Zengrong Zhang

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.

Circadian clock genes are rhythmically expressed in specific segments of the hen oviduct

In animals, core clock genes are expressed in many peripheral tissues throughout the body that contribute to tissue specific temporal regulation including those that comprise the reproductive system. The chicken ovulatory cycle seems to provide an example of a system in which circadian and interval timing mechanisms operate during ovulation-oviposition. However, little is known about the possible role of circadian regulation during egg formation and laying. To this end, we determined the rhythmic expression of several known canonical clock genes and clock controlled genes in the 4 segments of the chicken oviduct (infundibulum, magnum, isthmus, and uterus) taken from the same biological state (laying sequence and oviposition time) using real time RT-PCR. Except for Cry1, the other genes we analyzed were expressed in all 4 segments of the oviduct. Intriguingly, in a daily light-dark cycle, Bmal1, Clock, Per2, Per3, Cry2, and Rev-erbβ have highly significant rhythmic expression in the infundibulum and uterus but not in the magnum and isthmus. These results show that there is spatial specificity in the localization of clock cells in the hen reproductive tract and that peripheral clocks might have a direct role in the infundibulum and uterus where yolk is captured and the eggshell is formed, respectively.

Correlation Analysis on Single Nucleotide Polymorphism of CAPN1 Gene and Meat Quality and Carcass Traits in Chickens

Abstract The selection of meat quality has received considerable focus in chicken breeding. This study was aimed at investigating the effect of CAPN1 gene on meat quality traits in chicken populations. Primer pairs for 3′UTR in CAPN1 were designed from database of chicken genomic sequence. Polymorphisms were detected using PCR-SSCP and DNA sequencing. A mutation at position 9950 nt (G/A, locus A) was found among individuals in each population. The allele and genotype frequencies significantly differed among eight lines with higher frequencies of allele A2 and genotype A1A2 ( P P A1A1 genotype was significantly higher ( P A2A2 genotype. It was concluded that the CAPN1 gene was the major gene affecting the muscle fiber traits of chicken or was linked with the major gene. These results were useful for studying the molecular mechanism that influences meat traits and were used as the base of molecular-assisted selection to meat quality traits. So, this site may be a potential marker affecting the muscle traits of chickens.

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.