Differential gene expression in cumulus oocyte complexes collected by ovum pick up from repeat breeder and normally fertile Holstein Friesian heifers

Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement

Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.

Current Insights in the Repeat Breeder Cow Syndrome

Cows can have difficulties becoming pregnant, and in certain cases, these reproductive failures do not have an evident cause. Furthermore, when these failures are repeated three or more times with estrous cycles of normal duration and in the absence of evident clinical signs, it is considered repeat breeder cow (RBC) syndrome. A substantive incidence of RBC syndrome has been reported all over the world, which severely affects the farm economy. This paper reviews those studies particularly focused on RBC syndrome from 2000 to 2023 but also includes consolidated information until this date. Hormonal imbalances, undetectable oviductal or uterine defects, or poor oocyte or embryo quality have been reported as causes of RBC syndrome, while subclinical endometritis has been considered a relevant causal agent. However, it is unresolved why this condition is recurrent in certain animals, despite the implementation of corrective management actions or treatments. Recent studies evaluate the putative role of certain genes, factors, hormones, or proteins in the pathogenesis of RBC syndrome. Numerous risk factors contribute to the appearance of this syndrome, and some of them could be mitigated to partially prevent this infertility, while others cannot be changed. Due to the complexity of this syndrome, it is important to increase knowledge about the mechanisms involved, develop new diagnostic tools to differentiate causal agents, and implement new treatments to restore fertility. There is consensus about the huge repercussions of this syndrome on farm profitability, but further studies are now needed to describe its economic impact.

Ovarian luteal category at the time of exogenous progesterone treatment alters pre-ovulatory follicle size and pregnancy outcome but not initial GnRH treatment in repeat-breeder crossbred dairy heifers submitted to the 7-day fixed-time AI protocol

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Ovarian and fertility outcomes were similar for repeat-breeder crossbred dairy heifers with or without initial GnRH treatment.

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Presence of luteal tissue at the time of progesterone (P4) treatment in infertile heifers resulted in a 68.6% pregnancy rate (PR).

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The likelihood of PR was higher in infertile heifers bearing luteal tissue on the day of exogenous P4 trigger.

Repeat breeding is a substantial problem in heifer and cow breeding leading to greater infertility for female dairy herds. The aim of present study was to investigate the impact of corpus luteum (CL) presence and category and the first gonadotropin-releasing hormone (GnRH) administration concurrent with exogenous progesterone (P4) treatment on the largest follicle (LF) size and pregnancy rate (PR) in repeat-breeder crossbred dairy heifers submitted to the fixed-time artificial insemination (AI) protocol. Heifers (n= 243) were synchronised with (+GnRH) or without (–GnRH) first GnRH in the 7-day P4-GnRH-prostaglandin F2α-based programme. Each GnRH group was divided on presence of CL into two groups (+CL and –CL) in a 2 × 2 factorial arrangement. The PR was similar among –GnRH–CL (20.7%), –GnRH+CL (68.8%), +GnRH–CL (30.4%), and +GnRH+CL (68.3%) groups. However, presence of CL in heifers produced a 43.6% increase in PR compared to PR of heifers without CL (odds ratio = 6.550). Heifers bearing large-sized CL had greater large-sized LF on the day of fixed-time AI and PR. Plasma P4 concentration was positively related with CL diameter (r= 0.845; p < 0.001). The diameter of ovarian LF on the day of fixed-time AI was positively associated with P4 concentrations (r= 0.512; p < 0.001). We highlight that ovarian CL presence and category at the time of exogenous P4 treatment alters pre-ovulatory follicle size and PR but not initial GnRH treatment in repeat-breeder crossbred dairy heifers submitted to service with the 7-day fixed-time AI programme.

Bovine models for human ovarian diseases

During early embryonic development, late fetal growth, puberty, adult reproductive years, and advanced aging, bovine and human ovaries closely share molecular pathways and hormonal signaling mechanisms. Other similarities between these species include the size of ovaries, length of gestation, ovarian follicular and luteal dynamics, and pathophysiology of ovarian diseases. As an economically important agriculture species, cattle are a foundational species in fertility research with decades of groundwork using physiologic, genetic, and therapeutic experimental techniques. Many technologies used in modern reproductive medicine, such as ovulation induction using hormonal therapy, were first used in cows before human trials. Human ovarian diseases with naturally occurring bovine correlates include premature ovary insufficiency (POI), polycystic ovarian syndrome (PCOS), and sex-cord stromal tumors (SCSTs). This article presents an overview of bovine ovary research related to causes of infertility, ovarian diseases, diagnostics, and therapeutics, emphasizing where the bovine model can offer advantages over other lab animals for translational applications.

Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes

Background

Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic.

Results

There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits.

Conclusions

These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08555-z.

The effects of H22 tumor on the quality of oocytes and the development of early embryos from host mice: A single-cell RNA sequencing approach

The association between cancer and female reproduction remains largely unknown. Here we investigated the quality of oocytes and the developmental potential of zygotes using H22 tumor-bearing mice model. The results showed that the number of oocytes was decreased in tumor-bearing mice compared with the control mice, and accompanied scattered chromosomes was observed. Further study revealed an abnormal epigenetic reprogramming occurred in the zygotes from the H22 tumor-bearing mice, as exemplified by the aberrant 5hmC/5mC modifications in the pronuclei. Finally, single-cell RNA sequencing was performed on the oocytes collected from the H22 tumor-bearing mice. Our data showed that 45 of the 202 differentially expressed genes in tumor-bearing group were closely associated with oocyte quality. Protein interaction analysis indicated that the potential interaction among these 45 genes. Collectively, our study uncovered that the quality of oocytes and early embryonic development were affected by H22 tumor bearing via the altered expression patterns of genes related with reproduction, providing new insights into the reproductive capability of female cancer patients.

Lactoferrin levels in cervical fluid from in vitro fertilization (IVF) patients - correlation with IVF parameters

Since our previous results suggest that lactoferrin (LF) might have roles in the reproductive process and that its levels might change in the female tract as a response to various factors, the aim of this investigation was to assess whether LF levels in cervical secretions correlate with reproductive parameters from in vitro fertilization (IVF) patients. Cervical fluid samples were obtained from 34 women under 40 years old enrolled for assisted reproduction techniques, and LF concentration was measured. The mean total protein concentration in all cervical fluid samples was 842.8 ± 116.9 µg/mL. The mean concentration of LF was 0.73 ± 0.06 ng LF/µg of total proteins. We observed that higher LF levels in cervical fluid correlated with lower IVF rates when all patients were analyzed; this negative correlation was also sustained when only patients ≥35 years were studied. The mean LF concentration in cervical fluid was significantly lower among patients with normal IVF rates than in those with values 50% or less. Using a LF cutoff value of 0.83 ng/μg of total proteins, the study revealed a significant association between the LF levels below 0.83 ng/µg of total proteins and IVF rates above 50%. LF levels in cervical mucus could potentially be used as a marker of fertilization outcome.

Improvement of fertility in repeat breeder dairy cattle by embryo transfer following artificial insemination: possibility of interferon tau replenishment effect

Repeat breeder cattle do not become pregnant until after three or more breeding attempts; this represents a critical reproductive disorder. Embryo transfer (ET) following artificial insemination (AI) in repeat breeder cattle reportedly improves pregnancy rate, leading to speculation that interferon tau (IFNT) is associated with this phenomenon. However, the reason why the conception rate improves remains unknown. We investigated the effect of ET following AI on repeat breeder cattle in field tests, and determined whether adding an embryo affects the maternal immune cells detected by interferon-stimulated genes (ISGs), marker genes of IFN response. In total, 1122 repeat breeder cattle were implanted with in vitro fertilization (IVF) embryos after previous AI. ET following AI resulted in pregnancy rates of 46.9% in repeat breeder dairy cattle. In basic in vivo tests, to investigate the effect of adding embryos, ISGs mRNA expression levels were significantly higher in the AI + ET group than in the AI + sham group (transfer of only embryonic cryopreservation solution). Then, we examined the effect of cultured conditioned media (CM) of IVF embryos on splenic immune cells and Madin-Darby bovine kidney (MDBK) cells with stably introduced ISG15 promoter-reporter constructs. These cells exhibited a specific increase in ISG15 mRNA expression and promoter activity when treated with the CM of IVF embryos, suggesting that IVF embryos have the potential to produce and release IFNT. In conclusion, ET following AI is beneficial for improving conception in repeat breeder cattle. Added embryos may produce and secrete IFNT, resulting in the increased expression of ISGs.

Interferon-stimulated gene 20-kDa protein (ISG20) in infection and disease: Review and outlook

Interferon-stimulated exonuclease gene 20 (ISG20) is an RNA exonuclease in the yeast RNA exonuclease 4 homolog (REX4) subfamily and the DEDDh exonuclease family, and this gene codes for a 20-kDa protein. Those exonucleases are involved in cleaving single-stranded RNA and DNA. ISG20 is also referred to as HEM45 (HeLa estrogen-modulated, band 45). Expression of ISG20 can be induced or regulated by both type I and II interferons (IFNs) in various cell lines. ISG20 plays a role in mediating interferon's antiviral activities. In addition, ISG20 may be a potential susceptibility biomarker or pharmacological target in some inflammatory conditions. Exonucleases are useful components of many physiological processes. Despite recent advances in our understanding of the functions of ISG20, much work remains to be done with regard to uncovering the mechanism of action of ISG20 in specific diseases and adapting ISG20 for use as a biomarker of disease. This review describes current information on ISG20 and its potential use in marking disease. This review describes several research achievements thus far and it seeks to provide some new ideas for future related research.

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.

Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection

BACKGROUND

A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds.

RESULTS

A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production.

CONCLUSIONS

Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production.

Biomedical applications of ovarian transvaginal ultrasonography in cattle

Ovarian transvaginal ultrasonography (OTU) has been used world-wide for commercial ovum pick-up programs for in vitro embryo production in elite herds, providing an excellent model for the elucidation of factors controlling bovine oocyte developmental competence. Noninvasive sampling and treatment of ovarian structures is easily accomplished with bovine OTU techniques providing a promising system for in vivo delivery of transgenes directly into the ovary. The current review summarizes existing bovine OTU models and provides prospective applications of bovine OTU to undertake research in reproductive topics of biomedical relevance, with special emphasis on the development of in vivo gene transfer strategies.

Differences in cytoplasmic maturation between the BCB+ and control porcine oocytes do not justify application of the BCB test for a standard IVM protocol

The Brilliant Cresyl Blue (BCB) test relies on G6PDH activity and a simple protocol for the selection of higher quality oocytes. Although the BCB+ oocytes of all the species that have been investigated are characterized by superior quality when compared to BCB- counterparts, application of the test for embryo production still remains an open issue. The aim of our study was to compare BCB+ and the control oocytes (not subjected to the BCB test) in terms of selected aspects of cytoplasmic maturation (mtDNA copy number, mitochondria distribution, relative transcript abundance of six marker genes). The results of our study revealed more relevant differences within the BCB+ and the control oocytes (before and after IVM) than between the two categories of oocytes. There was no difference in the transcript abundance of the BCB+ and the control oocytes in 5 out of 6 analyzed genes (BMP15, GDF9, ATP5A1, EEF1A, ZAR1) and in mtDNA content (pre-IVM 179609 vs. 176595 and post-IVM 187243 vs. 246984, respectively). With regard to mitochondria distribution in pre- and post-IVM oocytes, there was nonsignificant tendency for a more frequent occurrence of the expected patterns in the BCB+ group. The results of the present study do not support the application of BCB staining in a routine IVM protocol due to relatively high similarity in selected parameters characterizing cytoplasmic maturation of BCB+ and control oocytes. This high similarity may results from the limited amount of less competent BCB- oocytes (10%) still present among nonselected oocytes of proper morphology.