Journal of Animal Production, Print ISSN: 2008-6776., Online ISSN: 2382-994X

Abstract Objective: Identifying selection signatures  can provide valuable insights into genomic regions that are under positive selection, which in turn leads to a better understanding of genotype-phenotype relationships Over the past few decades,, selection programs in broiler chicken have been based on fast growing and increased feed efficiency. On the other hand, this selection for rapid growth has been resulted an accumulation of fatty tissue and decrease of chicken meat quality, it has been new challenges in poultry breeding due to genetic correlation between rapid growing and fat deposition. The aim of the present study was to identify genomic regions under positive selection associated with body fat deposition in seven-week-old broiler chickens  using a statistical method based on linkage disequilibrium. Materials and Methods: In the present study, a total 475 chickens from two chicken lines divergently selected were obtained using the Illumina chicken 60 K SNP chip. The broilers used in this study were from two Chinese broiler lines. In the first step, for the detected regions of the genome were evaluated using the XP-EHH method based on linkage disequilibrium using Selscan software v.2.0. Candidate genomic regions and genes were identified by SNPs located at 1% upper range of XP-EHH values in ten creeping windows. Finally, GeneCards and DAVID databases were also used to interpret the function of the obtained genes. Additionally, the latest published version of Animal genome database was used for defining QTLs associated with fat deposition traits in identified locations. Results: Candidate genes STAB2, TAPT1, JDP2, FNDC3B, PTPN11, ADIPOR1 and SLC44A3 obtained these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with lipid metabolism, fatty acid transport, lipoprotein receptors, glucose metabolism and homeostasis. Various genes that were founded within these regions can be considered as candidates under selection based on function. Also, a survey on extracted QTLs showed that these QTLs involved in some economically important traits in chicken such as abdominal fat weight and carcass fat weight traits. Conclusion: However, will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in poultry breeding programs. The results of our research can be used to understand the genetic mechanism controlling fat deposition trait and using these findings could potentially be useful for genetic selection in chicken for increasing body weight while reducing body fat deposition during a broiler breeding.

Abstract The aim of present study was to investigate the effect of selection against ascites syndrome on different traits body growth, internal organs, and blood parameters in a broiler line. Therefore, by classifying different families based on the frequency of ascites under intense ascites inducing condition (AIC), 10 susceptible families (SUS) and 10 resistant families (RES) to ascites were selected and another set of offspring from the same families were bred under normal commercial condition (NCC). This process of selection and cross validation was carried out twice in the two distinct generations. The genetic relationship of different traits, the difference in the frequency of ascites between AIC and NCC, and the difference between different traits in SUS and RES were performed by correlation statistics, Chi-square test, and GLM procedure of SAS software (version 9.1), respectively. The correlation between ascites susceptibility in different families indicated that families that showed more ascites under AIC also had more ascites under NCC. Comparative study of different traits in susceptible and resistant groups showed that in SUS, body weight, growth rate and respiratory capacity were significantly lower and blood partial pressure of carbon dioxide was significantly higher than RES (P<0.05). In the present study it was shown that selection against this syndrome not only does not reduce growth rate in the investigated broiler line, but also improves growth traits and resistance to this syndrome in the mentioned line.

Abstract Ascites Syndrome is a costly metabolic disorder that has been linked to intense selection on growth rate and low feed conversion ratio in broilers. This Syndrome has become one of the most frequent causes of mortality within the broiler industry and leads to substantial economic losses and reduced animal welfare. To identify genes and genomic regions associated with Ascites Syndrome, genome wide association study was performed by the chicken 60K SNP panel on 101 birds from a F2 chicken population derived from the reciprocal cross between Arian broiler Line and Azerbaijan native fowls. Genomic best linear unbiased prediction procedure was used to calculate associations between each SNP and ascite related traits. Several SNPsfor the ratio of right ventricular to total ventricular, an indicator for Ascites syndrome, reached the suggestive threshold (8.25×10^-5) on chromosome 7. Two SNPs detected within CCDC141 and OSBPL6 genes were previously reported for human heart disorder. There are a large number of genes in this region (12745561-14602723) on chicken chromosome 7 that are related to hypertrophic cardiomyopathy, heart rate and human heart disorder. Selection for ascites resistance in broiler chicken using these findings could accelerate the genetic progress.

Abstract In order to identify loci and genes associated with meat quality traits, genome-wide association study (GWAS) were conducted in a F2 population derived from a reciprocal cross between Azerbaijan native chickens and Aryan broiler line by using Illumnia 60 K Chicken SNP Bead chip. For each bird, a total 6 traits including water holding capacity, meat color lightness (L*), redness (a*), yellowness (b*), shear force and ultimate pH were measured. The SNPs that were associated with meat quality traits were identified using both GLM and compressed mixed linear models (CMLM). A total of 36 SNPs were associated with meat quality traits in the genome–wide significance and suggestive levels, that 3 SNPs were significantly associated with meat color yellowness through CMLM model and 18 SNPs were suggestively associated with meat color yellowness, ultimate pH, water holding capacity and shear force through GLM model. The identified candidate genes have molecular functions related to meat quality traits. So, these candidate genes can be applied in the chicken breeding scheme.

Abstract The TLR4 gene structure as the main receptor for lipopolysaccharide recognition of Gram-negative bacteria was investigated in two strains of Iranian commercial Arian line and west Azerbaijan native chicks and its expression was studied in some major organs. Blood samples of the 120 birds were taken and total DNAs extracted. Then, the target gene was sequenced using four pairs of primers on four samples of each strain. The effects of amino acid changes on protein function were assessed by PANTHER software. To investigate the gene expression, total RNAs were extracted from liver, spleen, and lung tissues after slaughter of the birds. Gene expression was assessed by semi-quantitative RT-PCR. The amplified RNAs from tissues of liver, spleen and lungs. Then electrophoresis images were processed with the Image software and quantitative data analyzed by MINITAB. The results showed three new single polymorphisms (T1147C, C2246A and A1832G) in the sequence of TLR4 gene in the studied populations. The effects of variations on TLR4 protein structure indicated  a deleterious effect of mutations on  protein structure. The TLR4 gene expression in case of native and commercial strains did not show significant differences. Due to importance of the TLR4 in innate immunity and identification of some novel mutations affecting on protein structure, this gene could be a valuable candidate related to genetic resistance in poultry.