,143 milk samples included in the study, 147 (13%) did not coagulate, whereas 425 samples (approximately 37%) showed slow coagulation (samples with a record for A60 and a missing record for A30). Also, large mean values were observed for RCT (29.54 min) and logK20 (1.35 min). The heritabilities estimated for the cheese-making traits were moderate, ranging between 0.15 (for ILDCY) and 0.30 (A30 and ILCY). In general, within the pairs of related cheese-making traits, we found moderate-high phenotypic and genetic correlations. The RCT and logK20 traits showed high negative correlations with A30 and A60 at both the genetic and phenotypic levels. From the estimation of genetic parameters among these and several milk traits, the high and positive genetic correlations observed between PP and the two cheese yield traits should be highlighted. Based on the estimated phenotypic correlations, our study supports that subclinical mastitis is related to a delayed gelification of milk and lower curd firmness. Overall, this study provides the first report about the phenotypic and genetic parameters of cheese-making traits in a commercial population of Assaf sheep, offering preliminary information that might help to identify the cheese-making or related milk production traits that could be considered to improve Assaf population toward enhanced cheese performance features.