Genome-wide association study of antibody response to Newcastle disease virus in chicken

Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda

A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E-5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E-5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E-5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.

Heritability Estimate for Antibody Response to Vaccination and Survival to a Newcastle Disease Infection of Native chicken in a Low-Input Production System

The Newcastle disease virus (NDV) is the deadliest chicken pathogen in low-input village poultry, and selecting for NDV resistance has been recommended as a sustainable strategy in backyard poultry production systems. However, selecting for disease resistance needs precision data from either a big population sample size or on many generations with good pedigree records for effective prediction of heritability (h²) and breeding values of the foundation stock. Such conditions are almost impossible to meet in low-input backyard production systems. This study aimed at proposing a realistic method for estimating the heritability of the immune response to vaccination and survival of NDV infection in village poultry production to inform a breeding strategy for ND resistance in Cameroon. A 1 and 3% selection intensity of cocks and hens for higher antibody (ab) response (ABR) to vaccination followed by progeny selection of chickens who survived an experimental NDV infection was conducted from an initial population of 1,702 chickens. The selection induced an increase of 1012.47units/ml (p<0.01) of the NDV antibody of the progeny as well as an effective survival rate (ESR) increase of 11.75%. Three methods were used to estimate the heritability (h2) of NDV antibody response to vaccination. h2 was low irrespective of the method with estimates of 0.2227, 0.2442, and 0.2839 for the breeder’s equation method, the graphical method, and the full-sib/half-sib nested design, respectively. The mortality rate of infected chickens was high (86%). The antibody response to selection was not influenced by sex and genetic type even though the opposite was observed (p<0.05) for the ESR to NDV infection with naked neck chickens recording an ESR of 14% against 2.25% for the normal feather type. A very low heritability (0.0891) was observed for the survival against NDV infection. We confirm the evidence of disease resistance and the effect of selection for antibody response to vaccination on the improvement of the survival against NDV disease. Although the full sib/half sib nested design is more appropriate in case of availability of pedigree information, the direct methods are still useful in case of unavailability of full pedigree information. It is recommended that gene expression analysis should be prioritized for disease-resistance assessment and selection of native breeds of poultry.

Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs

Background

The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic data to study vaccine effectiveness in pigs.

Results

A cohort of 182 Large White pigs was vaccinated against Mycoplasma hyopneumoniae (M. hyo) at weaning (28 days of age), with a booster 21 days later. Vaccine response was assessed by measuring seric M. hyo antibodies (Ab) at 0 (vaccination day), 21 (booster day), 28, 35, and 118 days post-vaccination (dpv). Inter-individual variability of M. hyo Ab levels was observed at all time points and the corresponding heritabilities ranged from 0.46 to 0.57. Ab persistence was higher in females than in males. Genome-wide association studies with a 658 K SNP panel revealed two genomic regions associated with variations of M. hyo Ab levels at 21 dpv at positions where immunity-related genes have been mapped, DAB2IP on chromosome 1, and ASAP1, CYRIB and GSDMC on chromosome 4. We studied covariations of Ab responses with the pre-vaccination blood transcriptome obtained by RNA-Seq for a subset of 82 pigs. Weighted gene correlation network and differential expression analyses between pigs that differed in Ab responses highlighted biological functions that were enriched in heme biosynthesis and platelet activation for low response at 21 dpv, innate antiviral immunity and dendritic cells for high response at 28 and 35 dpv, and cell adhesion and extracellular matrix for high response at 118 dpv. Sparse partial least squares discriminant analysis identified 101 genes that efficiently predicted divergent responders at all time points. We found weak negative correlations of M. hyo Ab levels with body weight traits, which revealed a trade-off that needs to be further explored.

Conclusions

We confirmed the influence of the host genetics on vaccine effectiveness to M. hyo and provided evidence that the pre-vaccination blood transcriptome co-varies with the Ab response. Our results highlight that both genetic markers and blood biomarkers could be used as potential predictors of vaccine response levels and more studies are required to assess whether they can be exploited in breeding programs.

Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line

Two environmental factors, Newcastle disease and heat stress, are concurrently negatively impacting poultry worldwide and warrant greater attention into developing genetic resistance within chickens. Using two genetically distinct and highly inbred layer lines, Fayoumi and Leghorn, we explored how different genetic backgrounds affect the bursal response to a treatment of simultaneous Newcastle disease virus (NDV) infection at 6 days postinfection (dpi) while under chronic heat stress. The bursa is a primary lymphoid organ within birds and is crucial for the development of B cells. We performed RNA-seq and ChIP-seq targeting histone modifications on bursa tissue. Differential gene expression revealed that Leghorn, compared to Fayoumi, had significant down-regulation in genes involved in cell proliferation, cell cycle, and cell division. Interestingly, we also found greater differences in histone modification levels in response to treatment in Leghorns than Fayoumis, and biological processes enriched in associated target genes of H3K27ac and H3K4me1 were similarly associated with cell cycle and receptor signaling of lymphocytes. Lastly, we found candidate variants between the two genetic lines within exons of differentially expressed genes and regulatory elements with differential histone modification enrichment between the lines, which provides a strong foundation for understanding the effects of genetic variation on NDV resistance under heat stress. This study provides further understanding of the cellular mechanisms affected by NDV infection under heat stress in chicken bursa and identified potential genes and regulatory regions that may be targets for developing genetic resistance within chickens.

Genetic Basis of Response of Ghanaian Local Chickens to Infection With a Lentogenic Newcastle Disease Virus

Newcastle disease (ND) is a global threat to domestic poultry, especially in rural areas of Africa and Asia, where the loss of entire backyard local chicken flocks often threatens household food security and income. To investigate the genetics of Ghanaian local chicken ecotypes to Newcastle disease virus (NDV), in this study, three popular Ghanaian chicken ecotypes (regional populations) were challenged with a lentogenic NDV strain at 28 days of age. This study was conducted in parallel with a similar study that used three popular Tanzanian local chicken ecotypes and after two companion studies in the United States, using Hy-line Brown commercial laying birds. In addition to growth rate, NDV response traits were measured following infection, including anti-NDV antibody levels [pre-infection and 10 days post-infection (dpi)], and viral load (2 and 6 dpi). Genetic parameters were estimated, and two genome-wide association study analysis methods were used on data from 1,440 Ghanaian chickens that were genotyped on a chicken 600K Single Nucleotide Polymorphism (SNP) chip. Both Ghana and Tanzania NDV challenge studies revealed moderate to high (0.18 – 0.55) estimates of heritability for all traits, except viral clearance where the heritability estimate was not different from zero for the Tanzanian ecotypes. For the Ghana study, 12 quantitative trait loci (QTL) for growth and/or response to NDV from single-SNP analyses and 20 genomic regions that explained more than 1% of genetic variance using the Bayes B method were identified. Seven of these windows were also identified as having at least one significant SNP in the single SNP analyses for growth rate, anti-NDV antibody levels, and viral load at 2 and 6 dpi. An important gene for growth during stress, CHORDC1 associated with post-infection growth rate was identified as a positional candidate gene, as well as other immune related genes, including VAV2, IL12B, DUSP1, and IL17B. The QTL identified in the Ghana study did not overlap with those identified in the Tanzania study. However, both studies revealed QTL with genes vital for growth and immune response during NDV challenge. The Tanzania parallel study revealed an overlapping QTL on chromosome 24 for viral load at 6 dpi with the US NDV study in which birds were challenged with NDV under heat stress. This QTL region includes genes related to immune response, including TIRAP, ETS1, and KIRREL3. The moderate to high estimates of heritability and the identified QTL suggest that host response to NDV of local African chicken ecotypes can be improved through selective breeding to enhance increased NDV resistance and vaccine efficacy.

Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18–0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes.

Genetics and Genomic Regions Affecting Response to Newcastle Disease Virus Infection under Heat Stress in Layer Chickens

Newcastle disease virus (NDV) is a highly contagious avian pathogen that poses a tremendous threat to poultry producers in endemic zones due to its epidemic potential. To investigate host genetic resistance to NDV while under the effects of heat stress, a genome-wide association study (GWAS) was performed on Hy-Line Brown layer chickens that were challenged with NDV while under high ambient temperature to identify regions associated with host viral titer, circulating anti-NDV antibody titer, and body weight change. A single nucleotide polymorphism (SNP) on chromosome 1 was associated with viral titer at two days post-infection (dpi), while 30 SNPs spanning a quantitative trait loci (QTL) on chromosome 24 were associated with viral titer at 6 dpi. Immune related genes, such as CAMK1d and CCDC3 on chromosome 1, associated with viral titer at 2 dpi, and TIRAP, ETS1, and KIRREL3, associated with viral titer at 6 dpi, were located in two QTL regions for viral titer that were identified in this study. This study identified genomic regions and candidate genes that are associated with response to NDV during heat stress in Hy-Line Brown layer chickens. Regions identified for viral titer on chromosome 1 and 24, at 2 and 6 dpi, respectively, included several genes that have key roles in regulating the immune response.

Turkey humoral and cell-mediated immune responses to a Newcastle viscerotropic vaccine and its association with major histocompatibility complex

Immune responses to vaccines are mainly influenced by the nature of vaccines and host variation in response to vaccination. In this study we aimed to investigate turkey humoral and cell-mediated immune responses to a Newcastle viscerotropic vaccine and its association with major histocompatibility complex (MHC). Turkeys were vaccinated with Villegas–Glisson/University of Georgia (VG/GA) attenuated vaccine against Newcastle disease. The stimulation index of lymphocyte proliferation and antigen-specific local secretory IgA responses in bile, duodenum, ileum, as well as serum IgY and IgA responses were analysed by enzyme-linked immunosorbent assay. The turkey MHC class II B locus was selected as candidate gene for detection of associations with cellular and humoral immune responses. Significant differences were observed between both cellular and humoral responses of vaccinated and unvaccinated groups. A significant positive correlation was also found between ND specific IgY and ND specific IgA titres in serum, intestine (duodenum and ileum) and trachea. Moreover, the correlation between specific IgA titres in ileum and specific bile, duodenum and trachea was positively significant. High resolution melting analysis (HRM) was used to genotype MHC class II B exon 2. Eight melting profiles (A-G) were identified, among which, profile G showed a significant association with cellular response. The profile B revealed significant association with total IgA titres in serum and ileum. These findings help our understanding of the association of turkey MHC types with immune responses. Further correlation analysis between serum and mucosal antibody titres demonstrated that the levels of IgY and IgA in serum can give an impression about the levels of secretory IgA and situation of mucosal immunity. Based on the significant effects, ND specific IgY in serum appears to be a promising indirect marker for specific IgA in serum and trachea.

Genomic loci associated with antibody-mediated immune responses in an F2 chicken population

Immunity-related traits are heritable in chicken, therefore, it is possible to improve the inherent immunity by breeding programs. In this study using the Illumina chicken 60K single nucleotide polymorphisms (SNPs) chip, we performed a set of genome-wide association studies to determine candidate genes and loci responsible for primary and secondary antibody-mediated responses against sheep red blood cell. A F2 population descended from a commercial meat-type breed and an Iranian indigenous chicken was used for this study. Statistical analysis was based on a mixed linear model utilizing genomic relationship matrix to prevent spurious associations. Correction for multiple testing was done by applying 5% and 10% chromosomal false discovery rates (FDRs) for significant and suggestive thresholds, respectively. Nine significant and 17 suggestive associated SNPs were identified. Most of the SNPs that were suggestively associated with the primary response of total plasma immunoglobulins were also significantly associated with this trait in secondary response. Three SNPs were located within a narrow region of 23 kb on chromosome 16. Pathway analysis for the genes surrounding the associated SNPs showed that they are involve in antigen processing and presentation, primary immunodeficiency, vitamin digestion and absorption, cell adhesion molecules, phagosome, influenza A, folding, assembly and peptide loading of class I major histocompatibility complex, lipid digestion, mobilization, and transport (FDR &lt; 0.1). Interestingly, there were common regains associated with multiple immune-related traits.

SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium

Background

High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, this warrants pruning of genotyping data for high LD. We developed an algorithm, named SNPrune, which enables the rapid detection of any pair of SNPs in complete or high LD throughout the genome.

Methods

LD, measured as the squared correlation between phased alleles (r²), can only reach a value of 1 when both loci have the same count of the minor allele. Sorting loci based on the minor allele count, followed by comparison of their alleles, enables rapid detection of loci in complete LD. Detection of loci in high LD can be optimized by computing the range of the minor allele count at another locus for each possible value of the minor allele count that can yield LD values higher than a predefined threshold. This efficiently reduces the number of pairs of loci for which LD needs to be computed, instead of considering all pairwise combinations of loci. The implemented algorithm SNPrune considered bi-allelic loci either using phased alleles or allele counts as input. SNPrune was validated against PLINK on two datasets, using an r² threshold of 0.99. The first dataset contained 52k SNP genotypes on 3534 pigs and the second dataset contained simulated whole-genome sequence data with 10.8 million SNPs and 2500 animals.

Results

SNPrune removed a similar number of SNPs as PLINK from the pig data but SNPrune was almost 12 times faster than PLINK. From the simulated sequence data with 10.8 million SNPs, SNPrune removed 6.4 and 1.4 million SNPs due to complete and high LD. Results were very similar regardless of whether phased alleles or allele counts were used. Using allele counts and multi-threading with 10 threads, SNPrune completed the analysis in 21 min. Using a sliding window of up to 500,000 SNPs, PLINK removed ~ 43,000 less SNPs (0.6%) in the sequence data and SNPrune was 24 to 170 times faster, using one or ten threads, respectively.

Conclusions

The SNPrune algorithm developed here is able to remove SNPs in high LD throughout the genome very efficiently in large datasets.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0404-z) contains supplementary material, which is available to authorized users.

Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication

Background

Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process.

Results

We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes.

Conclusions

Our study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-1036-6) contains supplementary material, which is available to authorized users.

Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F₂ chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.

Genomewide association study of immune traits in chicken F2 resource population

Immune traits play pivotal roles in animal immune capacity development and disease resistance. Single nucleotide polymorphisms (SNPs) are common forms of genetic variations among individuals, which are thought to account for the majority of inherited phenotypic variations. In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10(-6) ) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10(-5) ) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10(-5) ) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven suggestive SNPs). Three significant SNPs (GGaluGA151406, Gga_rs14554319 and Gga_rs13593979) and candidate genes (LYRM4 and KTN1) were found to be associated with avian influenza antibody titres, and the first two SNPs are from the results of two-model analysis. For the immune organs, through the analysis of GLM, 19 SNPs were found to be significantly associated with the thymus weight, 61 SNPs were significantly associated with the bursa of Fabricius weight, six of which were located within a 34-Mb region (125 846 474-159 649 698 bp) on chicken chromosome 1 (GGA1). A candidate region relevant to haematological traits from GLM was found in GGA4 and 9 loci were located on it. Three loci (GGaluGA348521, Gga_rs16098446 and GGaluGA348518) within 179 kb (16 286 868-16 466 134 bp) on GGAZ from GLM provided evidence that this genomic segment may be relevant to red blood cell volume distribution width (RDW). Our study provides a list of significant SNPs and candidate genes that will be valuable information for unveiling the underlying molecular mechanism of immune regulation.

Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens

BACKGROUND

As a major economic trait in chickens, egg weight (EW) receives widespread interests in breeding, production and consumption. However, limited information is available for underlying genetic architecture of longitudinal trend in EW. Herein, we measured EWs at nine time points from onset of laying to 60 week of age, and conducted comprehensive genome-wide association studies (GWAS) in 1,534 F2 hens derived from reciprocal crosses between White Leghorn and Dongxiang chickens.

RESULTS

Egg weights at all ages except the first egg weight (FEW) exhibited high SNP-based heritability estimates (0.47~0.60). Strong pair-wise genetic correlations (0.77~1.00) were found among all EWs. Nine separate univariate genome-wide screens suggested 73 signals showing significant associations with longitudinal EWs. After multivariate and conditional analyses, four variants on three chromosomes remained independent contributions. The minor alleles at two loci exerted consistent and positive substitution effects on EWs, and other two were negative. The four loci together accounted for 3.84 % of the phenotypic variance for FEW and 7.29~11.06 % for EWs from 32 to 60 week of age. We obtained five candidate genes, of which NCAPG harbors a non-synonymous SNP (rs14491030) causing a valine-to-alanine amino-acid substitution. Genome partitioning analysis indicated a strong linear correlation between the variance explained by each chromosome and its length, which provided evidence that EW follows a highly polygenic nature of inheritance.

CONCLUSIONS

Identification of significant genetic causes that together implicate EWs at different ages will greatly advance our understanding of the genetic basis behind longitudinal EWs, and would be helpful to illuminate the future breeding direction on how to select desired egg size.

Stories and Challenges of Genome Wide Association Studies in Livestock - A Review

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

The identification of loci for immune traits in chickens using a genome-wide association study

The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.

A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance

Background

Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus).

Results

A genomic region on linkage group 7 was found to be significantly associated with columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host.

Conclusion

The GWAS revealed four QTLs associated with columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for columnaris resistance.

Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology

Newcastle disease (ND) and avian infectious bronchitis (IB) are contagious diseases of chickens. To identify genes associated with antibody levels against ND and IB, a genome-wide association study was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in Jinghai yellow chickens. This determined six single-nucleotide polymorphisms (SNPs) that were associated with antibody levels against Newcastle disease virus (NDV): rsZ2494661, rsZ2494710, rs1211307701, rs1211307711, rs1218289310 and rs420701988. Of these, rsZ2494661 and rsZ2494710 reached the 5 % Bonferroni genome-wide significance level (5.5E-07) and they were both 134.7 kb downstream of the SETBP1 gene. The remaining four SNPs had 'suggestive' genome-wide significance levels (1.1E-05) and they were within or near the Plexin B1, LRRN1 and PDGFC genes. IB had two SNPs associated with antibody levels: rs149988433 and rs16170823; both reached chromosome-wide significance levels and they were near the USP7 and TRIM27 genes, respectively. Bioinformatics, GO annotation and pathway analysis indicated that five of these genes (Plexin B1, TRIM27, PDGFC, SETBP1 and USP7) may be important for the generation of protective antibodies against NDV and infectious bronchitis virus (IBV). This paves the way for further research on host immune responses against NDV.

Genomic selection for the improvement of antibody response to Newcastle disease and avian influenza virus in chickens

Newcastle disease (ND) and avian influenza (AI) are the most feared diseases in the poultry industry worldwide. They can cause flock mortality up to 100%, resulting in a catastrophic economic loss. This is the first study to investigate the feasibility of genomic selection for antibody response to Newcastle disease virus (Ab-NDV) and antibody response to Avian Influenza virus (Ab-AIV) in chickens. The data were collected from a crossbred population. Breeding values for Ab-NDV and Ab-AIV were estimated using a pedigree-based best linear unbiased prediction model (BLUP) and a genomic best linear unbiased prediction model (GBLUP). Single-trait and multiple-trait analyses were implemented. According to the analysis using the pedigree-based model, the heritability for Ab-NDV estimated from the single-trait and multiple-trait models was 0.478 and 0.487, respectively. The heritability for Ab-AIV estimated from the two models was 0.301 and 0.291, respectively. The estimated genetic correlation between the two traits was 0.438. A four-fold cross-validation was used to assess the accuracy of the estimated breeding values (EBV) in the two validation scenarios. In the family sample scenario each half-sib family is randomly allocated to one of four subsets and in the random sample scenario the individuals are randomly divided into four subsets. In the family sample scenario, compared with the pedigree-based model, the accuracy of the genomic prediction increased from 0.086 to 0.237 for Ab-NDV and from 0.080 to 0.347 for Ab-AIV. In the random sample scenario, the accuracy was improved from 0.389 to 0.427 for Ab-NDV and from 0.281 to 0.367 for Ab-AIV. The multiple-trait GBLUP model led to a slightly higher accuracy of genomic prediction for both traits. These results indicate that genomic selection for antibody response to ND and AI in chickens is promising.

An association between genetic variation in the roundabout, axon guidance receptor, homolog 2 gene and immunity traits in chickens

The roundabout, axon guidance receptor, homolog 2 (ROBO2) gene is one member of the roundabout (ROBO) family, which belongs to the immunoglobulin superfamily. The ROBO molecules are known to function in axon guidance and cell migration and are involved in SLIT/ROBO signaling. In this study, we obtained the full-length cDNA sequence of the chicken ROBO2 gene. Sequence analysis indicated that 3 SNP (1418G > A, 1421C > A and 2462T > C) exist in exons 5 and 12 of the ROBO2 gene. Genotyping results revealed that the allele frequency of SNP 1421C > A was similar in all tested breeds, but the allele frequencies of the other 2 SNP were different between White Leghorn and Chinese indigenous chickens. Allele G of 1418G > A and allele T of 2462T > C predominated in the Chinese indigenous breed, whereas alleles A and C predominated in the White Leghorn breed. Association analyses revealed that birds with the GG genotype of SNP 1418G > A or the TT genotype of SNP 2462T > C had significantly higher antibody responses to Newcastle disease virus (NDV_S/P; P < 0.01) than carriers of the A allele (GA and AA) or the C allele (TC), respectively. Real-time PCR further revealed that ROBO2 expression in the spleens of the birds with higher antibody responses (GG and TT genotypes at SNP 1418 and 2462, respectively) was significantly higher than in the spleens of birds with the AA and AG genotypes at SNP 1418 or the TC genotype at SNP 2462 (P < 0.01). The results demonstrated that genetic variation at the ROBO2 gene plays a key role in the immune response to Newcastle disease virus, and SNP 1418G > A and 2462T > C can be used as genetic markers for the selection of chickens with stronger immune responses to Newcastle disease virus.

A genome-wide association study identifies major loci affecting the immune response against infectious bronchitis virus in chicken

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The genetic basis of host responses to infectious bronchitis virus is unclear.

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We detected 20 significant markers for the antibody response to infectious bronchitis virus in chicken.

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Loci on chromosomes 1 and 5 explained 12% and 13% of phenotypic variation.

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The host immune response cluster had 13 beta-defensin and interleukin-17F genes.

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Our results will contribute to the control of outbreaks of infectious bronchitis.

Coronaviruses are a hot research topic because they can cause severe diseases in humans and animals. Infectious bronchitis virus (IBV), belonging to gamma-coronaviruses, causes a highly infectious respiratory viral disease and can result in catastrophic economic losses to the poultry industry worldwide. Unfortunately, the genetic basis of the host immune responses against IBV is poorly understood. In the present study, the antibody levels against IBV post-immunization were measured by an enzyme-linked immunosorbent assay in the serum of 511 individuals from a commercial chicken (Gallus gallus) population. A genome-wide association study using 43,211 single nucleotide polymorphism markers was performed to identify the major loci affecting the immune response against IBV. This study detected 20 significant (P < 1.16 × 10⁻⁶) effect single nucleotide polymorphisms for the antibody level against IBV. These single nucleotide polymorphisms were distributed on five chicken chromosomes (GGA), involving GGA1, GGA3, GGA5, GGA8, and GGA9. The genes in the 1-Mb windows surrounding each single nucleotide polymorphism with significant effect for the antibody level against IBV were associated with many biological processes or pathways related to immunity, such as the defense response and mTOR signaling pathway. A genomic region containing a cluster of 13 beta-defensin (GAL1–13) and interleukin-17F genes on GGA3 probably plays an important role in the immune response against IBV. In addition, the major loci significantly associated with the antibody level against IBV on GGA1 and GGA5 could explain about 12% and 13% of the phenotypic variation, respectively. This study suggested that the chicken genome has several important loci affecting the immune response against IBV, and increases our knowledge of how to control outbreaks of infectious bronchitis.