X chromosome variants are associated with male fertility traits in two bovine populations.

BACKGROUND: Twenty-five phenotypes were measured as indicators of bull fertility (1099 Brahman and 1719 Tropical Composite bulls). Measurements included sperm morphology, scrotal circumference, and sperm chromatin phenotypes such as DNA fragmentation and protamine deficiency. We estimated the heritability of these phenotypes and carried out genome-wide association studies (GWAS) within breed, using the bovine high-density chip, to detect quantitative trait loci (QTL). RESULTS: Our analyses suggested that both sperm DNA fragmentation and sperm protamine deficiency are heritable (h2 from 0.10 to 0.22). To confirm these first estimates of heritability, further studies on sperm chromatin traits, with larger datasets are necessary. Our GWAS identified 12 QTL for bull fertility traits, based on at least five polymorphisms (P < 10-8) for each QTL. Five QTL were identified in Brahman and another seven in Tropical Composite bulls. Most of the significant polymorphisms detected in both breeds and nine of the 12 QTL were on chromosome X. The QTL were breed-specific, but for some traits, a closer inspection of the GWAS results revealed suggestive single nucleotide polymorphism (SNP) associations (P < 10-7) in both breeds. For example, the QTL for inhibin level in Braham could be relevant to Tropical Composites too (many polymorphisms reached P < 10-7 in the same region). The QTL for sperm midpiece morphological abnormalities on chromosome X (QTL peak at 4.92 Mb, P < 10-17) is an example of a breed-specific QTL, supported by 143 significant SNPs (P < 10-8) in Brahman, but absent in Tropical Composites. Our GWAS results add evidence to the mammalian specialization of the X chromosome, which during evolution has accumulated genes linked to spermatogenesis. Some of the polymorphisms on chromosome X were associated to more than one genetically correlated trait (correlations ranged from 0.33 to 0.51). Correlations and shared polymorphism associations support the hypothesis that these phenotypes share the same underlying cause, i.e. defective spermatogenesis. CONCLUSIONS: Genetic improvement for bull fertility is possible through genomic selection, which is likely more accurate if the QTL on chromosome X are considered in the predictions. Polymorphisms associated with male fertility accumulate on this chromosome in cattle, as in humans and mice, suggesting its specialization.

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing.

Animal metagenomic studies, in which host-associated microbiomes are profiled, are an increasingly important contribution to our understanding of the physiological functions, health and susceptibility to diseases of livestock. One of the major challenges in these studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of metagenomic profiling. This is the first study comparing the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. We compared the new method of Oxford Nanopore Technologies (ONT) adaptive sequencing, which can be used to target or eliminate defined genetic sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. The efficiency of each method in recovering the metagenomic data and recalling the metagenomic profiles was assessed. ONT adaptive sequencing yielded a higher amount of metagenomic data than the other methods per 1 Gb of sequence data. The increased sequencing efficiency of ONT adaptive sequencing consequently reduced the amount of raw data needed to provide sufficient coverage for the metagenomic samples with high host-to-microbe DNA ratio. Additionally, the long reads generated by ONT adaptive sequencing retained the continuity of read information, which benefited the in-depth annotations for both taxonomical and functional profiles of the metagenome. The different methods resulted in the identification of different taxa. Genera Clostridium, which was identified at low abundances and categorized under Order "Unclassified Clostridiales" when using the 16S rDNA amplicon sequencing method, was identified to be the dominant genera in the sample when sequenced with the three other methods. Additionally, higher numbers of annotated genes were identified with ONT adaptive sequencing, which also produced high coverage on most of the commonly annotated genes. This study illustrates the advantages of ONT adaptive sequencing in improving the amount of metagenomic data derived from microbiome samples with high host-to-microbe DNA ratio and the advantage of long reads in preserving intact information for accurate annotations.

Candidate Gene Expression in Bos indicus Ovarian Tissues: Prepubertal and Postpubertal Heifers in Diestrus.

Growth factors such as bone morphogenetic proteins 6, 7, 15, and two isoforms of transforming growth factor-beta (BMP6, BMP7, BMP15, TGFB1, and TGFB2), and insulin-like growth factor system act as local regulators of ovarian follicular development. To elucidate if these factors as well as others candidate genes, such as estrogen receptor 1 (ESR1), growth differentiation factor 9 (GDF9), follicle-stimulating hormone receptor (FSHR), luteinizing hormone receptor (LHR), bone morphogenetic protein receptor, type 2 (BMPR2), type 1 insulin-like growth factor receptor (IGFR1), and key steroidogenic enzymes cytochrome P450 aromatase and 3-ß-hydroxysteroid dehydrogenase (CYP19A1 and HSD3B1) could modulate or influence diestrus on the onset of puberty in Brahman heifers, their ovarian mRNA expression was measured before and after puberty (luteal phase). Six postpubertal (POST) heifers were euthanized on the luteal phase of their second cycle, confirmed by corpus luteum observation, and six prepubertal (PRE) heifers were euthanized in the same day. Quantitative real-time PCR analysis showed that the expression of FSHR, BMP7, CYP19A1, IGF1, and IGFR1 mRNA was greater in PRE heifers, when contrasted to POST heifers. The expression of LHR and HSD3B1 was lower in PRE heifers. Differential expression of ovarian genes could be associated with changes in follicular dynamics and different cell populations that have emerged as consequence of puberty and the luteal phase. The emerging hypothesis is that BMP7 and IGF1 are co-expressed and may modulate the expression of FSHR, LHR and IGFR1, and CYP19A1. BMP7 could influence the downregulation of LHR and upregulation of FSHR and CYP19A1, which mediates the follicular dynamics in heifer ovaries. Upregulation of IGF1 expression prepuberty, compared to postpuberty diestrus, correlates with increased levels FSHR and CYP19A1. Thus, BMP7 and IGF1 may play synergic roles and were predicted to interact, from the expression data (P = 0.07, r = 0.84). The role of these co-expressed genes in puberty and heifers luteal phase merits further research.

Variability and laboratory factors affecting the sperm chromatin structure assay in human semen.

During the past decade, the sperm chromatin structure assay (SCSA) has become an important tool for assessing semen quality in the human andrology laboratory. The SCSA uses the metachromatic properties of the fluorescent dye acridine orange (AO) in combination with flow cytometry to determine the sperm DNA susceptibility to denaturation in situ. The objective of this study was to evaluate laboratory factors affecting the SCSA and the variation between replicates. Semen ejaculates from 3 healthy volunteers were analyzed using the SCSA protocol as described by Evenson and Jost (2000), determining the X-mean, Y-mean, DNA fragmentation index (DFI), standard deviation of DFI (SD-DFI), and high DNA stainability (HDS). In experiment 1, the effects of thawing time, time of day, day, laboratory technician, donor, and incubation period before analysis were investigated. In experiment 2, the effects of sheath fluid, AO equilibration buffer, day, laboratory technician, donor, and incubation period before analysis were investigated. A significant difference was found between the 3 donors with respect to the X-mean, Y-mean, DFI, SD-DFI, and HDS. It was shown that incubation of the semen samples on ice postthaw had a significant effect on the X-mean, Y-mean, DFI, and SD-DFI. The laboratory technician conducting the analysis accounted for up to 15.4% for the variation of the SCSA measurements. The time of day affected the variation for the Y-mean (23.5% of the total variation of the Y-mean), and the day affected the variation for the X-mean (82.8% of the total variation of the X-mean). Incubation on ice for 5 to 25 minutes postthaw had a significant effect on the DFI and SD-DFI in both experiments. This study shows that several protocol steps in the SCSA affect the results obtained from the assay. Precise protocol description and standardization of the SCSA are therefore essential to achieve high agreement within and between different laboratories.

Increasing storage time of extended boar semen reduces sperm DNA integrity.

There is an extensive use of artificial insemination (AI) in the pig industry. Extended liquid boar semen may be used for insemination for up to 5 days after collection. The objective of this study was to determine the changes in sperm quality, when boar semen was extended and stored at 18 degrees C for up to 72 h post-collection. The study included three ejaculates from five boars, for each of the four breeds: Duroc, Hampshire, Landrace and Danish Large White (n=60 ejaculates). The sperm chromatin structure assay (SCSA) showed an increase in DNA fragmentation index (DFI) after 72 h of incubation (P<0.001), with no differences between breeds (P=0.07). For two Hampshire boars, all ejaculates had a large increase in DFI after 24 h of incubation. The standard deviation of DFI (SD-DFI) differed between breeds, with the SD-DFI for Hampshire being significantly greater than for the other breeds. The SD-DFI did not change during the 72 h of storage. Sperm viability was determined using SYBR-14 and propidium iodide in combination with flow cytometry. The sperm viability did not differ between breeds (P=0.21), but a difference in viability during storage (P<0.001) was detected. In conclusion, the SCSA cytogram patterns were consistent for different ejaculates within boars and storage of extended boar semen at 18 degrees C for 72 h significantly decreased the integrity of sperm DNA.

DNA integrity in sexed bull sperm assessed by neutral Comet assay and sperm chromatin structure assay.

During the production of sex-sorted spermatozoa from bull semen, the cells are exposed to a number of potential hazards including: dilution, centrifugation, incubation, exposure to DNA stains and laser light. These factors may affect the survival capacity and fertilization potential of the sperm. The objective of this study was to determine whether sex-sorted bull spermatozoa have more DNA damage than sperm from conventional processed bull semen. Two methods were used to determine DNA integrity: the neutral Comet assay (NCA) and the sperm chromatin structure assay (SCSA). The NCA showed that the conventional samples had a higher tail moment (TM) (P < 0.017) than the sorted samples and that there was no difference between the samples in tail length (TL) (P = 0.36). The SCSA showed that the DNA fragmentation index (DFI) was higher for conventional than the sorted samples (P = 0.011), but the standard deviation of DFI (SD-DFI) was higher for the sorted samples (P < 0.001). We conclude that the NCA and SCSA can be used in assessing DNA integrity in bovine sperm and that cell sorting by flow cytometry improves the integrity of the sperm cell population. Additionally the results from the SCSA indicated that the sex-sorted sperm had less homogenous sperm chromatin. In the future assessment of sperm DNA integrity may be used to select bulls for sperm sex sorting and optimizing sperm sex sorting procedures.

Sperm chromatin in beef bulls in tropical environments.

Sperm chromatin status was assessed in 565 Zebu and Zebu crossbred beef bulls in extensive tropical environments using the sperm chromatin structure assay (SCSA). The SCSA involved exposure of sperm to acid hydrolysis for 0.5 or 5.0 minutes, followed by flow cytometry to ascertain relative amounts of double-stranded (normal) and single-stranded (denatured) DNA, which was used to generate a DNA fragmentation index (%DFI). With conventional SCSA (0.5-minute SCSA), 513 bulls (91%) had <15 %DFI, 24 bulls (4%) had 15 to 27 %DFI, and 28 bulls (5%) had >27 %DFI. In 5.0-minute SCSA, 432 bulls (76%) had <15 %DFI, 68 bulls (12%) had 15 to 27 %DFI and 65 bulls (12%) had >27 %DFI. For most bulls, the SCSA was repeatable on two to four occasions; however, because most bulls had <15 %DFI, repeatability of the SCSA will need to be determined in a larger number of bulls in the 15 to 27 %DFI and >27 %DFI categories. The %DFI was negatively correlated with several bull semen parameters and the strongest negative correlation was with normal sperm. There was a strong positive correlation between %DFI and sperm head abnormalities. Based on these findings, most Zebu beef bulls in extensive tropical environments had relatively stable sperm chromatin. Based on the apparent negative correlations with conventional semen parameters, we inferred that the SCSA measured a unique feature of sperm quality, which has also been suggested for other species. Further studies on the relationships between sperm chromatin stability and fertility are required in beef bulls before chromatin status can be used as an additional predictor of the siring capacity of individual bulls in extensive multiple-sire herds.