Milk Production Traits In Sheep Research Articles

Epigenetic regulation of functional candidate genes for milk production traits in dairy sheep subjected to protein restriction in the prepubertal stage

BackgroundAs the prepubertal stage is a crucial point for the proper development of the mammary gland and milk production, this study aims to evaluate how protein restriction at this stage can affect methylation marks in milk somatic cells. Here, 28 Assaf ewes were subjected to 42.3% nutritional protein restriction (14 animals, NPR) or fed standard diets (14 animals, C) during the prepubertal stage. During the second lactation, the milk somatic cells of these ewes were sampled, and the extracted DNA was subjected to whole-genome bisulfite sequencing.ResultsA total of 1154 differentially methylated regions (DMRs) were identified between the NPR and C groups. Indeed, the results of functional enrichment analyses of the genes harboring these DMRs suggested their relevant effects on the development of the mammary gland and lipid metabolism in sheep. The additional analysis of the correlations of the mean methylation levels within these DMRs with fat, protein, and dry extract percentages in the milk and milk somatic cell counts suggested associations between several DMRs and milk production traits. However, there were no phenotypic differences in these traits between the NPR and C groups.ConclusionIn light of the above, the results obtained in the current study might suggest potential candidate genes for the regulation of milk production traits in the sheep mammary gland. Further studies focusing on elucidating the genetic mechanisms affected by the identified DMRs may help to better understand the biological mechanisms modified in the mammary gland of dairy sheep as a response to nutritional challenges and their potential effects on milk production.

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.

Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping.

The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of 6 years (2006–2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities and repeatabilities within and across lactations were estimated, fitting parity, litter size, season of lambing and fortnights in milk, as fixed; and additive genetic, permanent environment within and across lactations, flock by test‐day interaction and residual as random effects. For the RHM analysis, the model included the same fixed and random effects as before, plus an additional regional genomic additive effect (specific for the region being tested) as random. While the whole genomic additive effect was estimated using the genomic relationship matrix (GRM) constructed from all SNPs, the regional genomic additive effect was estimated from a GRM matrix constructed from the SNPs within each region. Heritability estimates ranged between 0.06 and 0.15, with repeatabilities being between 0.14 and 0.24 across lactations and between 0.23 and 0.39 within lactation for all milk production traits. A substantial effect of flock‐test‐day on milk production traits was also estimated. Significant genomic regions at either genome‐wide (p < .05) or suggestive (i.e., one false positive per genome scan) level were identified on chromosome (OAR) 2, 3 and 20 for F% and on OAR3 for P%, with the regions on OAR3 in common between the two traits. Our results confirmed the role of LALBA and AQP genes, on OAR3, as candidate genes for milk production traits in sheep.

Single nucleotide polymorphism of the β-lactoglobulin gene in sheep breeds reared in Bulgaria

In the present study, single nucleotide polymorphism in exon II of the β-lactoglobulin gene was investigated in four Bulgarian sheep breeds: Bulgarian Dairy Synthetic Population sheep (BDSP), Copper-red Shumen sheep (CRSH), Stara Zagora sheep (STZG) and Pleven Blackhead sheep (PLBH). Two genetic variants of β-LG gene (A and B) have been identified through PCR-RFLP assay. A 103 bp fragment of the polymorphic β-LG locus were amplified and digested with endonuclease enzyme RsaI. The obtained restriction fragments revealed three genotypes: AA, AB and BB, observed in 31%, 65.5% and 3.5% of the BDSP population and in 48%, 28% and 24% of CRSH sheep population, respectively, with departure from the Hardy-Weinberg equilibrium (P&lt;0.05) in these groups. The allele frequencies demonstrated a prevalence of the A allele (0.638 and 0.620) over the B allele (0.362 and 0.380) in both populations. On the contrary, the distribution of allele frequencies in STZG and PLBH was 0.240 and 0.100 for allele A, respectively and 0.760 and 0.900 for allele B. Therefore, the homozygous BB genotype in these sheep populations was more frequently encountered (0.520 and 0.800) than the heterozygous AB genotype (0.480 and 0.200), with HWE correspondence (P&gt;0.1). The homozygous genotype AA was absent in STZG and PLBH sheep populations. The greatest Nei’s genetic distance calculated by UPGMA method was found between the populations BDSPand PLBH (0.5334), while the closest relationship (0.0006) was established between CRSH and BDSP. The results obtained from the present investigation confirmed the presence of the SNP polymorphism in exon II of the β-lactoglobulin gene. Therefore, the genetic variability established in this polymorphic locus could be applied in further association studies with milk production traits in sheep.

Investigation of myostatin and calpain 3 gene polymorphisms and their association with milk-production traits in Sfakia sheep

Context Genetic selection based on genetic markers for economically important traits in Sfakia sheep. Aims The aim of the present study was to investigate variation in the ovine myostatin gene (MSTN) and calpain 3 gene (CAPN3), and their association with milk-production traits. Methods Records for milk yield, milk fat content, protein content, lactose content, and non-fat solid content, pH and somatic-cell score (log), were obtained from 376 Sfakia ewes. Polymerase chain reaction–single-strand conformational polymorphism (PCR–SSCP) analyses were used to detect variation in intron 1 of MSTN and exon 10 of CAPN3. General linear models were then used to test for associations between the variation in MSTN and CAPN3, and milk-production traits. Key results The SSCP banding patterns for MSTN showed four variants (A1, A2, A3 and A4), which contained nine nucleotide sequence differences. Four SSCP banding patterns (C1, C2, C3 and C4) were observed for CAPN3 and these contained eight nucleotide-sequence differences. The MSTN variation was associated (P &amp;lt; 0.05) with variation in milk yield and non-fat milk solid content. Variation in CAPN3 was associated with milk yield (P &amp;lt; 0.001), fat content (P &amp;lt; 0.05) and lactose content (P &amp;lt; 0.05). Association analyses between the presence/absence of MSTN and CAPN3 variants and milk-production traits showed that a variant of MSTN that had previously between associated with muscle hypertrophy was associated with decreased milk yield (P &amp;lt; 0.05) and a lower non-fat milk solid content (P &amp;lt; 0.01). A CAPN3 variant that had previously been associated with increased sheep-carcass loin lean-meat yield was associated with a decreased milk yield (P &amp;lt; 0.01) and a decreased milk fat content (P &amp;lt; 0.05). Conclusions Our results have provided an insight into the effects of variation in ovine MSTN and CAPN3 on milk-production traits in sheep. Implications To preserve the dual-purpose characteristics of Sfakia sheep, breeding goals should take into account the possible antagonism between meat and milk traits.

Investigation on relationships of the FABP3 and SLC27A3 genes with milk production traits in sheep

Investigation on relationships of the FABP3 and SLC27A3 genes with milk production traits in sheep

Identification of quantitative trait loci underlying milk traits in Spanish dairy sheep using linkage plus combined linkage disequilibrium and linkage analysis approaches

In this study, 2 procedures were used to analyze a data set from a whole-genome scan, one based on linkage analysis information and the other combing linkage disequilibrium and linkage analysis (LDLA), to determine the quantitative trait loci (QTL) influencing milk production traits in sheep. A total of 1,696 animals from 16 half-sib families were genotyped using the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) and analysis was performed using a daughter design. Moreover, the same data set has been previously investigated through a genome-wide association (GWA) analysis and a comparison of results from the 3 methods has been possible. The linkage analysis and LDLA methodologies yielded different results, although some significantly associated regions were common to both procedures. The linkage analysis detected 3 overlapping genome-wise significant QTL on sheep chromosome (OAR) 2 influencing milk yield, protein yield, and fat yield, whereas 34 genome-wise significant QTL regions were detected using the LDLA approach. The most significant QTL for protein and fat percentages was detected on OAR3, which was reported in a previous GWA analysis. Both the linkage analysis and LDLA identified many other chromosome-wise significant associations across different sheep autosomes. Additional analyses were performed on OAR2 and OAR3 to determine the possible causality of the most significant polymorphisms identified for these genetic effects by the previously reported GWA analysis. For OAR3, the analyses demonstrated additional genetic proof of the causality previously suggested by our group for a single nucleotide polymorphism located in the α-lactalbumin gene (LALBA). In summary, although the results shown here suggest that in commercial dairy populations, the LDLA method exhibits a higher efficiency to map QTL than the simple linkage analysis or linkage disequilibrium methods, we believe that comparing the 3 analysis methods is the best approach to obtain a global picture of all identifiable QTL segregating in the population at both family-based and population-based levels.

Investigation of polymorphisms and association of the ABCG2 gene with milk production traits in sheep

The ATP-binding casette sub-family G member 2 (ABCG2) gene was chosen as a candidate gene influencing milk production traits in sheep based on its function and chromosomal localization. A number of fragments were sequenced, including the 3′UTR region, 16 exons, and regions within introns 4, 5 and 6, in samples collected from 11 Awassi and 2 Gyimesi Racka sheep. A single 35-base insertion/deletion, and a total of 13 single nucleotide polymorphisms (SNPs) were identified. SNP mutations found in exons (n=3) were synonymous. Two SNPs (g.703T>C, c.863+40G>A) and the insertion/deletion (c.683-80_46del) were chosen for further investigation, and an association study between these three polymorphisms and milk production traits was performed in both breeds (Awassi n=310, Gyimesi Racka n=75). The analysis revealed significant effect of two of the studied SNPs in Gyimesi Racka. Mutation g.703T>C showed significant effect on protein percentage (p<0.05) while the c.683-80_46del had a significant effect on somatic cell score (p<0.01). However, further studies are needed to evaluate these possible associations more effectively.

Genetic polymorphism of β-lactoglobulin in sheep raised for milk production

To investigate β-lactoglobulin polymorphism using polymerase chain reaction – restriction fragment length polymorphism in Polish Mountain, East Friesian, Polish Merino and Austrian Bergschaf sheep raised for milk production, three β-LGB genotypes (AA, AB and BB) were found in all the groups, AB being the most frequent genotype in all the groups. The frequency of β-LGB A genes was 0.66 in Friesian, 0.55 in Bergschaf, 0.5 in Polish Mountain and 0.48 in Polish Merino sheep with no deviations from genetic equilibrium according to Hardy-Weinberg law. The relationship between β-lactoglobulin genotype and milk yield and milk composition was investigated, but no statistical differences were found. The present findings provide no conclusive evidence about the effect of different β-LGB variants on milk production traits in sheep.

Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

An (Awassi × Merino) × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P < 0.01) and additional 25 suggestive (P < 0.05) QTL were detected across both single QTL methods and all traits. In preparation of a meta-analysis, all QTL results were compared with a meta-assembly of QTL for milk production traits in dairy ewes from various public domain sources and can be found on the ReproGen ovine gbrowser http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

Quantitative trait loci underlying milk production traits in sheep

Improvement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half-sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome-wise multi-marker regression analysis revealed a genome-wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production-related traits.

Genetic and Environmental Trends for Milk Production Traits in Sheep Estimated with Test-day Model

Data from milk performance testing were used to analyze genetic and environmental trends for purebred Tsigai, Improved Valachian and Lacaune sheep. 103,715 (Tsigai), 212,962 (Improved Valachian) and 2,196 (Lacaune) test-day records gathered by the State Breeding Institute of the Slovak Republic entered the analyses. The respective pedigree data comprised 23,724 (Tsigai), 51,401 (Improved Valachian) and 438 (Lacaune) records. The multiple-trait, mixed model methodology was used to predict the breeding values for daily milk yield, fat and protein content and to estimate the fixed and remaining random effects assumed to affect the above mentioned traits, separately for each breed. The breeding values for daily milk yield were adjusted for 150-day standardized lactation length by multiplying with the constant 150, as the breeding goal of the selection scheme in Slovakian sheep is to increase 150-day milk production and constant heritability throughout the whole lactation is assumed. The genetic trends were expressed as changes in averages of breeding values across birth years of animals. For Tsigai and Lacaune breeds, cumulative genetic changes over the analyzed period were 3.8 and 5.1 kg for 150-day milk, 0 and -0.16% for fat content and 0 and -0.12% for protein content. For Improved Valachian breed, either a low (1.6 kg for 150-day milk yield) or zero (fat and protein content) cumulative genetic change was found. The environmental trends were calculated as averages of solutions for flock-test day effect across years and months in which measurements were taken. A distinctive cyclical pattern which reflected short-time variation in milk production traits was found. Possible explanations for this phenomenon are given and discussed.

Estimation of genetic and environmental parameters of milk production traits in Slovak purebred sheep using test-day model

Covariance matrices and genetic parameters for milk production traits in sheep were estimated for the Improved Valachian and Tsigai breeds. These multipurpose breeds are of local importance, and are bred for milk, meat and wool. The traits under study were daily milk yield and fat and protein content. Genetic analyses were based on test-day records gathered over the period from 1995 to 2001. Each breed was analyzed separately. Only purebred animals with at least four test days per lactation were considered. The data set for the Improved Valachian consisted of 117,959 test-day records of 28,753 lactations belonging to 18,867 ewes. The corresponding pedigree comprised information on 32,804 animals. For the Tsigai breed, the data set consisted of 52,191 test-day records of 12,382 lactations belonging to 8,132 ewes and the pedigree comprised 14,576 animals. The three-trait animal model was used for analyses. To account for different lactation stage, a fixed regression on individual test days was employed. In addition to the function describing, effects of days in milk, effects of lactation, litter size, number of milkings per day, age at lambing, and flock-test day as well as additive genetic and permanent environmental effect of the animal were included in the model. Of these, flock-test day, additive genetic and permanent environmental effects were treated as random. Restricted maximum likelihood (REML) algorithm was used to estimate genetic parameters and covariance matrices. Heritabilities were 0.10 and 0.19 for daily milk yield, 0.06 and 0.12 for fat content, 0.07 and 0.17 for protein content for the Improved Valachian and Tsigai breeds, respectively. Genetic correlations between milk yield and fat content for the two breeds were −0.29 and −0.23 and those between milk yield and protein content were −0.30 and −0.27. Genetic correlations between fat and protein content were 0.58 and 0.57. Higher values (either positive or negative) were found for the breed with the larger number of records. Variance ratios and correlations were also estimated for nongenetic effects for both breeds. Variance ratios for the flock-test-day effects were rather high, ranging from 0.34 to 0.48. Higher values for these effects were found in the Improved Valachian sheep, reflecting more variability in management conditions in this breed. The genetic parameters estimated in this study should be used in routine genetic evaluation of milk production traits of local sheep breeds to replace present selection criteria based on phenotype values of dam milk yield.