Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum)

The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (P_adj  < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.

Endometrial transcriptional profiling of a bovine fertility model by Next-Generation Sequencing

Studying the multitude of molecular networks and pathways that are potentially involved in a complex trait such as fertility requires an equally complex and broad strategy. Here, we used Next-Generation Sequencing for the characterization of the transcriptional signature of the bovine endometrial tissue. Periovulatory endocrine environments were manipulated to generate two distinctly different fertility phenotypes. Cycling, non-lactating, multiparous Nelore cows were manipulated to ovulate larger (> 13 mm; LF group; high fertility phenotype) or smaller (< 12 mm; SF group) follicles. As a result, greater proestrus estrogen concentrations, corpora lutea and early diestrus progesterone concentrations were also observed in LF group in comparison to SF group. Endometrial cell proliferation was estimated by the protein marker MKI67 on tissues collected 4 (D4) and 7 (D7) days after induction of ovulation. Total RNA extracts from D7 were sequenced and compared according to the transcriptional profile of each experimental group (LF versus SF). Functional enrichment analysis revealed that LF and SF endometria were asynchronous in regards to their phenotype manifestation. Major findings indicated an LF endometrium that was switching phenotypes earlier than the SF one. More specifically, a proliferating SF endometrium was observed on D7, whereas the LF tissue, which expressed a proliferative phenotype earlier at D4, seemed to have already shifted towards a biosynthetically and metabolically active endometrium on D7. Data on MKI67 support the transcriptomic results. RNA-Seq-derived transcriptional profile of the endometrial tissue indicated a temporal effect of the periovulatory endocrine environment, suggesting that the moment of the endometrial exposure to the ovarian steroids, E2 and P4, regulates the timing of phenotype manifestation. Gene expression profiling revealed molecules that may be targeted to elucidate ovarian steroid-dependent mechanisms that regulate endometrial tissue receptivity. Data was deposited in the SRA database from NCBI (SRA Experiment SRP051330) and are associated with the Bio-Project (PRJNA270391). An overview of the gene expression data has been deposited in NCBI's Gene Expression Omnibus (GEO) and is accessible through GEO Series accession number GSE65450. Further assessment of the data in combination with other data sets exploring the transcriptional profile of the endometrial tissue during early diestrus may potentially identify novel molecular mechanisms and/or markers of the uterine receptivity.

The Receptive Endometrial Transcriptomic Signature Indicates an Earlier Shift from Proliferation to Metabolism at Early Diestrus in the Cow

This study aimed to characterize the endometrial transcriptome and functional pathways overrepresented in the endometrium of cows treated to ovulate larger (≥13 mm) versus smaller (≤12 mm) follicles. Nelore cows were presynchronized prior to receiving cloprostenol (large follicle [LF] group) or not (small follicle [SF] group), along with a progesterone (P4) device on Day (D) -10. Devices were withdrawn and cloprostenol administered 42-60 h (LF) or 30-36 h (SF) before GnRH agonist treatment (D0). Tissues were collected on D4 (experiment [Exp.] 1; n = 24) or D7 (Exp. 2; n = 60). Endometrial transcriptome was obtained by RNA-Seq, whereas proliferation and apoptosis were assessed by immunohistochemistry. Overall, LF cows developed larger follicles and corpora lutea, and produced greater amounts of estradiol (D-1, Exp. 1, SF: 0.7 ± 0.2; LF: 2.4 ± 0.2 pg/ml; D-1, Exp. 2, SF: 0.5 ± 0.1; LF: 2.3 ± 0.6 pg/ml) and P4 (D4, Exp. 1, SF: 0.8 ± 0.1; LF: 1.4 ± 0.2 ng/ml; D7, Exp. 2, SF: 2.5 ± 0.4; LF: 3.7 ± 0.4 ng/ml). Functional enrichment indicated that biosynthetic and metabolic processes were enriched in LF endometrium, whereas SF endometrium transcriptome was biased toward cell proliferation. Data also suggested reorganization of the extracellular matrix toward a proliferation-permissive phenotype in SF endometrium. LF endometrium showed an earlier onset of proliferative activity, whereas SF endometrium expressed a delayed increase in glandular epithelium proliferation. In conclusion, the periovulatory endocrine milieu regulates bovine endometrial transcriptome and seems to determine the transition from a proliferation-permissive to a biosynthetic and metabolically active endometrial phenotype, which may be associated with the preparation of an optimally receptive uterine environment.

SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition

Genetic improvement is important for the poultry industry, contributing to increased efficiency of meat production and quality. Because breast muscle is the most valuable part of the chicken carcass, knowledge of polymorphisms influencing this trait can help breeding programs. Therefore, the complete genome of 18 chickens from two different experimental lines (broiler and layer) from EMBRAPA was sequenced, and SNPs and INDELs were detected in a QTL region for breast muscle deposition on chicken chromosome 2 between microsatellite markers MCW0185 and MCW0264 (105,849-112,649 kb). Initially, 94,674 unique SNPs and 10,448 unique INDELs were identified in the target region. After quality filtration, 77% of the SNPs (85,765) and 60% of the INDELs (7828) were retained. The studied region contains 66 genes, and functional annotation of the filtered variants identified 517 SNPs and three INDELs in exonic regions. Of these, 357 SNPs were classified as synonymous, 153 as non-synonymous, three as stopgain, four INDELs as frameshift and three INDELs as non-frameshift. These exonic mutations were identified in 37 of the 66 genes from the target region, three of which are related to muscle development (DTNA, RB1CC1 and MOS). Fifteen non-tolerated SNPs were detected in several genes (MEP1B, PRKDC, NSMAF, TRAPPC8, SDR16C5, CHD7, ST18 and RB1CC1). These loss-of-function and exonic variants present in genes related to muscle development can be considered candidate variants for further studies in chickens. Further association studies should be performed with these candidate mutations as should validation in commercial populations to allow a better explanation of QTL effects.

Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens

Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative trait loci (QTL) related to fat deposition have been detected, the resolution for these regions is low and functional variants are still unknown. The current study was conducted aiming at increasing resolution for a region previously shown to have a QTL associated with fat deposition, to detect novel variants from this region and to annotate those variants to delineate potentially functional ones as candidates for future studies. To achieve this, 18 chickens from a parental generation used in a reciprocal cross between broiler and layer lines were sequenced using the Illumina next-generation platform with an initial coverage of 18X/chicken. The discovery of genetic variants was performed in a QTL region located on chromosome 3 between microsatellite markers LEI0161 and ADL0371 (33,595,706-42,632,651 bp). A total of 136,054 unique SNPs and 15,496 unique INDELs were detected in this region, and after quality filtering, 123,985 SNPs and 11,298 INDELs were retained. Of these variants, 386 SNPs and 15 INDELs were located in coding regions of genes related to important metabolic pathways. Loss-of-function variants were identified in several genes, and six of those, namely LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1, were related to fat deposition. Therefore, these loss-of-function variants are candidate mutations for conducting further studies on this important trait in chickens.

201 USING THE TRANSCRIPTOME SIGNATURE TO PREDICT PREGNANCY SUCCESS IN BEEF COWS AT 6 DAYS AFTER ARTIFICIAL INSEMINATION

Pregnancy success is critical to the profitability of cattle operations. Attempts to reduce high rates of early embryonic loss mainly focus on the critical phase of embryo recognition by maternal tissue. However, the molecular events driving the uterine tissue toward a favourable stage, facilitating the maternal receptivity, are poorly understood. This study aimed to characterise the endometrial transcriptome profiles of pregnant versus nonpregnant beef cows during early pregnancy and attempted to define a potential set of marker genes that can be valuable for predicting pregnancy outcome. Therefore, pluriparous, cyclic Nellore (Bos indicus) cows were synchronized (n = 51) and artificially inseminated (n = 36) at detected oestrus using semen from a single high-fertility bull. Six days after AI (Day 6), jugular blood samples and an endometrial biopsy from the uterine horn contralateral to the ovary containing the CL were collected. Pregnancy diagnosis was performed by ultrasonography on Days 22 and 30. Based on pregnancy outcome, samples were retrospectively allocated to the following groups: pregnant (P; n = 6) and nonpregnant (NP; n = 5). Both groups had similar plasma progesterone concentrations on Day 6 (less than 1 ng mL–1 between lowest and greatest concentrations). Endometrial biopsies were submitted to RNA-Seq analysis in an Illumina single flow cell line (Illumina Inc., San Diego, CA). The 272 685 768 million filtered reads were mapped to the Bos taurus UMD3.1 reference genome and 14 654 genes were effectively analysed for differential expression between groups. Transcriptome data showed that 216 genes are differently expressed when comparing P v. NP endometrial tissue (adjusted P < 0.1). More specifically, 36 genes showed a significantly up-regulated expression for pregnant cows and 180 are up-regulated for non-pregant cows. Functional enrichment and pathway analyses revealed enriched expression of genes associated with extracellular matrix remodelling in NP cows and nucleotide binding, microsome, and vesicular fraction in P cows. From the 40 top-ranked genes, six that were down- and three that were up-regulated in pregnant cows were further analysed by qRT–PCR in an additional 26 cows. Subsequent quantitative expression data were evaluated using multivariate statistics. Both principal component analysis (PCA; R2 = 0.82 and Q2 = 0.40) and orthogonal projections to latent structures analysis (OPLS), using pregnancy as the dependent variable (R2Y = 0.95 and Q2 = 0.86), efficiently separated P from NP animals. In conclusion, this study characterizes a unique set of genes, expressed in the endometrium as early as 6 days after AI, that indicate a receptive state leading to pregnancy success. Furthermore, expression of such genes can be used as potential markers to efficiently predict pregnancy success.

102 SUPPLEMENTATION WITH ESTRADIOL CYPIONATE AT THE ONSET OF A SYNCHRONIZED PROESTRUS ALTERS THE UTERINE GENE EXPRESSION OF SUCKLED ANESTROUS BEEF COWS

The present study evaluated the effect of oestradiol cypionate (ECP) supplementation at the onset of a proestrus [i.e. at progesterone (P4) device removal of the synchronization of ovulation protocol] on the global endometrial gene expression of suckled anestrous beef cows. A total of 12 suckled cows presenting absence of corpus luteum detected by ultrasound received 2 mg of oestradiol benzoate IM and an intravaginal P4 device. Eight days later, P4 devices were removed, and the cows received 500 mg of sodium cloprostenol IM. Cows were blocked according to body condition score and diameter of largest follicle (LF) at P4 device removal and were randomly assigned to receive an IM treatment with 1 mg of ECP (ECP, n = 6) or not (CON, n = 6) at the P4 device removal. All cows received 10 μg of buserelin acetate 48 h after P4 device removal and were timed AI immediately after. Cows presenting a new corpus luteum formed 6 days after the gonadotropin-releasing hormone treatment had an endometrial fragment collected by transcervical biopsy. RNA-Seq analysis was performed and the transcriptome profile was obtained. The significance of differential gene expression was assessed with the package DESEqn 2 v.1.2.10 and the differential expression estimation was based on the GLM followed by the Wald test. The significance threshold was established as an FDR- Benjamini-Hochberg-adjusted P-value of <0.1. The integrated analysis was performed using DAVID database. In total, 135 transcripts were differentially expressed between ECP and CON groups, of which 73 genes were up-regulated by ECP supplementation and 62 genes were up-regulated in the CON cows. Two pathways were overrepresented by the ECP-induced transcripts: pathways in cancer (n = 5 genes) and small cell lung cancer (n = 3 genes). On the other hand, ECP-inhibited transcripts indicated the enrichment of 3 pathways: Parkinson's disease (n = 3 genes), oxidative phosphorylation (n = 3 genes), and Alzheimer's disease (n = 3 genes). More specifically, ECP-induced transcripts associated with pathways in cancer [gene symbol (fold change); respectively] were LAMC3 (1.55), PTCH1 (1.51), PTCH2 (1.52), PIK3R3 (1.22), and PIAS1 (1.18), whereas ECP-inhibited transcripts associated with oxidative phosphorylation were ATP5F1 (1.18), ATP5J (1.24), and NDUFB3 (1.37). Therefore, ECP supplementation at onset of the synchronized proestrous slightly alters the uterine transcriptome. The enriched pathways affected by the ECP supplementation described in this work need to be studied more but these results show candidate pathways that can be associated with uterine environment and receptivity and with possible regulation by oestradiol supplementation given at the onset of the proestrous.

Additional markers to refine the World Health Organization algorithm for diagnosis of pneumonia

INTRODUCTION

WHO guidelines for primary care of children with tachypnea indicate that all should receive antibiotics for presumed pneumonia. These guidelines have led to excessive antibiotic use.

OBJECTIVE

To examine the value of history of previous respiratory distress, chest indrawing and fever, and response to bronchodilator(BD) to refine these guidelines.

DESIGN

Prospective study.

SETTING

Urban tertiary care hospital.

SUBJECTS

Children, between the ages of 6 and 59 months, presenting with cough and tachypnea.

METHODS

182 children were enrolled. Each child had a chest X-ray that was read by two blinded, independent radiologists. Discordance between the two radiologists led to excluding 17 patients. The remaining 165 children were examined for fever and/or chest indrawing, and if they had a history of previous respiratory distress, challenge with a BD. The association of persistent tachypnea after BD and presence of pulmonary infiltrates was recorded.

RESULTS

The median age was 22 months (mean 25.1 +- 14.5 mo) and 75.8% were aged greater than 1 year. There were 58.8% males. Previous respiratory distress occurred in 65.0% and 79.2% of children aged less than 1 year and 1 year, respectively. Pneumonia was radiologically diagnosed in 26/165 (15.8%). 2/40 (5 %) of children without a history of previous respiratory distress had pneumonia diagnosed. Of 125 children with history of previous respiratory distress, pneumonia was identified in 24 (19.2 %). Persistence of tachypnea after BD was associated with pulmonary infiltrate in 14/24 (58.3%), whereas, tachypnea persisted in 32/101 (31.7%) children without pulmonary infiltrates (P = 0.02). The negative predictive value of resolution of tachypnea was 87.3% (95% CI 77.5 93.4). BD non-response was most useful in children without fever and/or with chest indrawing to indicate pneumonia as the cause of the tachypnea.

CONCLUSION

This study indicates that by adding the simple procedures of a history of previous respiratory distress, recording of fever and chest indrawing, and observing the response to bronchodilators, pneumonia can be reliably identified in children presenting with tachypnea and cough. It is probable that this approach to management of children with cough and tachypnea could reduce unnecessary use of antibiotics.