Toll-Like Receptor Gene Expression in Cecum and Spleen of Chicks Challenged with Salmonella Enterica Serovar Enteritidis

Toll-like receptors (TLR) recognize pathogenassociated molecular patterns (PAMP) of infectious microbes. Activation of TLR with PAMP can result in immune response by modulation of innate and adoptive immune system. This study aimed to investigate the acute effect of Salmonella challenge on TLR RNA expression in cecum and spleen of birds from different genetic lines. Chicks from broiler, Leghorn, and Fayoumi lines were challenged or mock challenged with Salmonella. The RNA expression levels of TLR2, TLR4 and TLR5 genes were assessed by quantitative RT-PCR in cecum and spleen tissue harvested at 2 or 18 h post-challenge. The results demonstrate a significant genetic line effect on TLR expression in the spleen of Salmonella infected birds, which may partly explain the genetic variability in immune response to Salmonella enterica serovar Enteritidis. The higher level of TLR2 and TLR4 RNA expression observed in the spleen of Fayoumi line compare to Leghorn and broiler lines in Salmonella enterica serovar Enteritidis challenged birds may be associated with the stronger immune response to the infection and might be useful characteristics to be considered in breeding immunocompetent chickens

SNPs in Region of NF-Kappa-B Gene Associated with Expression of Immune-Related Genes

Selection to enhance immune response is difficult. Gene expression was assessed in two advanced intercross lines of chickens for various immune-related genes. Single nucleotide polymorphisms, SNPs, were identified in regions local to each gene and around a distant transcription factor, NF-Kappa-B, NFKB. These SNPs were used to identify expression QTL, eQTL, to aid in selection of immune gene expression. These eQTL may provide effective resources to which marker assisted selection may be applied

Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data

The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5

<p>Abstract</p> <p>Background</p> <p>Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF) previously detected on chromosome 5 (GGA5).</p> <p>Results</p> <p>Hepatic transcriptome profiles for 45 offspring of a sire known to be heterozygous for the distal GGA5 AF QTL were obtained using a 20 K chicken oligochip. mRNA levels of 660 genes were correlated with the AF trait. The first approach was to dissect the AF phenotype by identifying animal subgroups according to their 660 transcript profiles. Linkage analysis using some of these subgroups revealed another QTL in the middle of GGA5 and increased the significance of the distal GGA5 AF QTL, thereby refining its localization. The second approach targeted the genes correlated with the AF trait and regulated by the GGA5 AF QTL region. Five of the 660 genes were considered as being controlled either by the AF QTL mutation itself or by a mutation close to it; one having a function related to lipid metabolism (HMGCS1). In addition, a QTL analysis with a multiple trait model combining this 5 gene-set and AF allowed us to refine the QTL region. The third approach was to use these 5 transcriptome profiles to predict the paternal Q versus q AF QTL mutation for each recombinant offspring and then refine the localization of the QTL from 31 cM (100 genes) at a most probable location confidence interval of 7 cM (12 genes) after determining the recombination breakpoints, an interval consistent with the reductions obtained by the two other approaches.</p> <p>Conclusion</p> <p>The results showed the feasibility and efficacy of the three strategies used, the first revealing a QTL undetected using the whole population, the second providing functional information about a QTL region through genes related to the trait and controlled by this region (HMGCS1), the third could drastically refine a QTL region.</p

Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations

A 3,072 single nucleotide polymorphism (SNP) panel was used to identify genetic markers linked to quantitative trait loci (QTL). Two association methods were used to search for QTL, SNP-wise and genome-wise models. The QTL associated with SNPs, found using both of these methods, can be applied to breeding programs in marker assisted selection (MAS). The extent and consistency of linkage disequilibrium (LD) was measured in two lines of commercial egg laying chickens by analysis of SNPs. Correlations were drawn between measurements of two consecutive years to determine consistency. At short distances, LD is retained which allows for markers at high LD with a trait to be effectively applied in MAS

A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes

BACKGROUND: The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. RESULTS: A total of 169 markers (21 microsatellites and 148 ESTs) were typed on the ChickRH6 RH panel, of which 134 were assigned to GGA5. The final map is composed of 73 framework markers extending over a 1315.6 cR distance. The remaining 61 markers were placed alongside the framework markers within confidence intervals. CONCLUSION: The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome

Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness

Quantitative trait loci (QTL) for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation