Transcriptome data of peripheral white blood cells from beef heifers collected at the time of artificial insemination.
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ABSTRACT:
SUBMITTER: Dickinson SE
PROVIDER: S-EPMC5996294 | biostudies-literature | 2018 Jun
REPOSITORIES: biostudies-literature
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Transcriptome data of peripheral white blood cells from beef heifers collected at the time of artificial insemination.
Dickinson Sarah E SE Biase Fernando H FH
Data in brief 20180321
The reproductive performance of heifers within their first breeding season influences the success of beef cattle operations. Therefore, a means to identify infertile and late breeding heifers before the start of the breeding season holds great promise for the future of the beef industry. Pubertal beef heifers were subjected to estrous synchronization and fixed time artificial insemination (FTAI). We collected peripheral blood from the heifers at the time of artificial insemination (AI) and gener ...[more]
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Project description:Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection for fertility is challenging. Beef cattle operations leverage estrous synchronization in combination with artificial insemination (AI) to breed heifers and benefit from an early and uniform calving season. A couple of weeks following AI, heifers are exposed to bulls for an opportunity to become pregnant by natural breeding (NB), but they may also not become pregnant during this time period. Focusing on beef heifers, in their first breeding season, we hypothesized that: a- at the time of AI, the transcriptome of peripheral white blood cells (PWBC) differs between heifers that become pregnant to AI and heifers that become pregnant late in the breeding season by NB or do not become pregnant during the breeding season; and b- the ratio of transcript abundance between genes in PWBC classifies heifers according to pregnancy by AI, NB, or failure to become pregnant.We generated RNA-sequencing data from 23 heifers from two locations (A: six AI-pregnant and five NB-pregnant; and B: six AI-pregnant and six non-pregnant). After filtering out lowly expressed genes, we quantified transcript abundance for 12,538 genes. The comparison of gene expression levels between AI-pregnant and NB-pregnant heifers yielded 18 differentially expressed genes (DEGs) (ADAM20, ALDH5A1, ANG, BOLA-DQB, DMBT1, FCER1A, GSTM3, KIR3DL1, LOC107131247, LOC618633, LYZ, MNS1, P2RY12, PPP1R1B, SIGLEC14, TPPP, TTLL1, UGT8, eFDR?0.02). The comparison of gene expression levels between AI-pregnant and non-pregnant heifers yielded six DEGs (ALAS2, CNKSR3, LOC522763, SAXO2, TAC3, TFF2, eFDR?0.05). We calculated the ratio of expression levels between all gene pairs and assessed their potential to classify samples according to experimental groups. Considering all samples, relative expression from two gene pairs correctly classified 10 out of 12 AI-pregnant heifers (P?=?0.0028) separately from the other 11 heifers (NB-pregnant, or non-pregnant).The transcriptome profile in PWBC, at the time of AI, is associated with the fertility potential of beef heifers. Transcript levels of specific genes may be further explored as potential classifiers, and thus selection tools, of heifer fertility.
| S-EPMC5807776 | biostudies-literature
Project description:Background: Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection for fertility is challenging. Beef cattle operations leverage estrous synchronization in combination with artificial insemination (AI) to breed heifers and benefit from an early and uniform calving season. A couple of weeks following AI, heifers are exposed to bulls for an opportunity to become pregnant by natural breeding (NB), but they may also not become pregnant during this time period. Focusing on beef heifers, in their first breeding season, we hypothesized that: a- at the time of AI, the transcriptome of peripheral white blood cells (PWBC) differs between heifers that become pregnant to AI and heifers that become pregnant late in the breeding season by NB or do not become pregnant during the breeding season; and b- the ratio of transcript abundance between genes in PWBC classifies heifers according to pregnancy by AI, NB, or failure to become pregnant. Results: We generated RNA-sequencing data from 23 heifers from two locations (A: six AI-pregnant and five NB-pregnant; and B: six AI-pregnant and six non-pregnant). After filtering out lowly expressed genes, we quantified transcript abundance for 12,538 genes. The comparison of gene expression levels between AI-pregnant and NB-pregnant heifers yielded 18 differentially expressed genes (DEGs) (ADAM20, ALDH5A1, ANG, BOLA-DQB, DMBT1, FCER1A, GSTM3, KIR3DL1, LOC107131247, LOC618633, LYZ, MNS1, P2RY12, PPP1R1B, SIGLEC14, TPPP, TTLL1, UGT8, eFDR≤0.02). The comparison of gene expression levels between AI-pregnant and non-pregnant heifers yielded six DEGs (ALAS2, CNKSR3, LOC522763, SAXO2, TAC3, TFF2, eFDR≤0.05). We calculated the ratio of expression levels between all gene pairs and assessed their potential to classify samples according to experimental groups. Considering all samples, relative expression from two gene pairs correctly classified 10 out of 12 AI-pregnant heifers (P=0.0028) separately from the other 11 heifers (NB-pregnant, or non-pregnant). Conclusion: The transcriptome profile in PWBC, at the time of AI, is associated with the fertility potential of beef heifers. Transcript levels of specific genes may be further explored as potential classifiers, and thus selection tools, of heifer fertility.
2018-01-13 | GSE103628 | GEO
Project description:Infertility remains the most prevalent reason for cattle being removed from production environments. We utilized metabolomic profiling to identify metabolites in the blood plasma that may be useful in identifying infertile heifers at the time of artificial insemination (AI). Prior to AI, phenotypic parameters including body condition, weight, and reproductive organ measurements were collected. These were determined not effective at differentiating between fertile and infertile heifers. Analysis of the resulting metabolomic profiles revealed 15 metabolites at significantly different levels (T-test P???0.05), with seven metabolites having a greater than 2-fold difference (T-test P???0.05, fold change ?2, ROC-AUC???0.80) between infertile and fertile heifers. We further characterized the utility of using the levels of these metabolites in the blood plasma to discriminate between fertile and infertile heifers. Finally, we investigated the potential role inflammation may play by comparing the expression of inflammatory cytokines in the white blood cells of infertile heifers to that of fertile heifers. We found significantly higher expression in infertile heifers of the proinflammatory markers tumor necrosis factor alpha (TNF?), interleukin 6 (IL6), and the C-X-C motif chemokine 5 (CXCL5). Our work offers potentially valuable information regarding the diagnosis of fertility problems in heifers undergoing AI.
| S-EPMC6123494 | biostudies-literature
Project description:The gene expression profiles were measured using RNA-Seq beef heifers sampled at weaning and retrospectively classified as pregnant through artificial insemination (AI-P, n = 8) or non-pregnant (NP, n = 7). In brief, crossbred heifers (Angus-Simmental) were used in this study. At the time of weaning (~238 days after birth), blood samples (10 mL) were collected from the jugular vein into vacutainers containing EDTA. The blood was processed to extract PWBC and was stored at -80 until further processing. During the breeding season, all the heifers followed the same breeding protocol, estrus synchronization, and fixed-time artificial insemination (AI). Fourteen days following the fixed-time AI, the non-pregnant heifers were exposed to fertile bulls for 60 days. Depending on the presence or absence of conceptus at 75 days following AI, heifers were classified as pregnant to AI (AI-P), pregnant to natural breeding (P-NB) or non-pregnant (NP). Heifers that were pregnant to AI (N = 8) and non-pregnant (N = 7) were considered for the study. Total RNA was extracted from peripheral white blood cells of 15 samples (AI-P and NP) and was subjected to sequencing. The RNA-Seq data were subjected to quality control and mapped with STAR aligner to Ensemble’s ARS UCD1.2 Bos taurus reference genome. Read quantification was performed using a STAR aligner to obtain raw counts per gene. Genes with low counts were filtered out. After filtering, the read counts were analyzed using DESeq2 v 1.26.0 to identify differentially expressed genes (DEGs). The DEGs with padj < 0.05 and absolute (log2 fold change) > 0.5 were considered significant. The NP heifers were considered as the reference group, and the DEGs up or downregulated were classified based on the log2 fold change direction. We identified 92 DEGs between AI-P and NP groups. The top pathways identified with DEGs were the immune system, cytokine production and defense response, hematopoietic cell lineage, positive regulation of reactive oxygen species metabolic process, and negative regulation of cysteine-type endopeptidase activity involved in the apoptotic process.
2023-02-28 | GSE221903 | GEO
Project description:The miRNA profiles were measured using small-RNA sequencing in beef heifers sampled at weaning that was retrospectively classified as fertile or subfertile following the breeding protocol. To accomplish this, the miRNA profiles were generated from the blood samples (10 mL) collected from crossbred heifers (Angus-Simmental) at the time of weaning (~238 days after birth). Peripheral white blood cells (PWBC) were extracted from the blood samples and stored at -80°C until further processing. During the breeding season, all the heifers followed the same breeding protocol, estrus synchronization, and fixed-time artificial insemination (AI). Fourteen days following the fixed-time AI, the non-pregnant heifers were exposed to fertile bulls for 60 days. Depending on the presence or absence of conceptus at 75 days following AI, heifers were classified as fertile for those who were pregnant through artificial insemination, pregnant to natural breeding (P-NB), or subfertile for those who were not pregnant. Heifers from fertile (n = 7) and subfertile (n = 7) groups were considered for the study. Total RNA was extracted from the PWBC of 14 samples and was subjected to small RNA library preparation and sequencing. After quality control, adapter trimming, and alignment, mature miRNAs were used for differential expression analysis. The read counts were transformed to counts per million (CPM), and raw counts with CPM < 1 in 50% of the samples were filtered out. The filtered raw counts were analyzed using DESeq2 v 1.26.0 to identify differentially expressed miRNAs (DEMIs). The DEMIs identified with a p-value < 0.05 and absolute (log2 fold change) > 0.5 were considered significant. With the subfertile heifers as the reference group, we identified 16 DEMIs between fertile and subfertile groups. To determine the genes targeting the DEMIs, we downloaded the target genes for each DEMI and retained only those genes expressed in the PWBCs. For the miRNA-gene correlation, we used the partial correlation and information theory (PCIT) approach to identify the significant gene-miRNA correlated pairs. The significant genes correlated with the miRNAs identified pathways including MAPK, ErbB, HIF-1, FoxO, p53, mTOR, T-cell receptor, insulin and GnRH signaling, apoptosis, and pathways regulating pluripotency of stem cells in the fertile group while cell cycle, p53 signaling pathway and apoptosis pathways in the subfertile group.
2023-07-17 | GSE225854 | GEO
Project description:The knowledge surrounding the bovine vaginal microbiota and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal bacterial community and estradiol concentrations at the time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + controlled internal drug release estrus synchronization protocol. At AI, a double-guarded uterine culture swab was used to sample the anterior vaginal tract. Immediately after swabbing the vaginal tract, blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) vs. nonpregnant (n = 49) between 41 and 57 d post-AI. Additionally, heifers were classified into low (1.1 to 2.5 pg/mL; n = 21), medium (2.6 to 6.7 pg/mL; n = 30), and high (7.2 to 17.6 pg/mL; n = 27) concentration of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4 region from the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via ANOVA and beta diversity was compared via PERMANOVA. There were no differences in the Shannon diversity index (alpha diversity; P = 0.336) or Bray-Curtis dissimilarity (beta diversity; P = 0.744) of pregnant vs. nonpregnant heifers. Overall, bacterial community composition in heifers with high, medium, or low concentrations of estradiol did not differ (P = 0.512). While no overall compositional differences were observed, species-level differences were present within pregnancy status and estradiol concentration groups. The implications of these species-level differences are unknown, but these differences could alter the vaginal environment thereby influencing fertility and vaginal health. Therefore, species-level changes could provide better insight rather than overall microbial composition in relation to an animal's reproductive health.
| S-EPMC7281872 | biostudies-literature
Project description:Supplementation of cattle diets with n-3-polyunsaturated fatty acids (PUFA) can improve reproductive efficiency. Conversely, short-term fluctuations in feed supply can impact pregnancy establishment. The objectives of this study were to examine the effects of (1) dietary supplementation with n-3-PUFA and (2) post-insemination plane of nutrition on the endometrial transcriptome. Beef crossbred heifers were offered concentrate based diets fortified with n-3-PUFA (PUFA; n = 32) or not (CONT; n = 28) for 30 days prior to breeding at a synchronised oestrous. Following artificial insemination, heifers were allocated within treatment to either a high or low plane of nutrition. Heifers were maintained on these diets for 16 days following which endometrial tissue was harvested at slaughter for subsequent RNAseq analysis. The influence of pregnancy status on the endomentrial transcriptome, within each dietary treatment group, was also examined. Post-insemination diet affected (P < 0.05) the endometrial transcriptome. Specifically, within n-3-PUFA-supplemented heifers, genes involved in embryonic development and mTOR signalling pathways, important in pregnancy establishment, were identified as differentially expressed. Results indicate that dietary supplementation of cattle diets with n-3-PUFA may have a positive effect on the expression of key fertility-related genes and pathways, during the critical window of maternal recognition of pregnancy, particularly where animals are underfed.
| S-EPMC7695717 | biostudies-literature
Project description:Our aim was to investigate insemination techniques in order to improve pregnancy rates of artificial insemination (AI) using sex-sorted semen (sexed AI) in cattle in tropical and subtropical (T/ST) regions. In T/ST regions, the pregnancy rates by sexed AI are reportedly the lowest in the hottest months of the year, with less than 15% in cows and 35-40% in heifers (PMID 24048822). We compared sexed AI by depositing the semen into the uterine body (UB-AI, n = 12) versus the unilateral uterine horn (UUH-AI, n = 14) of pre-ovulation heifers. The ovary and follicle were assessed by rectal ultrasound before AI. After insemination, pregnancy was determined by ultrasound at approximately 40 days and approximately 70 days. In the present study, we demonstrated that high pregnancy rates (>70%) by sexed AI in the hottest season in a subtropical region such as Taiwan can be achieved when heifers with pre-ovulation follicles are used. The overall pregnancy rates were 54% higher in the UUH-AI (71%) group than in the UB-AI (42%) group (P = 0.06), examined on approximately 40 days post-sexed AI. Surprisingly, however, the pregnancy outcome appeared to be higher in the hot season (62%) than in the cool season (46%) although this difference was not statistically significant. Based on the present study, we recommend that cattle breeders perform UUH-AI using sex-sorted semen for heifers with pre-ovulation follicles in order to achieve satisfactory pregnancy outcome in the hot seasons in T/ST regions.
| S-EPMC5519643 | biostudies-other
Project description:Two experiments investigated the effects of supplementing Ca salts of soybean oil (CSSO) during early gestation on reproductive function and pregnancy rates to AI in Bos taurus beef cows. In Exp. 1, 771 suckled, lactating, multiparous Angus cows were divided into 22 groups of approximately 35 cows per group and timed inseminated on day 0. After AI, groups were assigned randomly to receive (as-fed basis) 100 g of ground corn + 100 g of soybean meal per cow/d, in addition to 1) 100 g/cow daily of CSSO (n = 11) or 2) 87 g of prilled saturated fat + 13 g of limestone per cow/d (CON; n = 11). Groups were maintained in individual tall fescue-dominated pastures and offered treatments from day 0 to 21. Pregnancy status was determined between days 45 and 55 via transrectal ultrasonography. Cows receiving CSSO had greater (P = 0.01) pregnancy rates to timed AI compared with CON (60.2 vs. 51.7%; SEM = 4.2). In Exp. 2, 90 suckled, lactating, multiparous Angus × Hereford cows housed in 18 drylot pens (5 cows per pen) were assigned to the same timed AI program and treatments from Exp. 1 (9 pens per treatment) and received 20 kg/d (DM basis) of grass-alfalfa hay. Transrectal ultrasonography was performed to verify ovulation and corpus luteum (CL) volume before AI (day 0), on days 7 and 15. After ultrasonography on day 15, cows diagnosed without a CL on day 0, but with a CL greater than 0.38 cm3 in volume on days 7 and 15 (2 or 3 cows per pen; CSSO, n = 20; CON, n = 24), were assigned to conceptus collection via transcervical flushing and endometrial biopsy in the uterine horn ipsilateral to the CL. Blood samples were collected for FA analysis on days 0, 7, and 15. Blood was collected from cows not assigned to conceptus collection for whole-blood RNA extraction on day 20 and for pregnancy diagnosis on day 30 by measuring concentrations of pregnancy-associated glycoproteins. Cows receiving CSSO had greater (P ≤ 0.04) mean plasma concentrations of linoleic acid and ω-6 FA compared with CON on days 7 and 15. Moreover, CSSO supplementation increased (P = 0.05) mRNA expression of interferon-tau by the conceptus and blood mRNA expression of interferon-stimulated gene 15 and 20,50-oligoadenylate synthetase on day 20 in gestating cows. Hence, post-AI CSSO supplementation to B. taurus beef cows improved pregnancy rates to timed AI, which can be associated with increased mRNA expression of interferon-tau by the conceptus when CSSO is supplemented during early gestation.
| S-EPMC6095382 | biostudies-literature
Project description:We aimed with this study through RNAseq, found diferentially expressend genes (DEGs) that can be used as a new pregnancy markers in peripheral blood mononuclear cells (PBMC) on day 18 post artificial insemination; and to assess the mRNA profile by RT-qPCR of new pregnancy markers in PBMC and peripheral blood polymorphonuclear cells (PMN) at early pregnancy Methods: Nelore heifers (N=21) were artificially inseminated in a fixed time (D0). On Day 10, 14, 16, 18 and 20, blood was collected for isolation of PBMC and PMN, and P4 concentration assay and color Doppler ultrasonography was performed to evaluate the corpus luteum (CL) . Pregnancy diagnosis was done on Day 28 and heifers were classified in pregant (N=9) and non-pregant (N=12). Heifers (N=6/group) with different (P<0.05) plasma P4 concentration, CL area and blood perfusion on Day 18 were selected and RNAseq was done on PBMC samples. RNAseq analysis indicated 220 DEGs (200 up regulated in P). Twenty DEGs found on RNAseq of PBMC with the highest fold-changes or no overlapping between pregant and non-pregant, were assessed by RT-qPCR from Day10 to 20 (N=6/group). Conclusions: nine DEGs studied by RT-qPCR presented increased expression on PBMC for Pregnant group in at least one-time point from Day16 to 20; but only 4 of these DEGs retained the expression increased on PMN (IFI6, IFI44, RSAD2 and LGALS3BP). Thus, results indicate potential genes to be used as novel pregnancy predictors in immune cells in cattle at early gestation.
2019-08-22 | GSE136102 | GEO