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Background: Salmonella enteritidis (SE), a previously widespread infectious disease, is still cited as a major factor in economic losses in commercial chicken production. The host's genetic immune system determines the pathogenicity of a particular bacterium. To shed light on this topic, it was necessary to understand the key candidate genes essential for regulating susceptibility and resistance to the target disease. The field of poultry farming in particular has benefited greatly from the connection between quantitative and molecular genetics. Objectives: This study aims to identify the most important immune‐related genes and their signalling pathways (gene ontology, co‐expression and interactions) and to analyse their accumulation in host‐resistant SE diseases by combining gene expression assays with model‐based in silico evidence. Methods: A two‐step experimental design is followed. To start, we used free computational tools and online bioinformatics resources, including predicting gene function using a multiple association network integration algorithm (geneMania), the Kyoto Encyclopedia of Genes and Genomes, the Annotation, Visualization and Integrated Discovery (DAVID) database and the stimulator of interferon genes. Natural resistance‐associated macrophage protein 1 (NRAMP1), Toll‐like receptor 4 (TLR4), interferon‐γ (IFNγ), immunoglobulin Y (IgY) and interleukin 8 (IL8) were among the five genes whose expression levels in liver, spleen, and cecum were evaluated at 1107 SE after 48 h of inoculation. This molecular study was developed in the second phase of research to validate the in silico observations. Next, we use five promising biomarkers for relative real‐time polymerase chain reaction (PCR) quantification: TLR4, IL8, NRAMP1, IFNγ and IgY genes in two case and control assays. The 2−∆∆Ct Livak and Schmittgen method was used to compare the expression of genes in treated and untreated samples. This method normalizes the expression of the target gene to that of actin, an internal control and estimates the change in expression relative to the untreated control. Internal control was provided by the Beta actin gene. Next, statistically, the postdoc test was used for the evaluation of treatments using SAS version 9.4, and p values of 0.05 and 0.01 were chosen for significant level. Results: Interestingly, the results of our study suggest the involvement of various factors in the host immune response to Salmonella. These include inducible nitric oxide synthase, NRAMP1, immunoglobulin light chain (IgL), transforming growth factor B family (TGFb2, TGFb3 and TGFb4), interleukin 2 (IL2), apoptosis inhibitor protein 1 (IAP1), TLR4, myeloid differentiation protein 2 (MD2), IFNγ, caspase 1 (CASP1), lipopolysaccharide‐induced tumour necrosis factor (LITAF), cluster of differentiation 28 (CD28) and prosaposin (PSAP). The summary of gene ontology and related genes found for SE resistance was surprisingly comprehensive and covered the following topics: positive regulation of endopeptidase activity, interleukin‐8 production, chemokine production, interferon‐gamma production, interleukin‐6 production, positive regulation of mononuclear cell proliferation and response to interferon‐gamma. The role of these promising biomarkers in our networks against SE susceptibility is essentially confirmed by these results. After 48 h, the spleen showed significant expression of the tissue‐specific gene expression patterns for NRAMP1 and IL8 in the cecum, spleen and liver. Based on this information, this report searches for resistance and susceptibility lineages in most genomic regions for SE. Conclusions: In conclusion, the development of an appropriate selection program to improve resistance to salmonellosis can be facilitated by a comprehensive understanding of the immune responses of the chicken immune system after SE exposure. [ABSTRACT FROM AUTHOR]

Background: The domestic cat (Felis catus) is a newly evolved species in the family Felidae that has developed some great features among mammals. It is critical to conserve these species and prevent inbreeding from reducing their genetic diversity by understanding their genetic relationships and applying the information to breeding management. The diverse population was an excellent choice for studying genetic diversity and inbreeding phenomena. Objectives: To conduct this research, 128 individuals from 8 populations, including Azerbaijan, Persian, Ahar, Uermia, Tehran, Karaj, Turkish and Shop cat (both genders), were randomly selected from different geographical regions. We selected eight STR markers with different chromosomal locations based on polymorphism and observed allele numbers in the next step. DNA extraction was performed using tail hair root, PCR and electrophoresis, and gel staining was performed according to routine laboratory protocol. For statistical analysis, CONVERT versions POPGENE, ARLEQUIN GenAlEx and R script analysis. Results: Remarkably, our results showed that 23 alleles were identified in 128 samples. The highest number of alleles belonged to the FCa096 locus (eight alleles) in the Persian population, followed by FCa045 (seven alleles) in the Persian and Ahar populations. Another new finding is that the lowest number of alleles belonged to the 35 and FCa77 locus (two alleles). In addition, pairwise differentiation between and within populations was examined using the genetic distance index. Overall, the results showed that the degree of differentiation within the population is high in the Turkish population compared to other population groups and lower in the Azerbaijan population. In addition, principal component discriminant analysis‐based analysis based on the ADAGENET package shows the distribution of samples by geographical location. The results show that genetic mixing between populations is high. Conclusions: On this basis, we conclude that randomly bred domestic cats have a higher level of diversity than Persian domestic cats. This is an interesting topic for future work. [ABSTRACT FROM AUTHOR]

Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome‐wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome‐wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovine database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue‐based transcriptome records. Also, we used the david database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the genemania and string databases were used. Also, the available z‐scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that LYNX1, DGAT1, C14H8orf33, and LY6E were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, FBXL6 was detected as a significant gene associated with mastitis trait. CLN3 and ZNF34 genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high‐yielding dairy cows. [ABSTRACT FROM AUTHOR]

This study focuses on designing a conservation indigenous Awassi sheep breeding program based on the analysis of genetic variation using the simple sequence repeat markers (SSR). The allele frequency distribution of six SSR markers distributed on three different chromosomes was used to determine the genetic variation among 50 Awassi sheep (15 from the north, 20 from the middle, and 15 from the south of Babylon city) that were collected from the private herds. The results showed that the RM32 marker exhibited high frequency and the most genotypes existed compared to other markers. The mean number of alleles (NA), the effective number of alleles (NE), the Shannon index (I), and the polymorphism information content (PIC) values per loci were 2.66 ± 0.81, 2.05 ± 0.87, 0.73 ± 0.42, and 0.37± 0.26 respectively. Also, the average observed (Obs_Hom), expected (Exp_Hom) homozygosity, observed (Obs_Het), expected (Exp_Het) heterozygosity, Nei's expected heterozygosity, and inbreeding coefficient (FIS) were 0.77± 0.18, 0.56 ±0.25, 0.23 ± 0.18, 0.44 ±0.25, 0.43± 0.24, and 0.41± 0.12, respectively. The results of the Bayesian analysis revealed that all populations were homogenous there was a clear overlap between the individuals of the three distinct clusters were formed. On this basis, we conclude that the indigenous Awassi sheep in Babylon city have reasonable genetic variation. [ABSTRACT FROM AUTHOR]

Genomic selection (GS) plays an essential role in livestock genetic improvement programs. In dairy cattle, the method is already a recognized tool to estimate the breeding values of young animals and reduce generation intervals. Due to the different breeding structures of beef cattle, the implementation of GS is still a challenge and has been adopted to a much lesser extent than dairy cattle. This study aimed to evaluate genotyping strategies in terms of prediction accuracy as the first step in the implementation of GS in beef while some restrictions were assumed for the availability of phenotypic and genomic information. For this purpose, a multi-breed population of beef cattle was simulated by imitating the practical system of beef cattle genetic evaluation. Four genotyping scenarios were compared to traditional pedigree-based evaluation. Results showed an improvement in prediction accuracy, albeit a limited number of animals being genotyped (i.e., 3% of total animals in genetic evaluation). The comparison of genotyping scenarios revealed that selective genotyping should be on animals from both ancestral and younger generations. In addition, as genetic evaluation in practice covers traits that are expressed in either sex, it is recommended that genotyping covers animals from both sexes. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the influence of dietary supplementation of bovine lactoferrin (bLF) on growth performance, carcass traits, histomorphology of jejunum, immune function and hepatic and splenic gene expression of interferon‐gamma (IFN‐γ) and interleukine‐2 (IL‐2) in broiler chickens. A total of 240 one‐day‐old Ross 308 male broiler chickens were randomly allotted into six dietary treatments with four replicate pens (10 chicks per pen) and fed experimental diet in 3 feeding phases (starter: d 0–10, grower: d 11–24 and finisher: d 25–42). The experimental treatments were (1) corn–soya bean meal‐based basal diet (control), (2–5) basal diet supplemented with 200, 400, 600, 800 mg/kg bLF, respectively, and (6) basal diet supplemented with 200 mg/kg oxytetracycline (OTC). The average body weight gain (ABWG) of broilers fed 800 mg/kg bLF was 8.48% higher than those fed a corn–soybean meal‐based diet during the starter period (d 0–10) (linear effect, p = 0.002; quadratic effect, p = 0.24). Average daily feed intake (ADFI) and the feed conversion ratio (FCR) were not affected (p>0.05) by bLF supplementation. At 42 days of age, the breast meat percentage and carcass yield of broilers fed 800 mg/kg bLF compared with the control group significantly increased by 9.51% and 6.03% respectively (p < 0.05). Compared with the chicks fed the control diet, the chicks fed diets supplemented with bLF had higher villus height, muscle thickness and villus surface area (p > 0.05). Dietary bLF inclusion increased the total immunoglobulin (IgT) titre against sheep red blood cells (SRBCs) antigen (linear effect, p = 0.031; quadratic effect, p = 0.035) and improved the phytohaemagglutinin‐P (PHA‐P)‐skin test of broilers. Compared with the control, bLF enhanced the gene expression of IFN‐γ in spleen (p = 0.048, linear effect, p = 0.009; quadratic effect, p = 0.093) and liver (p = 0.012, linear effect, p = 0.008; quadratic effect, p = 0.01) and IL‐2 expression in spleen (p = 0.021, linear effect, p = 0.026; quadratic effect, p = 0.103). The bLF supplementation had no effect on IL‐2 gene expression in liver (p > 0.05, linear effect, p = 0.213; quadratic effect, p = 0.159). In conclusion, we found that supplementation of broiler diets with 800 mg/kg bLF can improve the growth performance, carcass yield, cell‐mediated and antibody‐mediated immune responses and enhance the IL‐2 and IFN‐γ gene expression of broilers. [ABSTRACT FROM AUTHOR]

Salmonella infection is an important risk to public health, as newly hatched chicks are very sensitive to Salmonella and the infection transfers to humans through contaminated meat and eggs. Vaccination and antibiotic treatment are common strategies to control salmonellosis. However, it is doubtful whether these strategies succeed, because immune functions depend on the activity of several genes. Genetic improvement of the immune system is an effective method to control salmonellosis. There is genetic variation among breeds and individuals inside breeds in terms of resistance to infection. Genes responsible for resistance to disease can be identified through quantitative trait loci and gene expression analysis. High-throughput technologies assist us to detect single nucleotide polymorphisms (SNPs) and to analyse the regulation of several genes simultaneously. By now, several SNPs have been detected in the chicken genome that influence the function of immune genes. Additionally, the expression level of genes varies during infection depending on the breed and age of chicken and environmental conditions. This review summarizes the results of previous studies on the identification of genes and gene regulation during Salmonella infection in chickens. [ABSTRACT FROM AUTHOR]