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Background: Our hypothesis centred on the potential to mitigate ascites outbreaks in birds exposed to cold stress by inhibiting pulmonary artery contraction through dietary intervention. Objective: This study aimed to evaluate the effect of natural and synthetic medications on growth performance, ascites‐related parameters and the expression of ascites‐related genes in the lung tissue of broiler chickens under low ambient temperature. Methods: We randomly assigned 450 one‐day‐old male Ross 308 chicks to six dietary treatments across five replicate pens, each containing 15 chicks. The treatments included a basal diet (control), and the basal diet was supplemented with hydroalcoholic extracts of sumac (HES, 200 mg/kg), Syrian mesquite (HEM, 200 mg/kg), l‐arginine (40% above requirement), captopril (15 mg/kg) and vitamin E (100 mg/kg). Results: Diets containing HEM, l‐arginine and vitamin E resulted in increased average daily gain on days 8–14 and 0–28, whereas HES showed a similar effect only during days 8–14 compared to the control diet (p < 0.05). Additionally, feed additives decreased packed cell volume, left and right ventricle volumes and systolic blood pressure (p < 0.05). Moreover, chickens fed the control and l‐arginine diets exhibited higher levels of angiotensin converting enzyme (ACE) mRNA in lung tissue compared to those fed HES, HEM and captopril (p < 0.05). Meanwhile, supplementation with HEM and l‐arginine increased the expression of inducible nitric oxide synthase (iNOS) mRNA in lung tissue compared to other treatments (p < 0.05). Regarding Cu/Zn‐superoxide dismutase (Cu/Zn‐SOD) expression, feed additives increased mRNA level in lung tissue, except for captopril (p < 0.05). Conclusions: This study demonstrates that the plant extracts may reduce the incidence of ascites syndrome not only through their antioxidant properties but also by modulating the expression of ACE, iNOS and Cu/Zn‐SOD genes. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are large‐scale changes in the DNA sequence that can affect the genetic structure and phenotype of an organism. The purpose of this study was to investigate the existing CNVs and their associations with the shank diameter (ShD) and shank length (ShL) traits using data from an F2 crossbred chicken population. To carry out the study, 312 chickens were genotyped using the Illumina 60k SNP Beadchip. The shank traits of the birds were measured from day 1 to 12 weeks of age. penncnv and cnvruler tools were used to find copy numbers and regions with copy number changes (CNVR), respectively. The CNVRanger package was used to perform a genome‐wide association study between shank traits and CNVs. Gene ontology research in CNVRs was carried out using the david database. In this investigation, 966 CNVs and 606 regions with copy number changes were discovered. The copy number states and variations were randomly distributed along the length of the autosomal chromosomes. Weeks 1–4, 9 and 12 of growth revealed a significant association of copy number variations with shank traits, false discovery rate (FDR‐corrected p‐value < 0.01), and the majority of CNVs that were statistically significant were found on chromosomes 1–3. These CNV segments are nearby genes such as KCNJ12, FGF6 and MYF5, which are fundamental to growth and development. In addition, gene set analyses revealed terms related to muscle physiology, regulation of cellular processes and potassium channels. [ABSTRACT FROM AUTHOR]

The cryopreservation process induces alterations in cellular parameters and epigenetic patterns in bull sperm, which can be prevented by adding cryoprotectants in the freezing extenders. The purpose of this study was to compare the protective effects of two extenders based on soybean lecithin (SLE) and egg yolk (EYE) on epigenetic patterns and quality parameters of sperm such as motility parameters, mitochondrial membrane integrity, DNA fragmentation, viability, and apoptotic‐like changes of bull sperm after cryopreservation. Results demonstrated that cryopreservation significantly (p <.05) reduced the level of DNA global methylation, H3K9 histone acetylation, and H3K4 histone methylation in both frozen groups compared to the fresh sperm. Also, the level of H3K9 acetylation was lower in the frozen SLE group (21.2 ± 1.86) compared to EYE group (15.2 ± 1.86). In addition, the SLE frozen group had a higher percentage of viability, progressive motility, and linearity (LIN) in SLE frozen group compared to EYE frozen group. However, no difference was observed in mitochondrial membrane integrity and DNA fragmentation between SLE and EYE frozen groups. While soybean‐lecithin‐based extender showed some initial positive impacts of epigenetics and semen parameters, further investigations can provide useful information for better freezing. [ABSTRACT FROM AUTHOR]

Context: As evaluation of carcass components is costly and time consuming, models for prediction of broiler carcass components are useful. Aims: The aim was to investigate the feasibility of machine learning methods in the prediction of carcass components from measurements on live birds during the rearing period. Methods: Three machine learning methods, including regression tree, random forest and gradient-boosting trees, were applied to predict carcass yields, and benchmarked against classical linear regression. Two scenarios were defined for prediction. In the first scenario, carcass yields were predicted by live bodyweight, shank length and shank diameter features, recorded at 2, 3 and 4 weeks of age. In the second scenario, predictor features recorded at 5, 6 and 7 weeks of age were used. The two scenarios were reanalysed by including effective single-nucleotide polymorphisms associated with bodyweight, shank length and shank diameter as new predictor features. Key results: The correlation coefficient between predicted and observed values for predicting weight of carcass traits ranged from 0.50 for wing to 0.59 for thigh in the first scenario, and from 0.63 for wing to 0.74 for carcass in the second scenario. These predictions for the percentage of carcass components ranged from 0.30 for wing to 0.39 for carcass and breast in the first scenario, and from 0.34 for thigh to 0.43 for carcass in the second scenario when random forest was used. Conclusions: Predictive accuracy in the first scenario was lower than in the second scenario for all prediction methods. Including single-nucleotide polymorphisms as predictor features in either scenario did not increase the accuracy of the prediction. Implications: In general, random forest had the best performance among machine learning methods, and classical linear regression in two scenarios, suggesting that it may be considered as an alternative to conventional linear models for prediction of carcass traits in broiler chickens. Evaluation of carcass component yields is costly and time consuming, thus models for the prediction of broiler carcass yields are useful. Three advanced predictive models were applied to predict carcass component yields, and benchmarked against the classical linear regression. Random forest had the best performance among machine learning methods, suggesting that it may be considered as an alternative to conventional linear models for prediction of carcass yields in broiler chickens. In all of the predictive model tested in this study, inclusion of single-nucleotide polymorphisms as predictor features lowered the predictive performance of the model. [ABSTRACT FROM AUTHOR]

Sheep is the primary source of animal protein in Iran. Birth type is one of the significant features that determine total meat output. Little is known about how long non-coding RNAs (LncRNAs) affect litter size. The purpose of this research is to investigate the DE–LncRNAs in ovarian tissue between multiparous and uniparous Shal ewes. Through bioinformatics analyses, LncRNAs with variable expression levels between ewes were discovered. Target genes were annotated using the DAVID database, and STRING and Cytoscape software were used to evaluate their interactions. The expression levels of 148 LncRNAs were different in the multiparous and uniparous ewe groups (false discovery rate (FDR) < 0.05). Eight biological process terms, nine cellular component terms, 10 molecular function terms, and 38 KEGG pathways were significant (FDR < 0.05) in the GO analysis. One of the most significant processes impacting fertility is mitogen-activated protein kinase (MAPK) signaling pathway, followed by oocyte meiosis, gonadotropin-releasing hormone signaling pathway, progesterone-mediated oocyte maturation, oxytocin signaling pathway, and cAMP signaling pathway. ENSOARG00000025710, ENSOARG00000025667, ENSOARG00000026034, and ENSOARG00000026632 are LncRNAs that may affect litter size and fertility. The most crucial hub genes include MAPK1, BRD2, GAK, RAP1B, FGF2, RAP1B, and RAP1B. We hope that this study will encourage researchers to further investigate the effect of LncRNAs on fertility. [ABSTRACT FROM AUTHOR]

Background: Trainability in dogs is affected by learning aptitude and memory capacity. While this trait has a heritable basis in canines, the specific genetic loci responsible for it remain unknown. Our previous results suggested that the BDNF, CCK and TAC1 genes are associated with learning and memory in canines. Experimental validation is crucial to confirm the effects of these candidate genes on trainability. Understanding the genetic foundation of this trait would offer insight into the inheritance pattern of complex behavioural characteristics. Objective: This study aimed to assess the genetic variations within candidate genes and explore their potential associations with behavioural phenotypes in dogs. Methods: The behavioural characteristics of 123 male Belgian Malinois dogs were assessed using a customised questionnaire. Target regions of candidate genes were screened for genetic variation by single‐strand conformational polymorphism (SSCP). Following that, SSCP banding patterns were sequenced, and putative transcription factor binding sites were predicted using bioinformatics tools. Quantitative association analysis between identified genetic variants and behavioural trait scores was performed using the general linear model (GLM). Results: Sequencing the coding and flanking regions revealed three mutations (c.‐89C>T, c.‐162G>C and c.*33T>A) in the dog TAC1 gene. Bioinformatics analysis predicted two single nucleotide polymorphisms (SNPs) were located within the putative TAC1 promoter and could disrupt transcription factor binding sites. Statistical tests revealed that the c.‐89C>T was significantly associated with excitability (p < 0.01), while the c.‐162G>C was significantly associated with trainability level (p < 0.05). Conclusion: In summary, we identified two regulatory SNPs in the 5'‐UTR promoter region of the TAC1 gene that are associated with excitability and trainability in Belgian Malinois dogs. These genetic variations have the potential to alter the binding sites of transcription factors NRF1 and OTX1, consequently influencing TAC1 expression and related behavioural characteristics. Our findings implicate TAC1 polymorphisms as candidates influencing breed‐specific behavioural characteristics in canines. Further studies on diverse breeds of dogs are necessary to validate these SNPs' effects. [ABSTRACT FROM AUTHOR]

Ovulation rate and litter size are the main reproductive traits with high economic value in the sheep breeding industry. In this study, three Shal ewes (multiparous) and three Sangsari ewes (uniparous) at the age of 5 were used. The live weight was between 45 and 50 kg at an extremely body condition score of 3. These breeds are marked seasonal reproduction activity and are often bred in semi‐closed breeding systems. Total RNAs were extracted from the ovarian tissues, and RNA sequencing was carried out. The DAVID (Database for Annotation, Visualization and Integrated Discovery) database was then used to annotate genes, and the string database and the Cytoscape software were used to investigate their interactions. Then path–act network analysis and gene–act network analysis were investigated. The results indicated that 19,932 genes were differentially expressed. The 5968 differentially expressed genes were identified in Shal ewe's ovarian tissue compared to Sangsari ewes (FDR < 0.05), of which 2921 genes were up‐regulated and 3047 genes were down‐regulated. Bioinformatics analysis exhibited that most of the biological processes and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways associated with significant DEGs (Differentially Expressed Genes) in the two studied breeds are associated with oocyte maturation and metabolism. MAPK signalling pathways and Ubiquitin‐mediated proteolysis are the most important biological pathways associated with reproductive and fertility traits in the Shal breed. AKT3, MAPK8, MAPK9 and RELA genes are also important genes related to the fertility of multiparous sheep. Analysis of ovarian RNA‐seq data identified that most of the differentially expressed genes were involved in various reproductive processes including folliculogenesis, ovulation, ovarian and embryonic development. The MAPK signalling pathway had the most interaction with other pathways, and the AKT3 gene could be a powerful candidate gene in the reproduction and fertility of Shal sheep. These results could pave the way for future efforts to address sheep prolificacy barriers. [ABSTRACT FROM AUTHOR]

Heat stress is a serious problem in the poultry industry. An effective tool for improving heat tolerance can be genomic selection based on single nucleotide polymorphisms. This study was performed to identify genomic regions controlling survivability to heat stress in a population of F2 chickens that accidentally experienced acute heat stress, using Illumina 60K Chicken SNP Bead Chip. After quality control in markers, 47,730 SNPs remained for genome‐wide association study (GWAS). The GWAS results indicated that markers Gga_rs16111480 (p = 8.503e‐08), GGaluGA354375 (p = 5.99e‐07) and Gga_rs14748694 (p = 7.085e‐07) located on Z chromosome showed significant association with heat stress tolerance trait. The Gga_rs16111480 marker was located inside the CEP78 gene. The marker GGaluGA354375 was located inside the LOC101752071 gene and next to the MEF2C gene. The Gga_rs14748694 marker was adjacent to LOC101752071 and MEF2C genes. Moreover, the SNP maker of Gga_rs16111480 was located on 243 kb downstream of the VPS13A gene, and the GGaluGA354375 and Gga_rs14748694 SNPs were located on 947 kb and 888 kb downstream of the ARRDC3 gene, respectively. The results of this study suggest that apart from the gene LOC101752071, which its function was unknown, each of the two MEF2C and CEP78 genes were found to be closely related to heat stress resistance in bird. [ABSTRACT FROM AUTHOR]

Background: The ovary has an important role in reproductive function. Animal reproduction is dominated by numerous coding genes and noncoding elements. Although long noncoding RNAs (LncRNAs) are important in biological activity, little is known about their role in the ovary and fertility. Methods: Three adult Shal ewes and three adult Sangsari ewes were used in this investigation. LncRNAs in ovarian tissue from two breeds were identified using bioinformatics analyses, and then target genes of LncRNAs were discovered. Target genes were annotated using the DAVID database, and their interactions were examined using the STRING database and Cytoscape software. The expression levels of seven LncRNAs with their target genes were assessed by real‐time PCR to confirm the RNA‐seq. Results: Among all the identified LncRNAs, 124 LncRNAs were detected with different expression levels between the two breeds (FDR < 0.05). According to the DAVID database, target genes were discovered to be engaged in one biological process, one cellular component, and 21 KEGG pathways (FDR < 0.05). The PES1, RPS9, EF‐1, Plectin, SURF6, CYC1, PRKACA MAPK1, ITGB2 and BRD2 genes were some of the most crucial target genes (hub genes) in the ovary. Conclusion: These results could pave the way for future efforts to address sheep prolificacy barriers. [ABSTRACT FROM AUTHOR]

Foie gras is a traditional dish in France that contains 50 to 60% of lipids. The high-fat content of the liver improves the organoleptic qualities of foie gras and reduces its technological yield at cooking (TY). As the valorization of the liver as foie gras products is strongly influenced by the TY, classifying the foie gras in their potential technological quality before cooking them is the main challenge for producers. Therefore, the current study aimed to identify hepatic biomarkers of foie gras qualities like liver weight (LW) and TY. A group of 120 male mule ducks was reared and overfed for 6–12 days, and their livers were sampled and analyzed by proton nuclear magnetic resonance (1H-NMR). Eighteen biomarkers of foie gras qualities were identified, nine for LW and TY, five specific to LW, and four specific to TY. All biomarkers were strongly negatively correlated to the liver weights and positively correlated to the technological yield, except for the lactate and the threonine, and also for the creatine that was negatively correlated to foie gras technological quality. As a result, in heavy livers, the liver metabolism was oriented through a reduction of carbohydrate and amino acid metabolisms, and the plasma membrane could be damaged, which may explain the low technological yield of these livers. The detected biomarkers have been strongly discussed with the metabolism of the liver in nonalcoholic steatohepatitis. [ABSTRACT FROM AUTHOR]

The foie gras is an emblematic product of French gastronomy composed of waterfowl fatty liver. The organoleptic qualities of this product depend on the liver characteristics such as liver weight (LW) and technological yield (TY) at cooking. One of the main issues for producers is to classify the foie gras with high or low technological quality before cooking them. Thus the study aims at identifying biomarkers of these characteristics with non-invasive biomarkers in duck. 1H-NMR (nuclear magnetic resonance of the proton) analyses were performed on plasma of male mule ducks at different time points during the overfeeding period to obtain a large range of liver characteristics so as to identify plasmatic biomarkers of foie gras. We used two methods, one based on bucket data from the 1H-NMR spectra and another one based on the fingerprints of several metabolites. PLS analyses and Linear models were performed to identify biomarkers. We identified 18 biomarkers of liver weight and 15 biomarkers of technological yield. As these two quality parameters were strongly correlated (−0.82), 13 biomarkers were common. The lactate was the most important biomarker, the other were mainly amino acids. Contrary to the amino acids, the lactate increased with the liver weight and decreased with the technological yield. We also identified 5 biomarkers specific to LW (3 carbohydrates: glucuronic acid, mannose, sorbitol and 2 amino acids: glutamic acid and methionine) that were negatively correlated to liver weight. It was of main interest to identify 2 biomarkers specific to the technological yield. Contrary to the isovaleric acid, the valine was negatively correlated to the technological yield. [ABSTRACT FROM AUTHOR]

Bayes Cπ methodology due to the simultaneous use of all SNPs in a random regression model is an alternative to overcome the overestimation of SNPs effects and excess of false positives. Hence, the present study was performed to identify causal single nucleotide polymorphisms (SNPs) associated with body weight (BW) and their pattern of significance over time from 2 to 8 weeks of age, in an F2 crossbred chicken population using Bayes Cπ methodology. Illumina 60 K SNP bead chip was used to genotype 312 F2 chicks. Sixteen SNPs distributed over 8 chromosomes had a Bayes Factor (BF) greater than 150 for BW in different ages. 14 different genes harbouring these SNPs (±250 kb), of which 12 were protein-encoding (DKK2, LEF1, RASGEF1C, FOXP1, LPCAT1, AKR1D1, GPR137C, EIF2AK3, ROR1, AKR1D1, LRFN5 and XPO7) and two were noncoding RNAs (LOC101751953 and LOC101751953). According to the obtained results, GGA1 and GGA4 were the most important chromosomes containing QTLs associated with observed traits. Different genetic regions were responsible for body weight in early and late ages. The various number of significant Bayes factors across different weeks of ages may indicate the artificial selection for market weight in a given age which has driven larger SNPs effects in intended weeks for desired market weight for the two groups. My research outputs resulted in discovering associated genes and pathways related to gain growth and body weight in chicken. The identified genes in this study can be used in poultry breeding programs. Therefore, this leads to reduced feed costs and increase revenue. [ABSTRACT FROM AUTHOR]

BACKGROUND: Animal breeds are often recognized through their specific characteristics, nevertheless, the breeds' anatomical and biochemical characteristics have not considered yet in many of the researches done on one-humped camels. There are some particular differences in camel breeds due to different climate conditions and rearing necessity OBJECTIVES: The aim of the current study was to compare differences in anatomical and plasma biochemical parameters of two Iranian one-humped camels, the Jammaz (racing) and Balouchi (dual-purpose) breeds. METHODS: Anatomical parameters were body length (BL), neck length (NL), chest girth (CG), barrel girth (BG), hump circumference (HC), fore limb length (FLL), hind limb length (HLL), height at hump (HH), fore limbs interval (FLI), hind limbs interval (HLI), fore hoof circumference (FHC), hind hoof circumference (HHC), abdominal circumference (AC), shank circumference (SC) and leg circumference (LC). Moreover, concentrations of Glucose, blood urea nitrogen (BUN), creatinine, cholesterol, total bilirubin (Bili-T), direct bilirubin (Bili- D), calcium (Ca), phosphorus (P), magnesium (Mg), aspartate aminotransferase (AST), creatine kinase (CK), lactate dehydrogenase (LDH), total protein (TP), albumin (Alb), triiodothyronine (T3) and thyroxine (T4) were measured as plasma biochemical parameters. Data analysis was conducted through t-test statistics. RESULTS: Results revealed significant differences between body type traits of breeds, especially in organs related to running ability, while the Jammaz breed has more height and longer limbs than the Balouchi breed. Some blood parameters (glucose, LDH, BUN, cortisol and T4) are considerably higher in Jammaz breed, too. CONCLUSIONS: Results of the current study suggest some anatomical (especially fore and hind limb lengths, neck length and body height at hump) and physiological characteristics (lactate dehydrogenase, blood urea nitrogen, cortisol, glucose and T4) of Iranian racing and dual purpose camels as breed markers. [ABSTRACT FROM AUTHOR]

The present study was conducted to investigate the effects of two plant extracts as alternatives to dietary antibiotics in broiler chickens exposed to low ambient temperature. A total of 300 one-day-old male broiler chickens were randomly assigned to four dietary treatments (5 replicate pens; 15 broiler chickens each) which consisted of starter (d 0 to 10), and grower (d 10 to 28) diets. Dietary treatments included a basal diet (negative control, NC) and three similar diets that were either supplemented with 200 mg/kg of Prosopis farcta extract (PFE), Rhus coriaria L. extract (RCE) or an antibiotic premix containing oxytetracycline (positive control, PC). In order to simulate low ambient temperature, room temperature was maintained at 32°C during the first 3 d of the trial and afterwards, the temperature was gradually reduced by approximately 1.5°C each day to 14°C on d 21. PFE and PC treatments exerted a significant effect on body weight gain at d 28. Diet PFE was effective in reducing mortality when compared with diet NC (p < 0.05). Furthermore, diet PFE caused increases in ileal digestibility of gross energy, dry matter and organic matter when compared with diet NC (p < 0.05). Diets PFE and PC decreased coliforms, total aerobic bacteria and total anaerobic bacteria loads in the caeca when compared with diet NC (p < 0.05). Moreover, the addition of PFE to the diet improved villous height in all small intestinal segments as well as villous height:crypt depth ratio in the duodenum when compared with diet NC (p < 0.05). The results indicated that PFE is not only a valid alternative to oxytetracycline under cold stress conditions, with no antibiotic resistance, but also has the potential to increase the resistance of broiler chickens against ascites syndrome. Moreover, the addition of RCE at the concentration of 200 mg/kg to the diet was not sufficient to improve the performance of broiler chickens (similar to diet PC) but maybe more effective at higher concentrations. [ABSTRACT FROM AUTHOR]

A case of lysosomal storage disease has been reported in a calf of Japanese Black cattle. Lysosomal storage diseases are hereditary diseases caused by deficiency of lysosomal hydrolases. The clinical and pathological features and accumulated substrates of the affected animal indicated a possibility of sialidosis or galactosialidosis caused by deficiency of neuraminidase (NEU1) or protective protein for β-galactosidase (PPGB). In the present study, we investigated nucleotide sequences of the genes encoding these two proteins to evaluate whether mutation of these genes is involved in this disease. We determined cattle genomic sequences of these two genes by using bovine EST sequences and the nucleotide sequences of all exons of these genes were compared between affected and normal animals. The results showed several nucleotide substitutions, but none of them was a functional mutation or specific to the affected animal. Furthermore, genotyping of the microsatellite markers in the vicinity of these two genes revealed no homozygosity of the chromosomal regions including these genes in the affected animal. These findings indicated that neither NEU1 nor PPGB gene is responsible for the lysosomal storage disease of Japanese Black cattle and therefore the disease is neither sialidosis nor galactosialidosis. [ABSTRACT FROM AUTHOR]

Forelimb-girdle muscular anomaly is a hereditary disorder of Japanese Black cattle characterized by tremors and astasia caused by hypoplasia of the forelimb-girdle muscles. The locus responsible for this disorder has been mapped on a middle region of bovine chromosome 26. In this study, we applied marker-assisted selection to identify the carriers of this disorder. Four microsatellite markers, DIK4440, BM4505, MOK2602 and IDVGA-59, linked to the disorder locus were genotyped in 37 unaffected offspring of a carrier sire. Transmission of the mutant or wild-type allele of the disorder locus of the sire to the 37 offspring was determined by examining the haplotypes of these markers. The results showed that nine and 18 of the 37 animals possessed the paternally transmitted mutant and wild-type alleles, respectively, and therefore, the nine animals with the mutant allele were identified as carriers. We concluded that the marker-assisted selection using these four markers can be applied for the identification of the carriers of forelimb-girdle muscular anomaly of Japanese Black cattle. [ABSTRACT FROM AUTHOR]