Huarui Du

Identification and association of the single nucleotide polymorphisms in calpain3 (CAPN3) gene with carcass traits in chickens

BackgroundThe aim of this study is to screen single nucleotide polymorphisms (SNP) of chicken Calpain3 (CAPN3) gene and to analyze the potential association between CAPN3 gene polymorphisms and carcass traits in chickens. We screened CAPN3 single nucleotide polymorphisms (SNP) in 307 meat-type quality chicken from 5 commercial pure lines (S01, S02, S03, S05, and D99) and 4 native breeds from Guangdong Province (Huiyang Huxu chicken and Qingyuan Ma chicken) and Sichuan Province (Caoke chicken and Shandi Black-bone chicken), China.ResultsTwo SNPs (11818T>A and 12814T>G) were detected by single strand conformation polymorphism (SSCP) method and were verified by DNA sequencing. Association analysis showed that the 12814T>G genotypes were significantly associated with body weight (BW), carcass weight (CW), breast muscle weight (BMW), and leg muscle weight (LMW). Haplotypes constructed on the two SNPs (H1, TG; H2, TT; H3, AG; and H4, AT) were associated with BW, CW (P < 0.05), eviscerated percentage (EP), semi-eviscerated percentage (SEP), breast muscle percentage (BMP), and leg muscle percentage (LMP) (P < 0.01). Diplotype H1H2 was dominant for BW, CW, and LMP, and H2H2 was dominant for EP, SEP, and BMP.ConclusionWe speculated that the CAPN3 gene was a major gene affecting chicken muscle growth and carcass traits or it was linked with the major gene(s). Diplotypes H1H2 and H2H2 might be advantageous for carcass traits.

Genotypes of IFIH1 and IFIT5 in seven chicken breeds indicated artificial selection for commercial traits influenced antiviral genes

Innate immunity is the first line against the invasion of pathogenic microorganisms. Previous reports only demonstrated production traits of commercial importance were often negatively correlated with innate disease resistance. However, whether different purpose of artificial selection influences innate immunity have not been understood. In this study, we cloned exon1, exon6 of IFIH1 and exon2 of IFIT5 by molecular biology techniques in seven different chicken breeds to detect the potential effect of artificial selection for commercial traits on disease resistance for the first time. In total, 8 single nucleotide polymorphisms(SNPs) of IFIH1 gene exon1 and exon6, 19 SNPs of IFIT5 gene exon2 were detected. We found all native chicken breeds had a relatively close relationship to broiler breeds but a remote relationship to layer breed. A great difference between CB and LLH with different selected purpose were observed. The allele frequencies of these two positive antiviral genes were associated with different purpose of artificial selection. Our experiment constituted the foundation for the interaction between commercial traits and immune trait.

Whole genome bisulfite sequencing reveals unique adaptations to high-altitude environments in Tibetan chickens

Background Tibetan chickens living at high altitudes show specific adaptations to high-altitude conditions, but the epigenetic modifications associated with these adaptations have not been characterized. Results We investigated the genome-wide DNA methylation patterns in Tibetan chicken blood by using whole genome bisulfite sequencing. Generally, Tibetan chickens exhibited analogous methylation patterns to that of lowland chickens. A total of 3.92% of genomic cytosines were methylcytosines and 51.22% of cytosines in CG contexts were methylated, which was less than those in lowland chicken (55.69%). Moreover, the base adjacent to the methylcytosines of mCHGs in Tibetan chickens had a preference for T, which was different from that in lowland chickens. In Tibetan chickens, the methylation levels in the promoter were relatively low, while the gene body was also maintained in a hypomethylated state. DNA methylation levels in regions upstream of the transcription start site of genes were negatively correlated with the level of gene expression, and DNA methylation of gene body regions was also negatively related to gene expression. Conclusions We generated the genome-wide DNA methylation patterns in Tibetan chickens and our results will be helpful for future epigenetic studies related to adaptations to high-altitude conditions.

Differences in expression of genes in the MyD88 and TRIF signalling pathways and methylation of TLR4 and TRIF in Tibetan chickens and DaHeng S03 chickens infected with Salmonella enterica serovar enteritidis

Salmonella enterica serovar (S. enteritidis) is a pathogenic bacterium that can cause symptoms of food poisoning, leading to death of poultry, resulting in serious economic losses. The MyD88 and TRIF signalling pathways play important roles in activating innate and adaptive immunity in chickens infected with S. enteritidis. The objective of the present study was to characterize in vivo mRNA expressions, protein levels and methylation levels of genes in the above two pathways in both Tibetan chickens and DaHeng S03 chickens infected with S. enteritidis. MyD88-dependent and TRIF-dependent signalling pathway were activated by infection, and the MyD88 signalling pathway induced cytokines LITAF and IL-8 played important roles in fighting against the S. enteritidis infection in vivo. The TLR4 methylation might alter expression of genes involved in the MyD88 signalling pathway, and thus different breeds of chickens might show differences in susceptibility to the S. enteritidis. The increased expression of INF β was activated by S. enteritidis, but its expressions were different in levels of mRNA and protein in Tibetan chickens and DaHeng chickens, suggesting its functions on the resistance to S. enteritidis infection in chickens. This study contributes to the understanding of two pathways activated in response to S. enteritidis infection, and gives indications on the mechanisms underlying resistance of Tibetan chickens and DaHeng chickens to S. enteritidis.

Tissue-Specific Expression of the Chicken Calpain2 Gene

We quantified chicken calpain 2 (CAPN2) expression in two Chinese chicken breeds (mountainous black-bone chicken breed [MB] and a commercial meat type chicken breed [S01]) to discern the tissue and ontogenic expression pattern and its effect on muscle metabolism. Real-time quantitative PCR assay was developed for accurate measurement of the CAPN2 mRNA expression in various tissues from chickens of different ages (0, 2, 4, 6, 8, 10, and 12 weeks). Results showed that the breast muscle and leg muscle tissues had the highest expression of CAPN2 compared to the other tissues from the same individual (P < .05). Overall, the CAPN2 mRNA level exhibited a “rise” developmental change in all tissues. The S01 chicken had a higher expression of the CAPN2 mRNA in all tissues than the MB chicken. Our results suggest that chicken CAPN2 expression may be related to chicken breeds and tissues.