Impact of crossing Fayoumi and Leghorn chicken breeds on immune response against Newcastle disease virus vaccines

Integrative study of chicken lung transcriptome to understand the host immune response during Newcastle disease virus challenge

Introduction

Newcastle disease is one of the significant issues in the poultry industry, having catastrophic effects worldwide. The lung is one of the essential organs which harbours Bronchus-associated lymphoid tissue and plays a vital role in the immune response. Leghorn and Fayoumi breeds are known to have differences in resistance to Newcastle disease. Along with genes and long non-coding RNAs (lncRNAs) are also known to regulate various biological pathways through gene regulation.

Methods

This study analysed the lung transcriptome data and identified the role of genes and long non-coding RNAs in differential immune resistance. The computational pipeline, FHSpipe, as used in our previous studies on analysis of harderian gland and trachea transcriptome was used to identify genes and lncRNAs. This was followed by differential expression analysis, functional annotation of genes and lncRNAs, identification of transcription factors, microRNAs and finally validation using qRT-PCR.

Results and discussion

A total of 8219 novel lncRNAs were identified. Of them, 1263 lncRNAs and 281 genes were differentially expressed. About 66 genes were annotated with either an immune-related GO term or pathway, and 12 were annotated with both. In challenge and breed-based analysis, most of these genes were upregulated in Fayoumi compared to Leghorn, and in timepoint-based analysis, Leghorn challenge chicken showed downregulation between time points. A similar trend was observed in the expression of lncRNAs. Co-expression analysis has revealed several lncRNAs co-expressing with immune genes with a positive correlation. Several genes annotated with non-immune pathways, including metabolism, signal transduction, transport of small molecules, extracellular matrix organization, developmental biology and cellular processes, were also impacted. With this, we can understand that Fayoumi chicken showed upregulated immune genes and positive cis-lncRNAs during both the non-challenged and NDV-challenge conditions, even without viral transcripts in the tissue. This finding shows that these immune-annotated genes and coexpressing cis-lncRNAs play a significant role in Fayoumi being comparatively resistant to NDV compared to Leghorn. Our study affirms and expands upon the outcomes of previous studies and highlights the crucial role of lncRNAs during the immune response to NDV.

Conclusion

This analysis clearly shows the differences in the gene expression patterns and lncRNA co-expression with the genes between Leghorn and Fayoumi, indicating that the lncRNAs and co-expressing genes might potentially have a role in differentiating these breeds. We hypothesise that these genes and lncRNAs play a vital role in the higher resistance of Fayoumi to NDV than Leghorn. This study can pave the way for future studies to unravel the biological mechanism behind the regulation of immune-related genes.

Breed and timepoint-based analysis of chicken harderian gland transcriptome during Newcastle disease virus challenge

Introduction: Newcastle disease is a highly infectious disease caused by the Newcastle Disease Virus (NDV) and has a devastating financial impact on the global chicken industry. It was previously established that Leghorn and Fayoumi breeds of chicken exhibit variable resistance against NDV infection. The harderian gland is the less studied tissue of the chicken, known to play an essential role in the immune response. Methods: Our previous study, we reported differential gene expression and long noncoding RNAs (lncRNAs) between challenged and non-challenged chickens in the Harderian gland transcriptomic data. Now, we report the analysis of the same data studying the differential expression patterns between Leghorn and Fayoumi and between different timepoints during disease. First, the pipeline FHSpipe was used for identification of lncRNAs, followed by differential expression analysis by edgeR (GLM), functional annotation by OmicsBox, co-expression analysis using WGCNA and finally validation of selected lncRNAs and co-expressing genes using qRT-PCR. Results: Here, we observed that Leghorn showed a higher number of upregulated immune-related genes than Fayoumi in timepoint-based analysis, especially during the initial stages. Surprisingly, Fayoumi, being comparatively resistant, showed little difference between challenged and non-challenged conditions and different time points of the challenge. The breed-based analysis, which compared Leghorn with Fayoumi in both challenged and non-challenged conditions separately, identified several immune-related genes and positive co-expressing cis lncRNAs to be upregulated in Fayoumi when compared to Leghorn in both challenged and non-challenged conditions. Discussion: The current study shows that Leghorn, being comparatively more susceptible to NDV than Fayoumi, showed several immune-related genes and positive co-expressing cis lncRNAs upregulated in challenged Leghorn when compared to non-challenged Leghorn and also in different timepoints during challenge. While, breed-based analysis showed that there were more upregulated immune genes and positive cis-lncRNAs in Fayoumi than Leghorn. This result clearly shows that the differences in the expression of genes annotated with immune-related GO terms and pathways, i.e., immune-related genes and the co-expressing cis-lncRNAs between Leghorn and Fayoumi, and their role in the presence of differences in the resistance of Leghorn and Fayoumi chicken against NDV. Conclusion: These immune-genes and cis-lncRNAs could play a role in Fayoumi being comparatively more resistant to NDV than Leghorn. Our study elucidated the importance of lncRNAs during the host defense against NDV infection, paving the way for future research on the mechanisms governing the genetic improvement of chicken breeds.

Integrated analysis of genes and long non-coding RNAs in trachea transcriptome to decipher the host response during Newcastle disease challenge in different breeds of chicken

Newcastle disease is a highly infectious economically devastating disease caused by Newcastle disease Virus in Chicken (Gallus gallus). Leghorn and Fayoumi are two breeds which show differential resistance patterns towards NDV. This study aims to identify the differentially expressed genes and lncRNAs during NDV challenge which could play a potential role in this differential resistance pattern. A total of 552 genes and 1580 lncRNAs were found to be differentially expressing. Of them, 52 genes were annotated with both Immune related pathways and Gene ontologies. We found that most of these genes were upregulated in Leghorn between normal and challenged chicken but several were down regulated between different timepoints after NDV challenge, while Fayoumi showed no such downregulation. We also observed that higher number of positively correlating lncRNAs was found to be downregulated along with these genes. This shows that although Leghorn is showing higher number of differentially expressed genes in challenged than in non-challenged, most of them were downregulated during the disease between different timepoints. With this we hypothesize that the downregulation of immune related genes and co-expressing lncRNAs could play a significant role behind the Leghorn being comparatively susceptible breed than Fayoumi. The computational pipeline is available at https://github.com/Venky2804/FHSpipe.

Productive qualities of geese when crossing breeds and using hepatoprotective complex

The study was on a one-way cross between Wanxi male and Lindov female geese, and tested the effects of a hepatoprotective compound on growth and other traits in the parental and one-way cross involving male and female progeny. The hybrids obtained from crossing had high viability and productivity; their level was also positively affected by giving a hepatoprotective complex. Female parents were the Lindov breed's geese, and male parents were 120 geese of the Chinese Wanxi breed. During the growing period, hybrid young birds were receiving a hepatoprotective complex in the amount of 1.0 mL per 1 L of water for 7 days. The research took into account geese' safety indices, live weight, and absolute and average daily gain. The interbreeding results prove that the resulting hybrids' safety index is 2.38%-4.54% higher than the parent forms' safety index. The hybrids' live weight increased by 8.4% due to a higher increase in live weight by 16.5%-22.1% allowing us to conclude the positive effect of crossing and using a hepatoprotective complex when breeding geese. The research made it possible to improve geese' productive qualities through hybridization and the use of a hepatoprotective complex. This information can contribute to the genetic improvement of body size in current breeding programs.

Crossbreeding impacts on caecal bacterial count and antibody titres in chickens

1. A crossbreeding experiment was conducted using 20 sires and 120 dams from each Fayoumi (F) and Rhode Island Red (R) breeds. The F₁ chicks of ½F½R and their reciprocal ½R½F crosses were used to estimate direct, maternal and heterotic effects.2. The caecal bacterial counts of Salmonella typhimurium and Enterococcus faecium and the IgA, IgG and IgM antibody titres were determined. Chicks of each genetic group (120 birds) were divided into three groups (40 birds per group) and chicks of the first group were assigned as the control group, while the second group was inoculated with S. typhimurium and E. faecium at 7 and 10 d of age (10⁶ cfu/chick) and the third was inoculated with S. typhimurium at 10 d of age (10⁶ cfu/chick).3. The generalised least square procedure was used to estimate cross-breeding effects. The S. typhimurium counts in the R breed was highly significant, followed by ½F½R cross, ½R½F cross, and F breed. The differences among genetic groups in E. faecium counts and caecal pH was not significant. The estimates of IgA, IgG, and IgM antibody titres were highly significant in the F breed, followed by ½R½F cross, ½F½R cross, and the R breed.4. The estimates of direct additive effects were highly significant F breed for the counts of S. typhimurium and antibody titres of IgA, IgG, and IgM. The maternal effects were highly significant F breed for S. typhimurium, E. faecium count, and antibody titres of IgA, IgG, and IgM. Estimates of direct heterosis were significant for S. typhimurium count and IgA antibody titre but not significant for E. faecium count, caecal pH, and antibody titres of IgG and IgM.5. The results showed that the Fayoumi breed could be used in breeding programmes to improve immunity traits against S. typhimurium in chickens.

Crossing effect for improving egg production traits in chickens involving local and commercial strains

Aim

This study aimed to contribute to the productivity improvement of the local chickens by enhancing their egg production traits using a crossbreeding program between Alexandria (local strain) and Lohmann White (commercial strain).

Materials and Methods

One thousand two-hundred and eighty-five 4-week-old chicks from two strains: Alexandria local strain (AA) and Lohmann White commercial strain (LL) and their reciprocal crosses obtained from 16 males and 160 females, were used to produce four genetic groups (AA, LL, AL, and LA). Differences among genotypes, direct additive, heterosis, and reciprocal effects were investigated regarding the following traits: Body weight at 4 and 8 weeks and at the age of sexual maturity, age at sexual maturity, egg production, average egg weight, and egg mass during the first 90 days of laying.

Results

Statistically significant effects of the genotypes were observed on traits studied. Analysis of direct additive effects showed that AA was superior as a sire strain for improving body weight at early age. For egg traits (age at sexual maturity, egg production, average egg weight, and egg mass), LL was better as a sire strain to improve these traits. Significant positive heterosis percentages were observed for body weight. The crosses (AL and reciprocal) were significantly superior in egg traits (egg production, average egg weight, and egg mass) compared to the local strain. The cross (LA) laid significantly earlier than the local strain. Analysis of reciprocal effects cleared that the local strain could be used as a strain of dam to improve body weight and egg traits.

Conclusion

Crossing improved egg production, egg weight, and egg mass in hybrids compared to the local strain.