Identification of candidate SNPs associated with embryo mortality and fertility traits in lactating Holstein cows
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ABSTRACT:
SUBMITTER: Gonzalez Berrios C
PROVIDER: S-EPMC11341358 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Embryo mortality (EM) contributes to infertility, but its exact mechanism is poorly understood. It was hypothesized that bovine EM pregnancies have impaired conceptus-derived interferon-tau (IFNT) release and action and are associated with altered transcriptome responses. The objective was to discover transcriptome response in EM tissues (endometrium [ENDO], corpus luteum [CL] and peripheral blood mononuclear cells [PBMC]) in lactating Holstein-Friesian cows. Two experiments (E1, E2) in day 16 pregnant (exposed to semen; E1:n=13, E2:n=15) or non-pregnant (NP; not exposed to semen; E1:n=7, E2:n=7) cows were completed. Uterine flushings (UF) and tissues were collected. Pregnant cows were also classified based on conceptus morphology and appearance for EM (E1:n=5, E2:n=6) or normal (N) conceptuses (E1:n=8, E2:n=9). Conceptuses and tissues were RNA sequenced and analyzed. The N conceptuses were longer (P<0.05) than EM conceptuses. The IFNT protein concentrations in UF were greater in N compared to EM and NP cows in E1 but not for E2. The ENDO conjugated ISG15 concentrations were greater in N (E1) than EM and NP cows but N (E2) were only greater than NP not EM cows. The major up-regulated canonical pathway in EM conceptuses was T helper 1 (Th1) and Th2. The ENDO had a massive increase in interferon stimulated genes in N and EM compared to NP cows. Estradiol-associated genes were up-regulated in EM compared to N ENDO for E2. The PBMC in E1 reflected up-regulation of genes associated Th1 immune responses in EM compared to N cows. Luteolytic pathways were upregulated in EM CL compared to N cows. This disruption of maternal recognition of pregnancy in EM pregnancies entails a massive T helper immune response within the conceptus, estradiol re-modelling of the ENDO, abnormal immune system in PBMC, luteolysis cascade in CL and, potentially, loss of pregnancy.
2024-08-09 | GSE233492 | GEO
Project description:A genome-wide association study (GWAS) of the daughter pregnancy rate (DPR), cow conception rate (CCR), and heifer conception rate (HCR) using 1,001,374-1,194,736 first-lactation Holstein cows and 75,140-75,295 SNPs identified 7567, 3798, and 726 additive effects, as well as 22, 27, and 25 dominance effects for DPR, CCR, and HCR, respectively, with log10(1/p) > 8. Most of these effects were new effects, and some new effects were in or near genes known to affect reproduction including GNRHR, SHBG, and ESR1, and a gene cluster of pregnancy-associated glycoproteins. The confirmed effects included those in or near the SLC4A4-GC-NPFFR2 and AFF1 regions of Chr06 and the KALRN region of Chr01. Eleven SNPs in the CEBPG-PEPD-CHST8 region of Chr18, the AFF1-KLHL8 region of Chr06, and the CCDC14-KALRN region of Chr01 with sharply negative allelic effects and dominance values for the recessive homozygous genotypes were recommended for heifer culling. Two SNPs in and near the AGMO region of Chr04 that were sharply negative for HCR and age at first calving, but slightly positive for the yield traits could also be considered for heifer culling. The results from this study provided new evidence and understanding about the genetic variants and genome regions affecting the three fertility traits in U.S. Holstein cows.
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Project description:Alpha-lactalbumin (α-LA) is a major whey protein in bovine and other mammalian milk, which regulates synthesis of lactose. Little is known about its genetic polymorphism and whether can be used as a potential marker for dairy ingredients, milk yield traits, and milk properties. To investigate its polymorphisms and their relationship with milk lactation traits in Chinese Holstein dairy cows, single-strand conformation polymorphism method (PCR-SSCP) and direct sequencing method were used to mark the α-LA gene SNPs. AA (0.7402) and AB (0.2598) genotypes were screened out by PCR-SSCP bands analysis in two independent populations. Direct sequencing revealed that there is one SNP at 1847th (T/C) bp in noncoding region of α-LA gene with highly polymorphic (0.5 < PIC = 0.5623 or 0.5822), of which T is in AA genotype while C in AB. Association analysis also showed that lactose content (p < 0.05) was negatively correlated with fat and protein contents within subgroup, indicating that the SNPs (1847th, T/C) in α-LA gene could be used as a novel potential molecular marker for lactation traits in Chinese Holstein dairy cows.
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Project description:Complete blood counts (CBCs) measure the abundance of individual immune cells, red blood cells, and related measures such as platelets in circulating blood. These measures can indicate the health status of an animal; thus, baseline circulating levels in a healthy animal may be related to the productive life, resilience, and production efficiency of cattle. The objective of this study is to determine the heritability of CBC traits and identify genomic regions that are associated with CBC measurements in lactating Holstein dairy cattle. The heritability of CBCs was estimated using a Bayes C0 model. The study population consisted of 388 cows with genotypes at roughly 75,000 markers and 16 different CBC phenotypes taken at one to three time points (n = 33, 131, and 224 for 1, 2, and 3 time points, respectively). Heritabilities ranged from 0.00 ± 0.00 (red cell distribution width) to 0.68 ± 0.06 (lymphocytes). A total of 96 different 1-Mb windows were identified that explained more than 1% of the genetic variance for at least one CBC trait, with 10 windows explaining more than 1% of the genetic variance for two or more traits. Multiple genes in the identified regions have functions related to immune response, cell differentiation, anemia, and disease. Positional candidate genes include RAD52 motif-containing protein 1 (RDM1), which is correlated with the degree of immune infiltration of immune cells, and C-X-C motif chemokine ligand 12 (CXCL12), which is critically involved in neutrophil bone marrow storage and release regulation and enhances neutrophil migration. Since animal health directly impacts feed intake, understanding the genetics of CBCs may be useful in identifying more disease-resilient and feed-efficient dairy cattle. Identification of genes responsible for variation in CBCs will also help identify the variability in how dairy cattle defend against illness and injury.
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Project description:Korean peninsula weather is rapidly becoming subtropical due to global warming. In summer 2018, South Korea experienced the highest temperatures since the meteorological observations recorded in 1907. Heat stress has a negative effect on Holstein cows, the most popular breed of dairy cattle in South Korea, which is susceptible to heat. To examine physiological changes in dairy cows under heat stress conditions, we analyzed the profiles circulating microRNAs isolated from whole blood samples collected under heat stress and non-heat stress conditions using small RNA sequencing. We compared the expression profiles in lactating cows under heat stress and non-heat stress conditions to understand the regulation of biological processes in heat-stressed cows. Moreover, we measured several heat stress indicators, such as rectal temperature, milk yield, and average daily gain. All these assessments showed that pregnant cows were more susceptible to heat stress than non-pregnant cows. In addition, we found the differential expression of 11 miRNAs (bta-miR-19a, bta-miR-19b, bta-miR-30a-5p, and several from the bta-miR-2284 family) in both pregnant and non-pregnant cows under heat stress conditions. In target gene prediction and gene set enrichment analysis, these miRNAs were found to be associated with the cytoskeleton, cell junction, vasculogenesis, cell proliferation, ATP synthesis, oxidative stress, and immune responses involved in heat response. These miRNAs can be used as potential biomarkers for heat stress.
| S-EPMC7458322 | biostudies-literature
Project description:BackgroundIdentification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. Semen from 550 Holstein bulls of high (≥ 1.7; n = 288) or low (≤ -2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Eleven reproduction and production traits were analyzed.ResultsA total of 40 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits.ConclusionSNPs in a total of 40 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be important for understanding the physiology of reproduction. Given the large number of SNPs associated with DPR that were not negatively associated with production traits, it should be possible to select for DPR without compromising production.
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Project description:This study investigated the mRNA of immune factors expressed by milk somatic cells from 72 healthy lactating Holstein cows on 1 farm. Milk samples were collected aseptically from the right front mammary gland before milking. The milk samples that had a negative reaction to the California mastitis test were used to analyze the mRNA of immune factors. Cows were divided into 2 groups based on the detection of bacteria in milk samples: positive group (n = 22 cows), which showed bacteria in cultures, and negative group (n = 50 cows), which did not show bacteria in cultures. There were significant positive correlations among the relative mRNA levels of interleukin (IL)-6, IL-8, arginase 1, chemokine (C-C motif) ligand (CCL) 1, and chemokine (C-X-C motif) ligand (CXCL) 13, as well as among the relative mRNA levels of IL-10, pentraxin 3, CCL5, and CCL14. Significantly high levels of IL-1β, IL-6, IL-8, arginase 1, Batf, CCL1, CXCL14, and toll-like receptor 4 in the positive group were discovered compared to the negative group. These results suggest that the presence of bacteria in lactating healthy dairy cows may affect mRNA levels of inflammatory mediators expressed by somatic cells.
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Project description:Mastitis is an infectious disease affecting the mammary gland, leading to inflammatory reactions and to heavy economic losses due to milk production decrease. One possible way to tackle the antimicrobial resistance issue stemming from antimicrobial therapy is to select animals with a genetic resistance to this disease. Therefore, aim of this study was to analyze the genetic variability of the SNPs found in candidate genes related to mastitis resistance in Holstein Friesian bulls. Target regions were amplified, sequenced by Next-Generation Sequencing technology on the Illumina® MiSeq, and then analyzed to find correlation with mastitis related phenotypes in 95 Italian Holstein bulls chosen with the aid of a selective genotyping approach. On a total of 557 detected mutations, 61 showed different genotype distribution in the tails of the deregressed EBVs for SCS and 15 were identified as significantly associated with the phenotype using two different approaches. The significant SNPs were identified in intergenic or intronic regions of six genes, known to be key components in the immune system (namely CXCR1, DCK, NOD2, MBL2, MBL1 and M-SAA3.2). These SNPs could be considered as candidates for a future genetic selection for mastitis resistance, although further studies are required to assess their presence in other dairy cattle breeds and their possible negative correlation with other traits.
| S-EPMC7912858 | biostudies-literature
Project description:The present study aimed to assess the relationship of Growth Differentiation Factor 9 (GDF9) genotypes with calving rate, Follicle-stimulating hormone (FSH), and Estradiol (E2) in the Iraqi Holstein-Friesian breed. A number of 15 blood samples were collected from a mother of dizygotic twin birth (DZTB) (with high calving rate records), and another blood sample was collected from 15 single birth (SB) cows. The DNA was extracted and six primers were designed for PCR and sequencing analysis. The FSH and E2 levels were tested through the estrus phase for the two groups (n=10 in each group). The sequence evaluation revealed the presence of two single nucleotide polymorphisms (SNPs) in exon II: A (1109) T and G (1133) A. The genotypic frequency for mutant genotypes was higher significantly (P<0.01) in DZTB cows (with calving rate), as compared to wild genotypes at the same loci. On the other hand, the wild genotypes recorded a significant increment (P<0.01) for SB cows, when compared to mutant genotypes in the same loci. Moreover, a significant rise (P<0.05) was reported in E2 and FSH levels for DZTB cows and mutant genotypes (P<0.01) against SB cows and wild genotypes in 0 and 24 h of estrus phase, respectively. Furthermore, non-significant differences were recorded in E2 concentration among the same genotypes at the same period. In conclusion, the GDF9 exon II SNPs increased the calving rate in Holstein-Friesian cows. The blood FSH and E2 concentrations were higher in the DZTB cows and control the superovulation. Finally, these SNPs can be regarded as markers to accelerate the breeding programs and used in embryo transfer and in vitro embryo production for Iraqi Holstein-Friesian cow breed.
| S-EPMC8790963 | biostudies-literature
Project description:BackgroundGenetic polymorphisms are known to influence milk production and composition. However, the genomic mechanisms involved in the genetic regulation of milk component synthesis are not completely understood. MicroRNAs (miRNAs) regulate gene expression. Previous research suggests that the high developmental potential of the mammary gland may depend in part on a specific miRNA expression pattern. The objective of the present study was to compare the mammary gland miRNomes of two dairy cow breeds, Holstein and Montbéliarde, which have different mammogenic potentials that are related to differences in dairy performance.ResultsMilk, fat, protein, and lactose yields were lower in Montbéliarde cows than in Holstein cows. We detected 754 distinct miRNAs in the mammary glands of Holstein (n = 5) and Montbéliarde (n = 6) midlactating cows using RNA-Seq technology, among which 738 were known and 16 were predicted miRNAs. The 25 most abundant miRNAs accounted for 90.6% of the total reads. The comparison of their abundances in the mammary glands of Holstein versus Montbéliarde cows identified 22 differentially expressed miRNAs (Padj ≤ 0.05). Among them, 11 presented a fold change ≥2, and 2 (miR-100 and miR-146b) were highly expressed. Among the most abundant miRNAs, miR-186 is known to inhibit cell proliferation and epithelial-to-mesenchymal transition. Data mining showed that 17 differentially expressed miRNAs with more than 20 reads were involved in the regulation of mammary gland plasticity. Several of them may potentially target mRNAs involved in signaling pathways (such as mTOR) and lipid metabolism, thereby indicating that they could influence milk composition.ConclusionWe found differences in the mammary gland miRNomes of two dairy cattle breeds. These differences suggest a potential role for miRNAs in mammary gland plasticity and milk component synthesis, both of which are related to milk production and composition. Further research is warranted on the genetic regulation of miRNAs and their role in milk synthesis.
| S-EPMC6668132 | biostudies-literature