Genome-wide association study identifies a novel candidate gene for egg production traits in chickens.

Qingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome-wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recorded and calculated, respectively. With a univariate linear mixed model, we detected one genome-wide significant single nucleotide polymorphism (SNP) and three chromosome-wide significant SNPs associated with egg laying rate. MTA2 is highly likely to be a functional gene for egg laying rate. Our study identifies MTA2 as the first time to be associated with egg laying rate. Findings in our study will advance our understanding of the genetic basis of egg production and have the potential to improve the efficiency of genomic selection in chickens.

Estimation of genetic parameters for important traits using a multi-trait model in late-feathering Qingyuan partridge hens in China.

Qingyuan partridge chicken is one of the most well-known Chinese indigenous yellow broilers. In breeding programmes, five traits are usually selected when the chickens are 105 days old, namely body weight (BW), comb height (CH), shank length (SL), shank girth (SG) and feather maturity (FM). The objective of this study was to estimate the genetic parameters of these five traits, especially direct additive genetic correlations, to lay the foundation for balanced selection of Qingyuan partridge chickens. Approximately 9600 records were used for estimation. Variance components for these five traits were estimated using three multi-trait models incorporating different effects via Gibbs sampling. Based on model 1 in which the random effects included direct additive genetic effects and residuals, the estimated direct heritabilities for BW, CH, SL, SG and FM were 0.29 ± 0.04, 0.53 ± 0.04, 0.47 ± 0.04, 0.43 ± 0.05 and 0.18 ± 0.03, respectively. The direct genetic correlations ranged from -0.08 to 0.46. When additionally considering maternal additive genetic effects (model 2), the estimates of direct heritabilities and absolute values of direct additive genetic correlations were smaller. The heritabilities were 0.14 ± 0.04, 0.40 ± 0.02, 0.34 ± 0.05, 0.27 ± 0.05 and 0.12 ± 0.03 for BW, CH, SL, SG and FM, respectively. The direct additive genetic correlations ranged from -0.33 to 0.36. More specifically, the direct additive genetic correlations between BW and CH, SL, SG and FM were 0.19 ± 0.13, 0.15 ± 0.15, 0.36 ± 0.15 and - 0.33 ± 0.21, respectively. The genetic correlations of FM with SL, SG and CH were - 0.15 ± 0.15, -0.08 ± 0.17 and 0.18 ± 0.15, respectively. The direct genetic correlations between CH and SG and SL were - 0.02 ± 0.11 and - 0.20 ± 0.11, respectively, and that between SL and SG was 0.19 ± 0.11. The total heritabilities and maternal additive genetic correlations ranged from 0.16 to 0.44 and from -0.13 to 0.61, respectively. The third model also included the maternal permanent environmental effect for BW. The estimates of direct heritability, direct additive genetic correlation, total heritability and maternal additive genetic correlation were only slightly different from those based on the second model. Therefore, the maternal additive genetic effect has a large effect on the estimation of genetic parameters, and it is better to consider this effect in the genetic evaluation of these five traits. Relatively high direct and maternal additive genetic correlations for most trait pairs suggested that it is better to jointly evaluate these five traits in breeding programmes.

Molecular cloning and functional studies on magang goose toll-like receptor 5.

Disease outbreaks heavily impact the economic viability of animal industries. Little is known about the mechanisms of immune system-related diseases in geese. Toll-like receptors (TLRs) play a major role in the anti-inflammatory immunity process in most animal species, but they have not been studied in the Magang goose. To elucidate the role of TLRs, reverse transcription polymerase chain reaction (RT-PCR) and PCR amplification of cDNA ends (Smart RACE) were used to clone the Magang goose TLR5 gene (mgTLR5). The full-length cDNA of mgTLR5 was 2967 bp in length, including a 5'-terminal untranslated region (UTR) of 215 bp, a 3'-terminal UTR of 384 bp, and an open reading frame of 2583 bp that encodes a protein of 860 amino acids. Structurally, mgTLR5 has a toll/interleukin-receptor (TIR) domain, a transmembrane domain, and seven leucine-rich repeats (LRRs) domains. Homology alignment of TLR5 and its TIR domains with other species revealed that mgTLR5 shared 98 % and 81.3 % of sequence similarity with white goose TLR5 and chicken TLR5, respectively. Quantitative RT-PCR showed that the mgTLR5 gene of the goose is widely expressed in all tested tissues, with the highest expression in the kidney and spleen. The increase in NF-κB promoter activity stimulated by flagellin was dependent on mgTLR5 expression in 293 T cells. Salmonella pullorum and flagellin significantly upregulated the expression of TLR5, IL-8, and IL-1 mRNA in peripheral blood mononucleotide cells of Magang goose cultured in vitro. Stimulation by S. pullorum for 24 h upregulated mgTLR5 expression in the cecum and kidney. We conclude that Magang goose TLR5 is a functional TLR5 homologue of the protein in other species and plays an important role in bacterial recognition.

Goose toll-like receptor 3 (TLR3) mediated IFN-γ and IL-6 in anti-H5N1 avian influenza virus response.

Induction of the innate immune pathways is critical for early anti-viral defense. How geese recognize viral molecules and activate these pathways is not well understood. In mammals, Toll-like receptor 3 (TLR3) recognizes double-stranded RNA. Activation of TLR3 induces the activation of NF-кB and the production of type-I interferon. In this study, the goose TLR3 gene was cloned using rapid amplification of cDNA ends. Goose TLR3 encoded an 896-amino-acid protein, containing a signal secretion peptide, 14 extracellular leucine-rich repeat domains, a transmembrane domain, a Toll/interleukin-1 receptor signaling domain, and shared 46.7-84.4% homology with other species. Tissue expression of goose TLR3 varied markedly and was highest in the pancreas and lowest in the skin. Human embryonic kidney 293 cells transfected with goose TLR3 and NF-κB-luciferase-containing plasmids responded significantly to poly i:c. The expression of TLR3, IL-6 and IFN-γ mRNA, but not IL-1 mRNA, was significantly upregulated after poly i:c or high pathogenic avian influenza virus (H5N1) stimulation in goose peripheral blood mononuclear cells cultured in vitro. Furthermore, geese infected with H5N1 showed significant upregulation of TLR3, especially in the lung and brain. We conclude that goose TLR3 is a functional TLR3 homologue of the protein in other species and plays an important role in virus recognition.

Identification and functional characterization of Toll-like receptor 2-1 in geese.

BACKGROUND: Toll-like receptor 2 (TLR2), an important pattern recognition receptor, activates proinflammatory pathways in response to various pathogens. It has been reported in humans and chicken, but not in geese, an important waterfowl species in China. Since some vaccines stimulate robust immune responsesl in chicken but not in geeeses we speculated that their immune systems are different. RESULTS: In this study, we cloned the goose TLR2-1 gene using rapid amplification of cDNA ends (RACE)and showed that geese TLR2-1 encoded a 793-amino-acid protein, containing a signal secretion peptide, an extracellular leucine-rich repeat domain, a transmembrane domain and a Toll/interleukin-1 receptor signaling domain deduced from amino acid sequence. TLR2-1 shared 38.4%-93.5% homology with its homologues in other species. Tissue expression of geese TLR2-1 varied markedly, and was higher in kidney, cloacal bursa, skin and brain compared to other organs/tissues. HEK293 cells transfected with plasmids carrying goose TLR2-1 and NF-κB-luciferase responded significantly to stimulation with Mycoplasma fermentans lipopeptide. Furthermore, geese infected with Mycoplasma gallisepticum (MG) and Salmonella enteritidis (SE) showed significant upregulation of TLR2-1 in both in vivo and in vitro. CONCLUSION: Geese TLR2-1 is a functional homologue of TLR2 present in other species and plays an important role in bacterial recognition in geese.