Genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep using parametric models and artificial neural networks.

This study aimed to assess the predictive ability of parametric models and artificial neural network method for genomic prediction of the following indicator traits of resistance to gastrointestinal nematodes in Santa Inês sheep: packed cell volume (PCV), fecal egg count (FEC), and Famacha© method (FAM). After quality control, the number of genotyped animals was 551 (PCV), 548 (FEC), and 565 (FAM), and 41,676 SNP. The average prediction accuracy (ACC) calculated by Pearson correlation between observed and predicted values and mean squared errors (MSE) were obtained using genomic best unbiased linear predictor (GBLUP), BayesA, BayesB, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayesian regularized artificial neural network (three and four hidden neurons, BRANN_3 and BRANN_4, respectively) in a 5-fold cross-validation technique. The average ACC varied from moderate to high according to the trait and models, ranging between 0.418 and 0.546 (PCV), between 0.646 and 0.793 (FEC), and between 0.414 and 0.519 (FAM). Parametric models presented nearly the same ACC and MSE for the studied traits and provided better accuracies than BRANN. The GBLUP, BayesA, BayesB and BLASSO models provided better accuracies than the BRANN_3 method, increasing by around 23% for PCV, and 18.5% for FEC. In conclusion, parametric models are suitable for genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep. Due to the small differences in accuracy found between them, the use of the GBLUP model is recommended due to its lower computational costs.

Economic values and selection index in different Angus-Nellore cross-bred production systems.

Bioeconomic models were developed to calculate economic values (EV) for economically important traits in beef cattle, to evaluate the impact of these traits on production profitability, to assess possible market changes with a payment system and to develop economic selection indexes for Angus cattle for two production systems. Two beef cattle production systems were simulated as follows: a cow-calf cycle (CC) and a complete cycle (CoC). Following selection, positive changes in the EV were observed. In the CC, each 1.0% increment in weaning weight (WW), weaning rate (WR) and pregnancy rate (PR) resulted in increases in US$ 1.30, US$ 3.68 and US$ 3.55 per cow/year in profit, respectively. In the CoC, EV of US$ 1.01, US$ 1.79, US$ 1.19, US$ 1.34, US$ 6.84 and US$ 7.86 per cow/year were obtained for WW, year weight, yearling weight, final weight, WR and PR, respectively. The payment system for carcass quality showed that the scenario considering that 100% of the animals displayed uniform carcasses exhibited the highest EV and was considered optimal. Considering the sensitivity analysis, the price paid per animal was the factor that most affected the EV in both systems. The selection indexes obtained may be used in similar production systems, and the use of EV and selection indexes are important tools for any production system with positive change in profit after selection.

Increased expression of ID2, PRELP and SMOC2 genes in patients with endometriosis.

Endometriosis is a benign, estrogen-dependent disease with symptoms such as pelvic pain and infertility, and it is characterized by the ectopic distribution of endometrial tissue. The expression of the ID2, PRELP and SMOC2 genes was compared between the endometrium of women without endometriosis in the proliferative phase of their menstrual cycle and the eutopic and ectopic endometrium of women with endometriosis in the proliferative phase. Paired tissue samples from 20 women were analyzed: 10 from endometrial and peritoneal endometriotic lesions and 10 from endometrial and ovarian endometriotic lesions. As controls, 16 endometrium samples were collected from women without endometriosis in the proliferative phase of menstrual cycle. Analysis was performed by real-time polymerase chain reaction (PCR). There was no significant difference between gene expression in the endometrium of women with and without endometriosis. The ID2 gene expression was increased in the most advanced stage of endometriosis and in ovarian endometriomas, the PRELP was more expressed in peritoneal lesions, and the SMOC2 was highly expressed in both peritoneal and endometrioma lesions. Considering that the genes studied participate either directly or indirectly in cellular processes that can lead to cell migration, angiogenesis, and inappropriate invasion, it is possible that the deregulation of these genes caused the development and maintenance of ectopic tissue.

Increased expression of ID2, PRELP and SMOC2 genes in patients with endometriosis

Endometriosis is a benign, estrogen-dependent disease with symptoms such as pelvic pain and infertility, and it is characterized by the ectopic distribution of endometrial tissue. The expression of the ID2, PRELP and SMOC2 genes was compared between the endometrium of women without endometriosis in the proliferative phase of their menstrual cycle and the eutopic and ectopic endometrium of women with endometriosis in the proliferative phase. Paired tissue samples from 20 women were analyzed: 10 from endometrial and peritoneal endometriotic lesions and 10 from endometrial and ovarian endometriotic lesions. As controls, 16 endometrium samples were collected from women without endometriosis in the proliferative phase of menstrual cycle. Analysis was performed by real-time polymerase chain reaction (PCR). There was no significant difference between gene expression in the endometrium of women with and without endometriosis. The ID2 gene expression was increased in the most advanced stage of endometriosis and in ovarian endometriomas, the PRELP was more expressed in peritoneal lesions, and the SMOC2 was highly expressed in both peritoneal and endometrioma lesions. Considering that the genes studied participate either directly or indirectly in cellular processes that can lead to cell migration, angiogenesis, and inappropriate invasion, it is possible that the deregulation of these genes caused the development and maintenance of ectopic tissue.

Growth curves of carcass traits obtained by ultrasonography in three lines of Nellore cattle selected for body weight.

The effect of selection for postweaning weight was evaluated within the growth curve parameters for both growth and carcass traits. Records of 2404 Nellore animals from three selection lines were analyzed: two selection lines for high postweaning weight, selection (NeS) and traditional (NeT); and a control line (NeC) in which animals were selected for postweaning weight close to the average. Body weight (BW), hip height (HH), rib eye area (REA), back fat thickness (BFT), and rump fat thickness (RFT) were measured and records collected from animals 8 to 20 (males) and 11 to 26 (females) months of age. The parameters A (asymptotic value) and k (growth rate) were estimated using the nonlinear model procedure of the Statistical Analysis System program, which included fixed effect of line (NeS, NeT, and NeC) in the model, with the objective to evaluate differences in the estimated parameters between lines. Selected animals (NeS and NeT) showed higher growth rates than control line animals (NeC) for all traits. Line effect on curves parameters was significant (P < 0.001) for BW, HH, and REA in males, and for BFT and RFT in females. Selection for postweaning weight was effective in altering growth curves, resulting in animals with higher growth potential.

Follicular fluid from infertile women with mild endometriosis may compromise the meiotic spindles of bovine metaphase II oocytes.

STUDY QUESTION: What is the potential impact of follicular fluid (FF) from infertile women with mild endometriosis (ME) on oocyte quality, especially on nuclear maturation and the meiotic spindle? SUMMARY ANSWER: FF from infertile women with ME may compromise nuclear maturation and the meiotic spindles of in vitro matured bovine oocytes. WHAT IS KNOWN ALREADY: Controversial studies have suggested that impaired oocyte quality may be involved in the pathogenesis of endometriosis-related infertility. Moreover, some studies have demonstrated alterations in the composition of FF from infertile women with endometriosis. However, to date no study has evaluated the effect of FF from infertile women with ME on the genesis of meiotic oocyte anomalies. STUDY DESIGN, SIZE, DURATION: We performed an experimental study. Samples of FF were obtained from February 2009 to February 2011 from 22 infertile women, 11 with ME and 11 with tubal or male factors of infertility (control group), who underwent ovarian stimulation for ICSI at our university IVF Unit. From March 2011 to February 2012 we performed in vitro maturation (IVM) experiments using immature bovine oocytes as described below. PARTICIPANTS/MATERIALS, SETTING, METHODS: FF free of blood and containing a mature oocyte was obtained from 22 infertile women during oocyte retrieval for ICSI. Immature bovine oocytes underwent IVM in the absence of FF (No-FF) and in the presence of four concentrations (1, 5, 10 and 15%) of FF from infertile women without endometriosis (C-FF) and with ME (ME-FF). Eleven replicates were performed, each one using FF from a control patient and a patient with ME. Each FF sample was used in only one experiment. After 22-24 h of IVM, oocytes were denuded, fixed and immunostained for morphological visualization of microtubules and chromatin by confocal microscopy. MAIN RESULTS AND THE ROLE OF CHANCE: A total of 1324 cumulus-oocyte complexes were matured in vitro. Of these, 1128 were fixed and 1048 were analyzed by confocal microscopy. The percentage of meiotically normal oocytes was significantly higher for oocytes that underwent IVM in the absence of FF (No-FF; 76.5%) and in the presence of 1% (80.9%), 5% (76.6%), 10% (75%) and 15% (76.2%) C-FF than in oocytes that underwent IVM in the presence of 1% (44.4%), 5% (36.7%), 10% (45.5%) and 15% (51.2%) ME-FF (P < 0.01). No differences were observed among FF concentrations within each group. When the four concentrations from each group were pooled, the number of oocytes in metaphase I stage was significantly higher in the ME-FF (50 oocytes) than in the C-FF (29 oocytes) group and the percentage of meiotic abnormalities was significantly higher when oocytes were matured with ME-FF (55.8%) than with C-FF (23.1%), P < 0.01. LIMITATIONS, REASONS FOR CAUTION: Owing to the strict selection criteria for FF donors, this study had a small sample size (11 cases and 11 controls), and thus further investigations using a large cohort of patients are needed to confirm these results. In addition, data obtained from studies using animal models may not necessarily be extrapolated to humans and studies evaluating in vivo matured oocytes from infertile women with ME are important to confirm our results. WIDER IMPLICATIONS OF THE FINDINGS: Our results open new insights into the pathogenic mechanisms of infertility related to mild endometriosis, suggesting that FF from infertile women with mild endometriosis may be involved in the worsening of oocyte quality of these women. STUDY FUNDING/COMPETING INTEREST(S): This study was supported by the National Council for Scientific and Technological Development (CNPq), Brazil. The authors declare no conflicts of interest.

Placental hydroxymethylation vs methylation at the imprinting control region 2 on chromosome 11p15.5.

In addition to methylated cytosines (5-mCs), hydroxymethylcytosines (5-hmCs) are present in CpG dinucleotide-enriched regions and some transcription regulator binding sites. Unlike methylation, hydroxymethylation does not result in silencing of gene expression, and the most commonly used methods to study methylation, such as techniques based on restriction enzymatic digestion and/or bisulfite modification, are unable to distinguish between them. Genomic imprinting is a process of gene regulation where only one member of an allelic pair is expressed depending on the parental origin. Chromosome 11p15.5 has an imprinting control region (ICR2) that includes a differentially methylated region (KvDMR1) that guarantees parent-specific gene expression. The objective of the present study was to determine the presence of 5-hmC at the KvDMR1 in human placentas. We analyzed 16 third-trimester normal human placentas (chorionic villi). We compared two different methods based on real-time PCR after enzymatic digestion. The first method distinguished methylation from hydroxymethylation, while the other method did not. Unlike other methylation studies, subtle variations of methylation in ICRs could represent a drastic deregulation of the expression of imprinted genes, leading to important phenotypic consequences, and the presence of hydroxymethylation could interfere with the results of many studies. We observed agreement between the results of both methods, indicating the absence of hydroxymethylation at the KvDMR1 in third-trimester placentas. To the best of our knowledge, this is the first study describing the investigation of hydroxymethylation in human placenta using a genomic imprinting model.

Placental hydroxymethylation vs methylation at the imprinting control region 2 on chromosome 11p15.5

In addition to methylated cytosines (5-mCs), hydroxymethylcytosines (5-hmCs) are present in CpG dinucleotide-enriched regions and some transcription regulator binding sites. Unlike methylation, hydroxymethylation does not result in silencing of gene expression, and the most commonly used methods to study methylation, such as techniques based on restriction enzymatic digestion and/or bisulfite modification, are unable to distinguish between them. Genomic imprinting is a process of gene regulation where only one member of an allelic pair is expressed depending on the parental origin. Chromosome 11p15.5 has an imprinting control region (ICR2) that includes a differentially methylated region (KvDMR1) that guarantees parent-specific gene expression. The objective of the present study was to determine the presence of 5-hmC at the KvDMR1 in human placentas. We analyzed 16 third-trimester normal human placentas (chorionic villi). We compared two different methods based on real-time PCR after enzymatic digestion. The first method distinguished methylation from hydroxymethylation, while the other method did not. Unlike other methylation studies, subtle variations of methylation in ICRs could represent a drastic deregulation of the expression of imprinted genes, leading to important phenotypic consequences, and the presence of hydroxymethylation could interfere with the results of many studies. We observed agreement between the results of both methods, indicating the absence of hydroxymethylation at the KvDMR1 in third-trimester placentas. To the best of our knowledge, this is the first study describing the investigation of hydroxymethylation in human placenta using a genomic imprinting model.

Characterization of the variable cow's age at last calving as a measurement of longevity by using the Kaplan-Meier estimator and the Cox model.

In most studies on beef cattle longevity, only the cows reaching a given number of calvings by a specific age are considered in the analyses. With the aim of evaluating all cows with productive life in herds, taking into consideration the different forms of management on each farm, it was proposed to measure cow longevity from age at last calving (ALC), that is, the most recent calving registered in the files. The objective was to characterize this trait in order to study the longevity of Nellore cattle, using the Kaplan-Meier estimators and the Cox model. The covariables and class effects considered in the models were age at first calving (AFC), year and season of birth of the cow and farm. The variable studied (ALC) was classified as presenting complete information (uncensored = 1) or incomplete information (censored = 0), using the criterion of the difference between the date of each cow's last calving and the date of the latest calving at each farm. If this difference was >36 months, the cow was considered to have failed. If not, this cow was censored, thus indicating that future calving remained possible for this cow. The records of 11 791 animals from 22 farms within the Nellore Breed Genetic Improvement Program ('Nellore Brazil') were used. In the estimation process using the Kaplan-Meier model, the variable of AFC was classified into three age groups. In individual analyses, the log-rank test and the Wilcoxon test in the Kaplan-Meier model showed that all covariables and class effects had significant effects (P < 0.05) on ALC. In the analysis considering all covariables and class effects, using the Wald test in the Cox model, only the season of birth of the cow was not significant for ALC (P > 0.05). This analysis indicated that each month added to AFC diminished the risk of the cow's failure in the herd by 2%. Nonetheless, this does not imply that animals with younger AFC had less profitability. Cows with greater numbers of calvings were more precocious than those with fewer calvings.

Genetic analysis on growth and carcass traits in Nelore cattle.

In this study, the objective was to estimate genetic parameters of body weight at 210 (BW210) and 365 (BW365) days of age in relation to rib eye area (REA), subcutaneous back fat thickness (BF) and rump fat (RF), and their respective genetic trends, in Nelore beef cattle. Estimates of genetic parameters and breeding values for the studied traits were obtained using the REML method. The direct and maternal heritability estimates were respectively: 0.25±0.02 and 0.21±0.01, for BW210, and 0.29±0.02 and 0.09±0.01, for BW365. The heritability estimates for transformed REA, BF and RF were 0.29±0.03, 0.21±0.02 and 0.23±0.03, respectively. There were genetic associations between BW210 and REA, BW365 and REA, and BF and RF, while the other correlations were low. The selection process that was conducted at the farms participating in the breeding program, taking the proposed selection index into consideration, caused genetic changes to these traits.

Genetic associations between age at first calving and heifer body weight and scrotal circumference in Nelore cattle.

Summary Age at first calving (AFC) measures the entry of heifers into the beef cattle production system. This trait can be used as a selection criterion for earlier reproductive performance. Using data from Nelore cattle participating in the 'Program for Genetic Improvement of the Nelore Breed' (PMGRN-Nelore Brazil), bi-trait analyses were performed using the restricted maximum likelihood method, based on an AFC animal model and the following traits: female body weight adjusted to 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted to 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. The heritability estimates for AFC ranged from 0.02 +/- 0.02 to 0.04 +/- 0.02. The estimates of additive direct heritabilities (with standard error) for BW365, BW450, SC365, SC450, SC550 and SC730 were 0.36 +/- 0.07, 0.38 +/- 0.07, 0.48 +/- 0.07, 0.65 +/- 0.07, 0.64 +/- 0.07 and 0.42 +/- 0.07, respectively, and the genetic correlations with AFC were -0.38, -0.33, 0.10, -0.13, -0.13 and 0.06, respectively. In the herds studied, selection for SC365, SC450, SC550 or SC730 should not cause genetic changes in AFC. Selection based on BW365 or BW450 would favor smaller AFC breeding values. However, the low magnitude of direct heritability estimates for AFC in these farms indicates that changes in phenotypical expression depend mostly on non-genetic factors.

Heritability estimates and genetic correlations for body weight and scrotal circumference adjusted to 12 and 18 months of age for male Nellore cattle.

Heritability estimates and genetic correlations were obtained for body weight and scrotal circumference, adjusted, respectively, to 12 (BW12 and SC12) and 18 (BW18 and SC18) months of age, for 10 742 male Nellore cattle. The adjustments to SC12 and SC18 were made using a nonlinear logistic function, while BW12 and BW18 were obtained by linear adjustment. The contemporary groups (CGs) were defined from animals born on the same farm, in the same year and birth season. The mean heritability estimates obtained using the restricted maximum likelihood method in bi-trait analysis were 0.25, 0.25, 0.29 and 0.42 for BW12, BW18, SC12 and SC18, respectively. The genetic correlations were 0.30 ± 0.11, 0.21 ± 0.13, 0.21 ± 0.11, -0.08 ± 0.15, 0.16 ± 0.12 and 0.89 ± 0.04 between the traits BW12 and BW18; BW12 and SC12; BW12 and SC18; BW18 and SC12; BW18 and SC18; and SC12 and SC18. The heritability for SC18 was considerably greater than for SC12, suggesting that this should be included as a selection criterion. The genetic correlation between BW18 and SC12 was close to zero, indicating that these traits did not influence each other. The contrary occurred between SC12 and SC18, indicating that selection using one of these could alter the other. Because of the mean magnitudes of heritabilities in the various measurements of weight and scrotal perimeter, it is suggested that the practice of individual selection for these traits is possible.

Association of an insulin-like growth factor 1 gene microsatellite with phenotypic variation and estimated breeding values of growth traits in Canchim cattle.

A population of 1398 Canchim (CA) cattle was genotyped to assess the association of an insulin-like growth factor 1 (IGF1) gene microsatellite with phenotypic variation and estimated breeding values of pre-weaning, weaning and post-weaning growth traits. After an initial analysis, the IGF1 genotype only had a significant effect (P < 0.05) on birth weight (BW) and weaning weight adjusted to 240 days (WW240). For these two traits, direct and maternal breeding values were estimated using the restricted maximum likelihood (reml). Two analyses were carried out. In the first (Model I), all fixed effects were fitted. In the second (Model II), the fixed effect of the IGF1 genotype was omitted. The estimated genetic and phenotypic components of variance were similar for every trait in both models. For Model I, estimated direct and maternal heritabilities were 0.26 and 0.16 for BW and 0.23 and 0.14 for WW240 respectively. The genetic and phenotypic correlations between BW and WW240 were 0.38 and 0.38 (Model I) and 0.19 and 0.38 (Model II) respectively. Fifty animals were classified according to their direct and maternal breeding values for both traits. Spearman rank-order correlation between animal rankings in the two models was used to assess the effect of including the IGF1 genotype in the model. Non-significant values from this correlation were indicative of a difference in breeding value rankings between the two approaches. The IGF1 gene was found to be associated with phenotypic variation and breeding values in the early phase of growth.

Temporal expression pattern of myostatin transcripts during chicken embryogenesis

No presente estudo, estimou-se a abundância dos transcritos da miostatina foi estimada durante a embriogênese de galinha por análises de RT-PCR competitiva. Níveis basais de mRNA desse gene foram detectados até o estádio HH15, enquanto acúmulos significativos nesses níveis foram observados apenas no estádio HH24, seguido por redução na abundância desses transcritos a partir do estádio HH26. Tais descobertas preliminares proporcionam informações relevantes sobre a ativação do fator de crescimento miostatina durante o desenvolvimento in ovo de aves.