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Background: Intramuscular fat (IMF) enhances marbling, improving meat quality and value. Transcriptome analysis enables the identification of genes and pathways involved in IMF deposition, supporting targeted breeding and nutritional strategies to improve beef quality. Methods: This study used RNA-Seq to compare gene expression in high- (Hereford; Her), moderate- (Holstein Friesian; Hf), and low-marbling (Limousine; Lim) Semitendinosus muscle. Using Illumina’s NovaSeqX Plus, sequencing data underwent quality control with FastQC to remove low-quality reads and adapters, followed by alignment to the bovine genome using HISAT2. Differential expression analysis was performed using DESeq2, and genes were filtered based on a threshold of p-value < 0.05 and |log2FC| > 0.5 to identify significantly regulated genes. Results: A total of 21,881 expressed genes were detected, with 3025 and 7407 significantly differentially expressed in Her and Hf vs. Lim, respectively (|log2FC| > 0.5, p < 0.05). Protein–protein interaction analysis revealed 20 hub genes, including SMAD3, SCD, PLIN2, SHH, SQLE, RXRA, NPPA, NR1H4, PRKCA, and IL10. Gene ontology and KEGG pathway analyses linked these genes to lipid metabolism and IMF-associated pathways, such as PPAR signaling, fatty acid metabolism, and PI3K–Akt signaling. Conclusions: These findings highlight RNA-Seq’s utility in uncovering the genetic basis of marbling and the importance of aligning beef production with consumer demands through genetic improvements. This study aimed to identify breed-independent molecular mechanisms of intramuscular fat deposition and shared metabolic processes in the Semitendinosus muscle to improve beef quality.

The ileal digestible energy (IDE), apparent metabolizable energy (AME), and AME-corrected for zero nitrogen retention (AMEn) values of soybean meal (SBM) and corn grain were determined using the regression method for growing Japanese quails. A reference diet based on corn and SBM was developed to meet all nutritional requirements of growing quails, and test ingredients, including corn and SBM, were replaced as part of the energy source in the reference diet by 100 or 200 g/kg. During the period of 14 to 21 days post-hatch, a total of 375 mixed-sex quail chicks (33.1 ± 1.99 g) were provided with the experimental diet. The chicks were randomly divided into five dietary treatments with five replicates and fifteen birds in each replication. Including SBM to the reference diet resulted in a linear increase in the ileal digestibility of nitrogen (P = 0.014), dry matter (P = 0.035), ether extract (P = 0.013), and energy digestibility (P = 0.039). Including corn or SBM at 100 or 200 g/kg in the reference diet had no effect on AME and AMEn, while nitrogen metabolizability linearly decreased (P = 0.016) with increasing SBM. Based on the regression equations, the IDE, AME, and AMEn values of corn grain were 3438, 3448, and 3217 kcal/kg, respectively. The corresponding values for SBM were 3236, 3301, and 2977 kcal/kg, respectively. The energetic value of major feed elements can improve the precise diet design for developing Japanese quail.

Non-additive genetic effects are important to increase the accuracy of estimating genetic parameters for growth traits. The aim of this study was to estimate genetic parameters and variance components, specially dominance and epistasis genetic effects, for growth traits (birth weight (BW), weaning weight (WW), 3 (W3), 6 (W6), 9 (W9), and 12 (W12) month weight) in Adani goats. Analyses were carried out using Bayesian method via Gibbs sampler animal model by fitting of 18 different models. All fixed effects (sex, type of birth, age of dam, and year) showed significant effects on BW, WW, W3, and W6, whereas the type of birth and age of dam were not significant on W9 and W12. With the best model, direct heritability estimates were 0.347, 0.178, 0.158, 0.359, 0.278, and 0.281 for BW, WW, W3, W6, W9, and W12 traits, respectively. Maternal permanent environmental effect was significant for BW and WW, but maternal genetic effect was significant only for W3. Dominance and epitasis effects were significant almost for all traits and as a proportion of phenotypic variance were ranged from 0.115 to 0.258 and 0.107 to 0.218, respectively. The range of accuracy of breeding values estimated for growth traits with appropriate evaluation models was from 0.521 to 0.652, 0.616 to 0.694, and 0.548 to 0.684 for the all animals, 10% of the best males and 50% of the best females, respectively. When dominance and epistasis effects added to models, the error variance was reduced and the accuracy of estimated breeding values increased. The accuracy of the best model showed a significant difference with the accuracy of other models (p < 0.01). The result of the present study suggests that non-additive genetic effects should be in genetic evaluation models for goat growth traits because of its effect on accuracy of estimated breeding values.

The main goal of breeding programmes is to maximise the genetic improvement of the economic traits of farm animals. Beside the economic traits, the birds' survival has directly influenced on the economic gain. Therefore, this study aimed to investigate the genetic relationship between survival and productive traits in Japanese quail. A total of 1854 records were collected during four generations from 2017 to 2019 in Khorasan Razavi Agricultural Research and Training Centre (KRARTC). Data were used to estimate the genetic correlations among quail survival (S) with egg weight (EW) and body weight gain (BWG) traits. Linear-threshold model was used to estimate (co)variance components, and genetic parameters of traits via the Gibbs sampling method. The heritability of EW was 0.04, and the heritability estimates for survival at different ages ranged from 0.138 to 0.399 in joint analysis with EW. The highest negative genetic correlation between EW and S 0-14 (i.e. survival up to 14 d) was obtained as −0.704. The highest and lowest heritability of weight gain traits for BWG 0-7 and BWG 7-14 were 0.583 and 0.116, respectively. The analyses of BWG traits with survival at different ages revealed that the genetic correlations ranged from 0.015 (between BWG 0-7 and S 0-14 ) to 0.638 (between BWG 0-7 and S 0-7 ). This study showed that the genetic selection for survival at different ages could be effective. On the other hand, selection for BWG 0-7 could also indirectly improve the survival in quails because of the positive and high genetic correlation between BWG 0-7 with S 0-7 . Highlights Genetic improvement of production traits in quail may lead to reduced survival in quail. Studies regarding on the survival of quail were yet not carried out. Heritability of the survival at different ages showed that genetic selection for this trait could improve the survival. Survival at different ages had a negative genetic correlation with egg weight (EW), and body weight gain (BWG) traits after 21 d of old.

Exploration of genetic variance has mostly been limited to additive effects estimated using pedigree data and non-additive effects have been ignored. This study aimed to evaluate the performance of single nucleotide polymorphisms (SNPs) marker models in the mixed and orthogonal framework including both additive and non-additive effects for estimating variances and genomic prediction in four diabetes-related traits in heterogeneous stock mice. Models have performed differently in detecting SNPs affecting traits. Dominance variances explained over 14.7 and 3.8% of genetic and phenotype variance in a Genomic prediction and variance component estimation method (GVCBLUP) framework. Reliabilities of additive Genomic best linear unbiased prediction model (GBLUP) in different traits ranged from 44.8 to 66.6%, for GVCBLUPs framework including both additive and dominance effects (MAD), and 46.1 to 69% for the model including additive effect (MA). Dominance GBLUP reliabilities ranged from 6 to 26.4% for MAD and from 22.5 to 50.5% in the model including dominance (MD). MA and MD had higher reliability for additive and dominance GBLUPs compared to MAD. Reliabilities of GBLUPs in MAD and MA for all traits were not significant except for growth slope (P < 0.01). In orthogonal framework models, epistasis variances accounted for a greater proportion (87.3, 89.1, 95.5, and 77.2%) of genetic variation for end weight, growth slope, body mass index, and body length, respectively. Heritability in a broad sense was estimated at 1.12, 1.67, 3.64, and 2.0%, in which non-additive heritability had a significant contribution. Genetic variances explained by dominance using GVCBLUPs were 16.8, 29.4, 14.6, and 14.9% for the traits. Generally, the non-additive models had a lower value of deviance information criterion (DIC) and performed better in estimating the variance component. Comparing the estimated variance by orthogonal framework models confirmed the results previously estimated by GVCBLUPs, with the difference that the estimates were shrinking. Following significant SNPs affecting diabetes-related traits by post-genome-wide studies could reveal unknown aspects and contribute to genetic control of the disease.

Small-scale fisheries substantially contribute to the reduction of poverty, local economies and food safety in many countries. However, limited and low-quality catches and effort data for small-scale fisheries complicate the stock assessment and management. Bayesian modelling has been advocated when assessing fisheries with limited data. Specifically, Bayesian models can incorporate information of the multiple sources, improve precision in the stock assessments and provide specific levels of uncertainty for estimating the relevant parameters. In this study, therefore, the state-space Bayesian generalised surplus production models will be used in order to estimate the stock status of fourteen Demersal fish species targeted by small-scale fisheries in Sistan and Baluchestan, Iran. The model was estimated using Markov chain Monte Carlo (MCMC) and Gibbs Sampling. Model parameter estimates were evaluated by the formal convergence and stationarity diagnostic tests, indicating convergence and accuracy. They were also aligned with existing parameter estimates for fourteen species of the other locations. This suggests model reliability and demonstrates the utility of Bayesian models. According to estimated fisheries’ management reference points, all assessed fish stocks appear to be overfished. Overfishing considered, the current fisheries management strategies for the small-scale fisheries may need some adjustments to warrant the long-term viability of the fisheries.

Abstract Minimizing bird mortality in the commercial quail breeding industry is important from an economic and welfare perspective. Genetic and non-genetic factors can influence on the cumulative survival of the birds (CS). Accordingly, this study aimed to investigate non-genetic factors on CSs (cumulative survival of the birds from hatch to 5 (CS1), 10 (CS2), 15 (CS3), 20 (CS4), 25 (CS5), 30 (CS6), 35 (CS7), 40 (CS8), and 45 (CS9) days of age), and estimation of the genetic parameters for CSs in crossbred population of quail. Data set included 1794 records from crossbred chicks hatched from 70 sires and 72 dams. The fixed effects were analyzed using an animal model by ASReml software, and all traits were analyzed using Bayesian method via Gibbs sampling by fitting of 6 threshold animal models including the direct genetic effect, the maternal permanent environmental effect, and the maternal genetic effect. The best fitted model for each trait was selected based on the deviance information criteria. Hatch number, the month of hatch, and combination of chickens showed a significant effect on CSs, but the sex of chickens does not have a significant effect on CSs. However, females have higher survival than males (except for CS1). With the best model, the highest and lowest direct heritability was estimated for CS5 (0.386) and CS3 (0.250), respectively. The maternal genetic effect was significant for CS1, CS2, CS3, and CS4 traits, but the maternal permanent environmental effect was significant only for CS1. The range of maternal heritability for CS1 to CS4 traits was estimated from 0.064 to 0.111, and ratio of the permanent environmental variance to phenotypic variance for CS1 was 0.021. The result showed that increasing of the birds’ survival could be performed by correcting non-genetic factors and genetic selection for CSs considering the maternal genetic effects in younger ages.Highlights• In the commercial quail breeding industry, the bird mortality is important from an economic and welfare perspective.• Improving quail survival can be achieved by controlling the genetic and non-genetic factors affecting on survival, so knowledge of these factors is necessary.• The combination of crossbred chickens had a significant effect on cumulative survival traits.• The Cumulative survival traits in the crossbred population had relatively high genetic diversity, so genetic selection for these traits could be effective.

The present study was conducted to evaluate aflatoxin B1 (AFB1) detoxification effects of some medicinal plants under both in vitro and in vivo. The in vitro experiment was performed with 25 treatments in 5 replications. The samples of medicinal plants were incubated with AFB1 for 72 h, and the toxin residual in the supernatant was determined. The highest aflatoxin elimination was found to be related to peppermint (81%). Thereafter, in vivo experiment was conducted to investigate the effects of peppermint dried leaves, essential oil, and menthol on liver, bone, and meat, as well as the performance of growing Japanese quail fed diet contaminated with AFB1. A total of 640 7-day-old Japanese quails were assigned using a completely randomized design as 2 × 4 factorial arrangement with two levels of AFB1 (including 0 and 2.5 mg/kg diet) and four treatments (including no additive; peppermint powder, 20 g/kg; peppermint essential oil, 800 mg/kg; and menthol powder, 400 mg/kg). Those birds fed AFB1-contaminated diet with no additives showed the worst liver health status by considering super oxide dismutase (P = 0.0399), glutathione peroxidase (P = 0.0139), alanine aminotransferase (P < 0.0001), and aspartate aminotransferase levels (P = 0.0512). However, the supplementation of AFB1 contaminated diet with additives improved their liver health status. Menthol receiving birds showed the highest tibia strength, while the birds fed with AFB1-contaminated diet with no additives had the weakest bone strength (P < 0.0001). A significant increase was also observed in malondialdehyde level of meat by dietary inclusion of AFB1, which was well-repressed by the dietary supplementation of peppermint essential oil and menthol (P = 0.0075). Body weight gain dramatically decreased by adding AFB1 to the diet, which was recovered with the dietary supplementation of additives (P = 0.0585). According to the results of the current study, peppermint and its derivatives can be used to suppress aflatoxin effects on the liver, bone, and meat quality and to improve the performance of Japanese quails.

Abstract Improved feed efficiency (FE) is one of the most important achievements in animal breeding programs. The present investigation aimed to determine the phenotypic correlations of residual feed intake (RFI) breeding value with some traits in growing Japanese quail. A total of 48 birds (24 males and 24 females) were selected from 220 quail chicks divided into three classes based on breeding values (BV) for RFI including low (LBV;n= 16), medium (MBV;n= 16), and high-BV (HBV;n= 16) were used to test FE. The effects of three groups of BV on the studied traits including carcass traits, meat quality, humoral immunity, and bone properties were evaluated. The BV for RFI was positively correlated with feed conversion ratio (FCR) and feed intake (FI) but not with metabolic BW (MBW0.75). Live body weight, carcass, breast, and thigh weight in the LBV-RFI group were significantly greater than those in the HBV-RFI group. The BV for RFI had a negative correlation with live body weight and thigh weight. Our findings suggested that the selection of LBV-RFI quails may be useful to increase live body weight without any adverse impact on meat quality and bone properties, and live body weight can be implemented in breeding programs as an indirect selection indicator for improvement of FE in quails.

Glioblastoma multiforme (GBM) is considered to be one of the most invasive human cancers, characterized by a high mortality rate and an average survival is <1 year. These tumors are highly aggressive and insensitive to conventional radio and chemotherapy. An interesting aspect of glioblastoma is the association of active human cytomegalovirus (HCMV) infection, which is evident by the presence of viral DNA, mRNA and protein level in most glioblastoma tissues. Although the presence of the HCMV infection in glioblastoma is well established, but the oncomodulatory role of HCMV is not defined yet. Enhancer of zeste human homolog 2 ( EZH2 ) is a key protein of the polycomb repressive complex 2, epigenetic gene silencers. There have been several reports that EZH2 activity is essential in GBM pathogenesis. In our previous research, we have found a high rate of HCMV infection in a cohort of Iranian glioblastoma patients. In this study, we investigated the expression of EZH2 in HCMV-negative versus HCMV-positive GBM tissues in comparison to non-tumor tissues. The level of expression was determined by real time PCR and the differences were calculated using the Livac or 2 −ΔΔCt and analysis of variance (ANOVA). Relative expression of EZH2 in HCMV-negative glioblastoma tissues were increased 6.053-fold compared to non-neoplastic brain tissues, while EZH2 gene expression was increased 41.098-fold in HCMV-positive glioblastoma tissues. ANOVA test showed that there is a significant difference in EZH2 expression between normal brain tissue, HCMV-negative and HCMV-positive glioblastoma tumors ( p value = 0.0001). Our data indicate that EZH2 expression can be considered a risk factor in glioblastoma and EZH2 inhibitors may serve as potential new treatment in glioblastoma. This would be an interesting new field to investigate in more detail.