A genome-wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease

Genome-wide re-sequencing reveals selection signatures for important economic traits in Taihang chickens

Taihang chickens is precious genetic resource with excellent adaptability and disease resistance, as well as high-quality eggs and meat. However, the genetic mechanism underlying important economic traits remain largely unknown. To address this gap, we conducted whole-genome resequencing of 66 Taihang and 15 White Plymouth rock chicken (Baiyu). The population structure analysis revealed that Taihang chickens and Baiyu are 2 independent populations. The genomic regions with strong selection signals and some candidate genes related to economic and appearance traits were identified. Additionally, we found a continuously selected 1.2 Mb region on chromosome 2 that is closely related to disease resistance. Therefore, our findings were helpful in further understanding the genetic architecture of the Taihang chickens and provided a worthy theoretical basis and technological support to improve high-quality Taihang chickens.

Epigenetic Factor MicroRNAs Likely Mediate Vaccine Protection Efficacy against Lymphomas in Response to Tumor Virus Infection in Chickens through Target Gene Involved Signaling Pathways

Epigenetic factors, including microRNAs (miRNAs), play an important role in affecting gene expression and, therefore, are involved in various biological processes including immunity protection against tumors. Marek's disease (MD) is a highly contagious disease of chickens caused by the MD virus (MDV). MD has been primarily controlled by vaccinations. MD vaccine efficacy might, in part, be dependent on modulations of a complex set of factors including host epigenetic factors. This study was designed to identify differentially expressed miRNAs in the primary lymphoid organ, bursae of Fabricius, in response to MD vaccination followed by MDV challenge in two genetically divergent inbred lines of White Leghorns. Small RNA sequencing and bioinformatic analyses of the small RNA sequence reads identified hundreds of miRNAs among all the treatment groups. A small portion of the identified miRNAs was differentially expressed within each of the four treatment groups, which were HVT or CVI988/Rispens vaccinated line 63-resistant birds and line 72-susceptible birds. A direct comparison between the resistant line 63 and susceptible line 72 groups vaccinated with HVT followed by MDV challenge identified five differentially expressed miRNAs. Gene Ontology analysis of the target genes of those five miRNAs revealed that those target genes, in addition to various GO terms, are involved in multiple signaling pathways including MAPK, TGF-β, ErbB, and EGFR1 signaling pathways. The general functions of those pathways reportedly play important roles in oncogenesis, anti-cancer immunity, cancer cell migration, and metastatic progression. Therefore, it is highly likely that those miRNAs may, in part, influence vaccine protection through the pathways.

Genome-wide allele frequency studies in Pacific oyster families identify candidate genes for tolerance to ostreid herpesvirus 1 (OsHV-1)

BACKGROUND

Host genetics influences the development of infectious diseases in many agricultural animal species. Identifying genes associated with disease development has the potential to make selective breeding for disease tolerance more likely to succeed through the selection of different genes in diverse signaling pathways. In this study, four families of Pacific oysters (Crassostrea gigas) were identified to be segregating for a quantitative trait locus (QTL) on chromosome 8. This QTL was previously found to be associated with basal antiviral gene expression and survival to ostreid herpesvirus 1 (OsHV-1) mortality events in Tomales Bay, California. Individuals from these four families were phenotyped and genotyped in an attempt to find candidate genes associated with the QTL on chromosome 8.

RESULTS

Genome-wide allele frequencies of oysters from each family prior to being planting in Tomales Bay were compared with the allele frequencies of oysters from respective families that survived an OsHV-1 mortality event. Six significant unique QTL were identified in two families in these genome-wide allele frequency studies, all of which were located on chromosome 8. Three QTL were assigned to candidate genes (ABCA1, PIK3R1, and WBP2) that have been previously associated with antiviral innate immunity in vertebrates.

CONCLUSION

The identification of vertebrate antiviral innate immunity genes as candidate genes involved in molluscan antiviral innate immunity reinforces the similarities between the innate immune systems of these two groups. Causal variant identification in these candidate genes will enable future functional studies of these genes in an effort to better understand their antiviral modes of action.

Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing

Background

Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers.

Results

In total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene.

Conclusions

The results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08236-3.

Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens

Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.

Genome-wide association study of body size traits in Wenshang Barred chickens based on the specific-locus amplified fragment sequencing technology

Chicken body size (BS) is an economically important trait, which has been assessed in many studies for genetic selection. However, previous reports detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) of purebred Wenshang Barred chickens. A total of 250 one-day-old male chickens were assessed in this study. Body size in individual birds was measured at 56 days. SLAF-seq was used to genotype and GWAS analysis was carried out using the general linear model (GLM) of the TASSEL program. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, of which 175,211 were tested as candidate SNPs for genome-wide association analysis using the TASSEL general linear model. Three SNPs markers reached genome-wide significance. Of these, chrZ:81729634, chrZ:81841715, and chrZ:81954149 at 81,729,634, 81,841,715, and 81,954,149 bp of GGA Z were significantly associated with body diagonal length at 56 days (BDL56); and tibia length at 56 days (TL56). These SNPs were close to three genes, including ZCCHC7, PAX5, and MELK. These results open new horizons for studies on BS and should promote the use of Chinese chickens, especially Wenshang Barred chickens.

Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data

Individuals differ widely in their contribution to the spread of infection within and across populations. Three key epidemiological host traits affect infectious disease spread: susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection to others) and recoverability (propensity to recover quickly). Interventions aiming to reduce disease spread may target improvement in any one of these traits, but the necessary statistical methods for obtaining risk estimates are lacking. In this paper we introduce a novel software tool called SIRE (standing for "Susceptibility, Infectivity and Recoverability Estimation"), which allows for the first time simultaneous estimation of the genetic effect of a single nucleotide polymorphism (SNP), as well as non-genetic influences on these three unobservable host traits. SIRE implements a flexible Bayesian algorithm which accommodates a wide range of disease surveillance data comprising any combination of recorded individual infection and/or recovery times, or disease diagnostic test results. Different genetic and non-genetic regulations and data scenarios (representing realistic recording schemes) were simulated to validate SIRE and to assess their impact on the precision, accuracy and bias of parameter estimates. This analysis revealed that with few exceptions, SIRE provides unbiased, accurate parameter estimates associated with all three host traits. For most scenarios, SNP effects associated with recoverability can be estimated with highest precision, followed by susceptibility. For infectivity, many epidemics with few individuals give substantially more statistical power to identify SNP effects than the reverse. Importantly, precise estimates of SNP and other effects could be obtained even in the case of incomplete, censored and relatively infrequent measurements of individuals' infection or survival status, albeit requiring more individuals to yield equivalent precision. SIRE represents a new tool for analysing a wide range of experimental and field disease data with the aim of discovering and validating SNPs and other factors controlling infectious disease transmission.

Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

Mapping QTL Associated with Resistance to Avian Oncogenic Marek's Disease Virus (MDV) Reveals Major Candidate Genes and Variants

Marek’s disease (MD) represents a significant global economic and animal welfare issue. Marek’s disease virus (MDV) is a highly contagious oncogenic and highly immune-suppressive α-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impact on animal health and on the poultry industry. Genetic selection provides an alternative and complementary method to vaccination. However, even after years of study, the genetic mechanisms underlying resistance to MDV remain poorly understood. The Major Histocompatability Complex (MHC) is known to play a role in disease resistance, along with a handful of other non-MHC genes. In this study, one of the largest to date, we used a multi-facetted approach to identify quantitative trait locus regions (QTLR) influencing resistance to MDV, including an F₆ population from a full-sib advanced intercross line (FSIL) between two elite commercial layer lines differing in resistance to MDV, RNA-seq information from virus challenged chicks, and genome wide association study (GWAS) from multiple commercial lines. Candidate genomic elements residing in the QTLR were further tested for association with offspring mortality in the face of MDV challenge in eight pure lines of elite egg-layer birds. Thirty-eight QTLR were found on 19 chicken chromosomes. Candidate genes, microRNAs, long non-coding RNAs and potentially functional mutations were identified in these regions. Association tests were carried out in 26 of the QTLR, using eight pure lines of elite egg-layer birds. Numerous candidate genomic elements were strongly associated with MD resistance. Genomic regions significantly associated with resistance to MDV were mapped and candidate genes identified. Various QTLR elements were shown to have a strong genetic association with resistance. These results provide a large number of significant targets for mitigating the effects of MDV infection on both poultry health and the economy, whether by means of selective breeding, improved vaccine design, or gene-editing technologies.

A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens

Background

Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which causes high mortality. Furthermore, an outbreak of SP infection can result in a considerable number of carriers that become potential transmitters, thus, threatening fellow chickens and offspring. In this study, we conducted a genome-wide association study (GWAS) to detect potential genomic loci and candidate genes associated with two disease-related traits: death and carrier state.

Methods

In total, 818 birds were phenotyped for death and carrier state traits through a SP challenge experiment, and genotyped by using a 600 K high-density single nucleotide polymorphism (SNP) array. A GWAS using a single-marker linear mixed model was performed with the GEMMA software. RNA-sequencing on spleen samples was carried out for further identification of candidate genes.

Results

We detected a region that was located between 33.48 and 34.03 Mb on chicken chromosome 4 and was significantly associated with death, with the most significant SNP (rs314483802) accounting for 11.73% of the phenotypic variation. Two candidate genes, FBXW7 and LRBA, were identified as the most promising genes involved in resistance to SP. The expression levels of FBXW7 and LRBA were significantly downregulated after SP infection, which suggests that they may have a role in controlling SP infections. Two other significant loci and related genes (TRAF3 and gga-mir-489) were associated with carrier state, which indicates a different polygenic determinism compared with that of death. In addition, genomic inbreeding coefficients showed no correlation with resistance to SP within each breed in our study.

Conclusions

The results of this GWAS with a carefully organized Salmonella challenge experiment represent an important milestone in understanding the genetics of infectious disease resistance, offer a theoretical basis for breeding SP-resistant chicken lines using marker-assisted selection, and provide new information for salmonellosis research in humans and other animals.

Whole Genome Resequencing of Arkansas Progressor and Regressor Line Chickens to Identify SNPs Associated with Tumor Regression

Arkansas Regressor (AR) chickens, unlike Arkansas Progressor (AP) chickens, regress tumors induced by the v-src oncogene. To better understand the genetic factors responsible for this tumor regression property, whole genome resequencing was conducted using Illumina Hi-Seq 2 × 100 bp paired-end read method (San Diego, CA, USA) with AR (confirmed tumor regression property) and AP chickens. Sequence reads were aligned to the chicken reference genome (galgal5) and produced coverage of 11× and 14× in AR and AP, respectively. A total of 7.1 and 7.3 million single nucleotide polymorphisms (SNPs) were present in AR and AP genomes, respectively. Through a series of filtration processes, a total of 12,242 SNPs were identified in AR chickens that were associated with non-synonymous, frameshift, nonsense, no-start and no-stop mutations. Further filtering of SNPs based on read depth ≥ 10, SNP% ≥ 0.75, and non-synonymous mutations identified 63 reliable marker SNPs which were chosen for gene network analysis. The network analysis revealed that the candidate genes identified in AR chickens play roles in networks centered to ubiquitin C (UBC), phosphoinositide 3-kinases (PI3K), and nuclear factor kappa B (NF-kB) complexes suggesting that the tumor regression property in AR chickens might be associated with ubiquitylation, PI3K, and NF-kB signaling pathways. This study provides an insight into genetic factors that could be responsible for the tumor regression property.

Evaluation of genetic resistance to Salmonella Pullorum in three chicken lines

Resistance to diseases varies considerably among populations of the same species and can be ascribed to both genetic and environmental factors. Salmonella Pullorum (SP) is responsible for significant losses in the poultry industry, especially in developing countries. To better understand SP resistance in chicken populations with different genetic backgrounds, we orally challenged 3 chicken lines with SP-a highly selected commercial breed (Rhode Island Red, RIR), a local Chinese chicken (Beijing You, BY), and a synthetic layer line (dwarf, DW)-at 4 d of age. Two traits related to SP resistance, survival, and bacterial carriage in the spleen were evaluated after infection. Survival rates were recorded up to 40 d of age when all chickens still alive were killed to verify the presence of SP in the spleen to determine carrier state. Mortalities for RIR, BY, and DW chicks were 25.1%, 8.3%, and 22.7%, respectively, and the corresponding carrier-states in the spleens were 17.9%, 0.6%, and 15.8%. Survival and carrier-state heritabilities were estimated using an animal threshold model. Survival heritability was 0.197, 0.091, and 0.167 in RIR, BY, and DW populations, respectively, and the heritabilities of carrier state for DW and RIR were 0.32 and 0.16, respectively. This is the first time that the heritability of the SP carrier state has been evaluated in chickens. Our study provides experimental evidence that chickens with various genetic background exhibited significantly different SP-resistant activities and heritabilities. These results may be useful for selecting lines with better disease resistance.

Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology

Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (PRSS23, ME3, FAM181B, NABP1, SDPR, TSSK6L2, and RBBP8). Moreover, 24 BW-associated SNPs reached "suggestive" genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.

The genetics of feed conversion efficiency traits in a commercial broiler line

Individual feed conversion efficiency (FCE) is a major trait that influences the usage of energy resources and the ecological footprint of livestock production. The underlying biological processes of FCE are complex and are influenced by factors as diverse as climate, feed properties, gut microbiota, and individual genetic predisposition. To gain an insight to the genetic relationships with FCE traits and to contribute to the improvement of FCE in commercial chicken lines, a genome-wide association study was conducted using a commercial broiler population (n = 859) tested for FCE and weight traits during the finisher period from 39 to 46 days of age. Both single-marker (generalized linear model) and multi-marker (Bayesian approach) analyses were applied to the dataset to detect genes associated with the variability in FCE. The separate analyses revealed 22 quantitative trait loci (QTL) regions on 13 different chromosomes; the integration of both approaches resulted in 7 overlapping QTL regions. The analyses pointed to acylglycerol kinase (AGK) and general transcription factor 2-I (GTF2I) as positional and functional candidate genes. Non-synonymous polymorphisms of both candidate genes revealed evidence for a functional importance of these genes by influencing different biological aspects of FCE.

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.

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.

Host genetic variants and gene expression patterns associated with Epstein-Barr virus copy number in lymphoblastoid cell lines

Lymphoblastoid cell lines (LCLs) are commonly used in molecular genetics, supplying DNA for the HapMap and 1000 Genomes Projects, used to test chemotherapeutic agents, and informing the basis of a number of population genetics studies of gene expression. The process of transforming human B cells into LCLs requires the presence of Epstein-Barr virus (EBV), a double-stranded DNA virus which through B-cell immortalisation maintains an episomal virus genome in every cell of an LCL at variable copy numbers. Previous studies have reported that EBV alters host-gene expression and EBV copy number may be under host genetic control. We performed a genome-wide association study of EBV genome copy number in LCLs and found the phenotype to be highly heritable, although no individual SNPs achieved a significant association with EBV copy number. The expression of two host genes (CXCL16 and AGL) was positively correlated and expression of ADARB2 was negatively correlated with EBV copy number in a genotype-independent manner. This study shows an association between EBV copy number and the gene expression profile of LCLs, and suggests that EBV copy number should be considered as a covariate in future studies of host gene expression in LCLs.

Genome-wide SNP scan in a porcine Large White×Minzhu intercross population reveals a locus influencing muscle mass on chromosome 2

A high-density single nucleotide polymorphism (SNP) array containing 62 163 markers was employed for a genome-wide association study (GWAS) to identify variants associated with lean meat in ham (LMH, %) and lean meat percentage (LMP, %) within a porcine Large White×Minzhu intercross population. For each individual, LMH and LMP were measured after slaughter at the age of 240±7 days. A total of 557 F2 animals were genotyped. The GWAS revealed that 21 SNPs showed significant genome-wide or chromosome-wide associations with LMH and LMP by the Genome-wide Rapid Association using Mixed Model and Regression-Genomic Control approach. Nineteen significant genome-wide SNPs were mapped to the distal end of Sus Scrofa Chromosome (SSC) 2, where a major known gene responsible for muscle mass, IGF2 is located. A conditioned analysis, in which the genotype of the strongest associated SNP is included as a fixed effect in the model, showed that those significant SNPs on SSC2 were derived from a single quantitative trait locus. The two chromosome-wide association SNPs on SSC1 disappeared after conditioned analysis suggested the association signal is a false association derived from using a F2 population. The present result is expected to lead to novel insights into muscle mass in different pig breeds and lays a preliminary foundation for follow-up studies for identification of causal mutations for subsequent application in marker-assisted selection programs for improving muscle mass in pigs.

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.

Improving the outcome of a Marek's disease challenge in multiple lines of egg type chickens

A challenge test following inoculation with a standard amount of a vv+ strain of the Marek's disease (MD) virus in multiple lines and multiple generations of egg type chicken and the corresponding phenotypic trend are described. This program significantly reduced mortality of progeny from selected sires for three to 11 generations in eight of the nine elite lines studied herein. In brown egg lines, a retrospective analysis of DNA indicated an association between the blood type B (major histocompatibility complex) of the sire and the MD mortality in the challenge of its progeny. As a result of the multigeneration stock amplification and crossbreeding processes used in the commercial breeding industry, improvement in survival after challenge at the elite level will translate to improved welfare for millions of birds at the commercial production level.