Bos taurus isolate:embryo | breed:Polish Holstein Friesian
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ABSTRACT:
PROVIDER: PRJNA1026627 | ENA |
REPOSITORIES: ENA
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Project description:We reported the bovine liver gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.
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Project description:We reported the bovine pituitary gland gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.
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Project description:The aim of the study was to fit the genomic evaluation model to Polish Holstein-Friesian dairy cattle. A training data set for the estimation of additive effects of single nucleotide polymorphisms (SNPs) consisted of 1227 Polish Holstein-Friesian bulls. Genotypes were obtained by the use of Illumina BovineSNP50 Genotyping BeadChip. Altogether 29 traits were considered: milk-, fat- and protein- yields, somatic cell score, four female fertility traits, and 21 traits describing conformation. The prediction of direct genomic values was based on a mixed model containing deregressed national proofs as a dependent variable and random SNP effects as independent variables. The correlations between direct genomic values and conventional estimated breeding values estimated for the whole data set were overall very high and varied between 0.98 for production traits and 0.78 for non return rates for cows. For the validation data set of 232 bulls the corresponding correlations were 0.38 for milk-, 0.37 for protein-, and 0.32 for fat yields, while the correlations between genomic enhanced breeding values and conventional estimated breeding values for the four traits were: 0.43, 0.44, 0.31, and 0.35. This model was able to pass the interbull validation criteria for genomic selection, which indicates that it is realistic to implement genomic selection in Polish Holstein-Friesian cattle.
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Project description:The aim of the present study was to evaluate the genotype and allele frequencies of 24 polymorphisms in casein alpha S1 (CSN1S1), casein alpha S2 (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3), and progestagen-associated endometrial protein (PAEP) genes. The study included 1900 Polish Black and White Holstein-Friesian dairy cows that were subjected to genotyping via microarrays. A total of 24 SNPs (Single Nucleotide Polymorphisms) within tested genes were investigated. Two CSN1S1 SNPs were monomorphic, while allele CSN1S1_3*G in CSN1S1_3 SNP dominated with a frequency of 99.39%. Out of seven CSN2 SNPs, four were polymorphic; however, only for CSN2_3 all three genotypes were detected. Only three out of nine SNPs within CSN3 were monomorphic. Three PAEP SNPs were also found to be polymorphic with heterozygotes being most frequent. Hardy-Weinberg equilibrium (HWE) was observed for eight variants. It was shown that only CSN3_6 was not in HWE. The fact that many of investigated SNPs were monomorphic may suggest that in the past the reproduction program favored one of these genotypes. SNPs that are included in commercially available microarrays should be monitored in relation to changes in their frequencies. If a SNP has turned monomorphic, maybe it should be considered for removal from the microarray.
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Project description:This study analyzed the associations between two single-nucleotide polymorphisms (C2239T and A1674C), used together as a genotype located in BNBD4, and milk traits and breeding values of productivity traits of Polish Holstein-Friesian dairy cows. The research was carried out on 322 cows, with 7070 milk parameter and somatic cell count records in daily milking, as well as 897 records covering data on whole lactations, and 2209 breeding value records for productivity traits. The DMU statistical package with a one-trait repeatability test-day animal model was used to estimate the associations. The differences between the genotype effects were analyzed using Duncan's post-hoc tests. The CC/AA and CT/AC genotypes had the highest frequencies (0.62 and 0.23, respectively). For use in marker-assisted selection, the CC/AC genotype is the most promising as an indicator of high-yielding cows potentially resistant to mastitis, because it was associated with the lowest somatic cell count (SCC), highest milk, fat, and protein yields in daily milking, as well as with milk yield in the whole lactation. The studied genotypes were also related to the breeding values of all the investigated production traits. However, some simulation studies have indicated a high rate of false-positives in GWAS based on classically calculated EBVs.
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Project description:In the recent years, antioxidant properties of food products have become an important aspect for consumers. Milk is a very good source of easily absorbable proteins and minerals, as well as a valuable source of antioxidants. Lipocalin-2 (LCN2), given that, inter alia, it is produced in large quantities by various types of cells in response to oxidative stress caused by physical or chemical factors, it can be considered a protein that determines the total antioxidant capacity of milk. The main objective of this study was to analyze polymorphisms within the lipocalin-2 gene and to determine their impact on antioxidant activity of milk from Holstein-Friesian cows. The genotyping was carried out by sequencing of PCR products. To determine the antioxidant activity of milk, the Trolox equivalent antioxidant capacity (TEAC) method was used. A total of four polymorphic sites were identified in the examined segment of the bovine lipocalin-2 gene. It was shown that cows of the CC genotype at the locus g.98793763G>C produced milk of significantly higher antioxidant capacity. The antioxidant capacity of milk also varied according to the age of cows, their daily milk yield, and SCC in milk.
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Project description:ObjectiveThe aim of this study was to verify the usefulness of artificial neural networks (ANN), multivariate adaptive regression splines (MARS), naïve Bayes classifier (NBC), general discriminant analysis (GDA), and logistic regression (LR) for dystocia detection in Polish Holstein-Friesian Black-and-White heifers and cows and to indicate the most influential predictors of calving difficulty.MethodsA total of 1,342 and 1,699 calving records including six categorical and four continuous predictors were used. Calving category (difficult vs easy or difficult, moderate and easy) was the dependent variable.ResultsThe maximum sensitivity, specificity and accuracy achieved for heifers on the independent test set were 0.855 (for ANN), 0.969 (for NBC), and 0.813 (for GDA), respectively, whereas the values for cows were 0.600 (for ANN), 1.000 and 0.965 (for NBC, GDA, and LR), respectively. With the three categories of calving difficulty, the maximum overall accuracy for heifers and cows was 0.589 (for MARS) and 0.649 (for ANN), respectively. The most influential predictors for heifers were an average calving difficulty score for the dam's sire, calving age and the mean yield of the farm, where the heifer was kept, whereas for cows, these additionally included: calf sex, the difficulty of the preceding calving, and the mean daily milk yield for the preceding lactation.ConclusionThe potential application of the investigated models in dairy cattle farming requires, however, their further improvement in order to reduce the rate of dystocia misdiagnosis and to increase detection reliability.
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Project description:Analysis of key genes and gene networks determining milk productivity of the dairy HF cows
2011-11-16 | GSE33680 | GEO
Project description:Greater progesterone (P4) concentrations during the follicular growth have been associated with greater quality of embryos produced by superovulated cows and heifers. However, it is yet to be determined the mechanisms by which oocyte exposure to greater P4 concentrations improves early embryo quality. The objective of this study was to evaluate the impact of different P4 concentrations during superovulation on the transcriptome profile of early bovine embryos. A total of 63 post-puberty Holstein heifers were randomly assigned into two experimental groups: High P4 (n = 31) and Low P4 (n = 32). Heifers received a pre-synchronization protocol followed by a protocol of superovulation that included the allocated P4 treatment. Embryo collection was performed 7 days post artificial insemination and embryos were evaluated for stage of embryonic development and grades of quality. Embryos graded as good/excellent quality (High P4: n = 27; Low P4: n = 27) were randomly allocated in 3 biological replicates per treatment group, balanced for stage of embryonic development. Transcriptome analysis suggested that exposure to different concentrations of P4 during superovulation promote changes in gene expression of 7 days old embryos that may be related to their developmental competence. These modifications are associated with downregulation of beta-estradiol pathway, upregulation of trophoblast-related genes and downregulation of WNT signalling pathway. Our results suggest a potential sensitivity of future embryos to follicular P4 levels but do not allow to conclude if the effect is from the oocyte, the oviduct, or the uterus response to P4.
2024-06-04 | GSE249344 | GEO