Marek’s disease (MD) is a highly infectious lymphoproliferative disease in chickens with a signif... more Marek’s disease (MD) is a highly infectious lymphoproliferative disease in chickens with a significant economic impact. Mardivirus gallidalpha 2, also known as Marek’s disease virus (MDV), is the causative pathogen and has been categorized based on its virulence rank into four pathotypes: mild (m), virulent (v), very virulent (vv), and very virulent plus (vv+). A prior comparative genomics study suggested that several single-nucleotide polymorphisms (SNPs) and genes in the MDV genome are associated with virulence, including nonsynonymous (ns) SNPs in eight open reading frames (ORF): UL22, UL36, UL37, UL41, UL43, R-LORF8, R-LORF7, and ICP4. To validate the contribution of these nsSNPs to virulence, the vv+MDV strain 686 genome was modified by replacing nucleotides with those observed in the vMDV strains. Pathogenicity studies indicated that these substitutions reduced the MD incidence and increased the survival of challenged birds. Furthermore, using the best-fit pathotyping method t...
The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG... more The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grassroots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.
For these experiments we used CO 2 gas euthanasia, following the current standards for poultry eu... more For these experiments we used CO 2 gas euthanasia, following the current standards for poultry euthanasia provided in AVMA Guidelines for the Euthanasia of Animals (2020 Edition). All experiments presented herein were carried out in accordance with the approval of the Institutional Animal Care and Use Committee,
Organismal evolution of the 3D genome The conformation of chromosomes within the nucleus can refl... more Organismal evolution of the 3D genome The conformation of chromosomes within the nucleus can reflect a cell's type or state. However, studies of the conservation and evolutionary history of the mechanisms regulating genome structure across species are lacking. Hoencamp et al. mapped three-dimensional (3D) genome organization in 24 eukaryote species, including animals, fungi, and plants. At interphase, species' telomeres and centromeres either clustered across chromosomes or oriented in a polarized state maintaining individual chromosomal territories within the cell, a difference attributed to condensin II. An experimental loss of condensin II in human cells promotes the formation of centromere clusters but has no effect on loop or compartment formation. Whether the structure of the 3D genome varies across species may thus depend on whether they carry a functional condensin II gene. Science , abe2218, this issue p. 984
Many livestock and human vaccines are leaky as they block symptoms but do not prevent infection o... more Many livestock and human vaccines are leaky as they block symptoms but do not prevent infection or onward transmission. This leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine...
Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic leth... more Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element. Specifically, the wg-2 mutation was initially mapped to a 7 Mb region of chromosome 12 using an Illumina 3 K SNP array. Subsequent SNP genotyping and exon sequencing combined with analysis from improved genome assemblies narrowed the region of interest to a maximum size of 227 kb. Within this region, 3 validated and 3 predicted candidate genes are found, and these are described. The wg-2 mutation is a valuable resource to contribute to an improved understanding of the developmental pathways involved in chicken and avian limb development as well as serving as a model for human development, as the resulting syndrome shares features with human congenital disorders.
Marek's disease (MD) is an infectious disease characterized by lymphomas and high mortality i... more Marek's disease (MD) is an infectious disease characterized by lymphomas and high mortality in susceptible chickens. The causative and ubiquitous alpha-herpesvirus known as MD virus (MDV) integrates into host telomeres during early infection through latency, known to be an important phase for oncogenic transformation. Herein, we sought to determine the influence of vaccination and host genetics on the temporal dynamics of MDV-host genome interactions. We studied integration profiles using 2 MD vaccines that vary in protective efficacy in 2 genetic lines that differ in MD resistance/susceptibility. Virus integration of both oncogenic MDV and vaccine strains was observed in both MD susceptible and resistant birds, however, the lines differed in their dynamic telomere-integration profiles. Notably, the resistant host genotype exhibited a smaller percentage of replicating cells with the virus telomere-integrated only phenotype as compared to the susceptible genotype. Vaccination wit...
It has previously been shown that effective probiotics can accelerate gut maturation and the deve... more It has previously been shown that effective probiotics can accelerate gut maturation and the development of a normal microflora in poultry. This results in increased resistance to enteric pathogens encountered by chicks early in life. Our objective in experiments 1 and 2 was to evaluate the effect of in ovo administration of FloraMax ®-B11 (FM) on Marek's disease (MD) herpesvirus of turkeys (HVT) vaccine protective efficacy. In Exp. 1, day 18 White Leghorn embryos were randomly distributed in four groups, 1) HVT vaccinated, no MDV challenge, 2) HVT + FM vaccinated, no MDV challenge, 3) HVT vaccinated, challenge with virulent MDV, 4) HVT+ FM vaccinated, challenge with virulent MDV. Exp. 2 was designed the same as Exp. 1, except chicks were challenged with a very virulent MDV strain. There was no significant difference (P> 0.05) in MD incidence between birds vaccinated with and without FM in the HVT vaccine. In Exp. 3 and 4, day 18 commercial broiler embryos were in ovo injected with either saline or FM to measure hatchability, microbiota composition, morphometric analysis, and Salmonella enterica serovar Enteritidis (SE) infection in chickens. The administration of the probiotic did not negatively affect hatchability, but significantly reduced (P<0.05) coliforms within the gut. In Exp. 4, the FM treated group showed significantly increased (P<0.05) BW at 7 days when compared to the controls. This is associated with the higher villi surface area observed in the FM group and reduced (P<0.001) SE incidence and (P<0.05) CFU recovery. The results of these studies suggest that the in ovo administration of FM into the amnion at 18 days of embryogenesis does not impact the protection of the HVT vaccine against MD or negatively affect hatchability. It also reduces the recovery of gram negative bacteria, improves BW during the first 7 days, and decreases SE recovery in broiler chickens.
Marek's disease (MD) is an important neoplastic disease of chickens caused by Marek's dis... more Marek's disease (MD) is an important neoplastic disease of chickens caused by Marek's disease virus (MDV), a highly oncogenic alphaherpesvirus. In this study using two chicken lines, one resistant and another susceptible to MD, splenic T cells and cecal microbiome were profiled to gain a better understanding of primary differences in these lines. The percent of splenic CD4(+) T cells were similar regardless of MDV challenge status in both bird lines. In contrast, CD8αα profiles were different (P < 0.005) between chicken lines under naïve status and under MDV challenge, suggesting that CD8αα T cells play a key role in mediating MDV infection. Microbiome composition was different between naïve resistant (Bluatia spp.) and susceptible birds (Streptococcus spp.) (P < 0.05) during initial colonization. With MDV-challenge, both chicken lines showed lower numbers of beneficial Faecalibacterium spp. and increased number of Lactobacillus spp. Metabolic profiles between naïve ch...
Microsatellites are tandem duplications with a simple motif of one to six bases as the repeat uni... more Microsatellites are tandem duplications with a simple motif of one to six bases as the repeat unit. Microsatellites provide an excellent opportunity for developing genetic markers of high utility because the number of repeats is highly polymorphic, and the assay to score microsatellite polymorphisms is quick and reliable because the procedure is based on the polymerase chain reaction (PCR). We have identified 404 microsatellite-containing clones of which 219 were suitable as microsatellite markers. Primers for 151 of these microsatellites were developed and used to detect polymorphisms in DNA samples extracted from the parents of two reference populations and three resource populations. Sixty, 39,46,49, and 61% of the microsatellites exhibited length polymorphisms in the East Lansing reference population, the Compton reference population, resource population No. 1 (developed to identify resistance genes to Marek's disease), resource population No. 2 (developed to identify genes involved in abdominal fat), and resource population No. 3 (developed to identify genes involved in production traits), respectively. The 91 microsatellites that were polymorphic in the East Lansing reference population were genotyped and 86 genetic markers were eventually mapped. In addition, 11 new random amplified polymorphic DNA (RAPD) markers and 24 new markers based on the chicken CR1 element were mapped. The addition of these markers increases the total number of markers on the East Lansing genetic map to 273, of which 243 markers are resolved into 32 linkage groups. The map coverage within linkage groups is 1,402 cM with an average spacing of 6.7 cM between loci. The utility of the genetic map is greatly enhanced by adding 86 microsatellite markers. Based on our current map,-2,550 cM of the chicken genome is within 20 cM of at least one microsatellite marker.
Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and p... more Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P < 0.05) were identified across the three lines. With GS, 70 selected regions were identified. Empirical thresholds for local allele frequency changes were de...
While rearing birds in confinement and at high density are very successful practices for producin... more While rearing birds in confinement and at high density are very successful practices for producing poultry meat and eggs, these conditions may promote the spread of infectious diseases. Consequently, the poultry industry places great emphasis on disease control measures, primarily at the animal husbandry level. The field of genomics offers great promise to complement these current control measures by providing information on the molecular basis for disease, disease resistance, and vaccinal immunity. This briefly summarizes some of our efforts to apply several genomic and functional genomics approaches to identify genes and pathways that confer genetic resistance to Marek's disease (MD), a herpesvirus-induced T cell lymphoma of chickens. By utilizing the "top-down" approach of QTL to identify genomics regions, and integrating it with "bottom-up" approaches of transcript profiling and Marek's disease virus (MDV)-chicken proteinprotein interactions, three genes that confer resistance to MD are revealed, plus a number of other positional candidate genes of high confidence. These genes can be further evaluated in poultry breeding programmes to determine if they confer genetic resistance to MD. This integrative genomics strategy can be applied to other infectious diseases. The impact of the genome sequence and other technological advancements are also discussed.
Three main aspects of chicken biodiversity are dealt within this report: (a) cluster analysis bas... more Three main aspects of chicken biodiversity are dealt within this report: (a) cluster analysis based on autosomal microsatellites, (b) microsatellites on the sex chromosomes, and (c) SNP-based biodiversity.(a) Cluster analysis of autosomal microsatellites: We used 29 microsatellites to genotype 2000 chickens randomly selected from 65 different populations representing various chicken types and various geographical regions. The computer program Structure placed the 65 populations into clusters that are in agreement with their geographic origin and breed history. Only at two predefined clusters, there is little admixture between non-commercial populations originating from Asia and those from Europe. In contrast, commercial broilers and brown egg layers appeared as admixed populations of these two main gene pools. Increasing the number of clusters resulted in generation of specific clusters of commercial lines, having very low admixture with other clusters. In addition, we identified se...
The resolution of genes that determine resistance to disease is described using chicken lines mai... more The resolution of genes that determine resistance to disease is described using chicken lines maintained at the Avian Disease and Oncology Laboratory (ADOL). This description includes a summary 1) of existing selected and inbred lines differing for resistance to viral-induced tumors, i.e., Marek's disease (MD) and lymphoid leukosis (LL), and of the use of inbred and line crosses to define relevant disease-resistant genes, e.g., TV, ALVE, B, R, LY4, TH1, BU1, and IGG1; 2) of the development of TVB*/ALVE congenic lines to establish the affects of endogenous virus (EV) expression on resis
Since the sequencing of the genome and the development of high-throughput tools for the explorati... more Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection (∼600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of ∼20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken.
The ChickenGTEx atlas: the genetic regulation of multi-tissue and single-cell transcriptome signatures in chickens
Chicken is a valuable model for understanding fundamental biology and vertebrate evolution, as we... more Chicken is a valuable model for understanding fundamental biology and vertebrate evolution, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional variation. Here, through integrating bulk RNA-Seq of 7,015 samples, single-cell RNA-Seq of 127,598 cells and 2,869 whole-genome sequences, we presented an atlas of regulatory variants across 28 chicken tissues and 43 cell types, including millions of regulatory effects on primary expression (protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3’ untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants and their context dependence and utility in interpreting genome-wide associations of 108 chicken complex traits. Finally, we illustrated linea...
Identification and evaluation of SNPs at the 3’ end of the tva gene segregating among ALSV resistance and susceptible lines of chickens
Avian leukosis and sarcoma virus (ALSV) is an oncogenic retrovirus consisting of six subgroups (A... more Avian leukosis and sarcoma virus (ALSV) is an oncogenic retrovirus consisting of six subgroups (A, B, C, D, E, and J). ALSV(A) is the second most common subgroup infecting commercial poultry. Molecular tools to identify the ALSV(A) receptor (tva) positive and negative chickens could be useful to the poultry industry in tracking genetically resistant chickens. Previously, no chicken tva cDNA clones had been found, but using a partial quail tva sequence (L22753), a homologous chicken EST sequence (BM488087) was identified. Primers were designed, and a segment of 1,636 bp of the chicken tva gene was isolated from each of three previously identified tva-positive BAC clones (http://poultry.mph.msu.edu/resources/Resources.htm#bacdata). New primers were then designed, and the sequence was extended at the 3’ end up to 3,155 bp. This region covers a 1,607 bp sequence gap in the draft chicken genome sequence at chr28:819894-821500. Using the original primers, fifteen SNPs were identified amon...
In order to generate an atlas of the functional elements driving genome expression in domestic an... more In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can...
Additional file 1: Table S1. of Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek's disease
Summary of identified CNVs and CNVRs in the two chicken lines. For CNVs reported by CNVnator, the... more Summary of identified CNVs and CNVRs in the two chicken lines. For CNVs reported by CNVnator, the copy number denoted the absolute copy number estimated by CNVnator, and for those predicted by Pindel, the absolute copy number was not available and represented by ratio of the total number of uniquely mapped reads in the population supporting the CNV to that supporting the reference. Besides, Pindel can detected some not pure deletions (some fragments are inserted in the deletion region), and the inserted fragments were listed in the "Note" column. (XLSX 1591 kb)
Additional file 4: Table S6-S7. of Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marekâ s disease
List of ASE genes used for comparison (Table S6) and Overlap between line-specific CNVRs of high ... more List of ASE genes used for comparison (Table S6) and Overlap between line-specific CNVRs of high frequency with ASE genes (Table S7). ASE: allele-specific expression. (XLSX 45 kb)
Marek’s disease (MD) is a highly infectious lymphoproliferative disease in chickens with a signif... more Marek’s disease (MD) is a highly infectious lymphoproliferative disease in chickens with a significant economic impact. Mardivirus gallidalpha 2, also known as Marek’s disease virus (MDV), is the causative pathogen and has been categorized based on its virulence rank into four pathotypes: mild (m), virulent (v), very virulent (vv), and very virulent plus (vv+). A prior comparative genomics study suggested that several single-nucleotide polymorphisms (SNPs) and genes in the MDV genome are associated with virulence, including nonsynonymous (ns) SNPs in eight open reading frames (ORF): UL22, UL36, UL37, UL41, UL43, R-LORF8, R-LORF7, and ICP4. To validate the contribution of these nsSNPs to virulence, the vv+MDV strain 686 genome was modified by replacing nucleotides with those observed in the vMDV strains. Pathogenicity studies indicated that these substitutions reduced the MD incidence and increased the survival of challenged birds. Furthermore, using the best-fit pathotyping method t...
The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG... more The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grassroots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.
For these experiments we used CO 2 gas euthanasia, following the current standards for poultry eu... more For these experiments we used CO 2 gas euthanasia, following the current standards for poultry euthanasia provided in AVMA Guidelines for the Euthanasia of Animals (2020 Edition). All experiments presented herein were carried out in accordance with the approval of the Institutional Animal Care and Use Committee,
Organismal evolution of the 3D genome The conformation of chromosomes within the nucleus can refl... more Organismal evolution of the 3D genome The conformation of chromosomes within the nucleus can reflect a cell's type or state. However, studies of the conservation and evolutionary history of the mechanisms regulating genome structure across species are lacking. Hoencamp et al. mapped three-dimensional (3D) genome organization in 24 eukaryote species, including animals, fungi, and plants. At interphase, species' telomeres and centromeres either clustered across chromosomes or oriented in a polarized state maintaining individual chromosomal territories within the cell, a difference attributed to condensin II. An experimental loss of condensin II in human cells promotes the formation of centromere clusters but has no effect on loop or compartment formation. Whether the structure of the 3D genome varies across species may thus depend on whether they carry a functional condensin II gene. Science , abe2218, this issue p. 984
Many livestock and human vaccines are leaky as they block symptoms but do not prevent infection o... more Many livestock and human vaccines are leaky as they block symptoms but do not prevent infection or onward transmission. This leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine...
Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic leth... more Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element. Specifically, the wg-2 mutation was initially mapped to a 7 Mb region of chromosome 12 using an Illumina 3 K SNP array. Subsequent SNP genotyping and exon sequencing combined with analysis from improved genome assemblies narrowed the region of interest to a maximum size of 227 kb. Within this region, 3 validated and 3 predicted candidate genes are found, and these are described. The wg-2 mutation is a valuable resource to contribute to an improved understanding of the developmental pathways involved in chicken and avian limb development as well as serving as a model for human development, as the resulting syndrome shares features with human congenital disorders.
Marek's disease (MD) is an infectious disease characterized by lymphomas and high mortality i... more Marek's disease (MD) is an infectious disease characterized by lymphomas and high mortality in susceptible chickens. The causative and ubiquitous alpha-herpesvirus known as MD virus (MDV) integrates into host telomeres during early infection through latency, known to be an important phase for oncogenic transformation. Herein, we sought to determine the influence of vaccination and host genetics on the temporal dynamics of MDV-host genome interactions. We studied integration profiles using 2 MD vaccines that vary in protective efficacy in 2 genetic lines that differ in MD resistance/susceptibility. Virus integration of both oncogenic MDV and vaccine strains was observed in both MD susceptible and resistant birds, however, the lines differed in their dynamic telomere-integration profiles. Notably, the resistant host genotype exhibited a smaller percentage of replicating cells with the virus telomere-integrated only phenotype as compared to the susceptible genotype. Vaccination wit...
It has previously been shown that effective probiotics can accelerate gut maturation and the deve... more It has previously been shown that effective probiotics can accelerate gut maturation and the development of a normal microflora in poultry. This results in increased resistance to enteric pathogens encountered by chicks early in life. Our objective in experiments 1 and 2 was to evaluate the effect of in ovo administration of FloraMax ®-B11 (FM) on Marek's disease (MD) herpesvirus of turkeys (HVT) vaccine protective efficacy. In Exp. 1, day 18 White Leghorn embryos were randomly distributed in four groups, 1) HVT vaccinated, no MDV challenge, 2) HVT + FM vaccinated, no MDV challenge, 3) HVT vaccinated, challenge with virulent MDV, 4) HVT+ FM vaccinated, challenge with virulent MDV. Exp. 2 was designed the same as Exp. 1, except chicks were challenged with a very virulent MDV strain. There was no significant difference (P> 0.05) in MD incidence between birds vaccinated with and without FM in the HVT vaccine. In Exp. 3 and 4, day 18 commercial broiler embryos were in ovo injected with either saline or FM to measure hatchability, microbiota composition, morphometric analysis, and Salmonella enterica serovar Enteritidis (SE) infection in chickens. The administration of the probiotic did not negatively affect hatchability, but significantly reduced (P<0.05) coliforms within the gut. In Exp. 4, the FM treated group showed significantly increased (P<0.05) BW at 7 days when compared to the controls. This is associated with the higher villi surface area observed in the FM group and reduced (P<0.001) SE incidence and (P<0.05) CFU recovery. The results of these studies suggest that the in ovo administration of FM into the amnion at 18 days of embryogenesis does not impact the protection of the HVT vaccine against MD or negatively affect hatchability. It also reduces the recovery of gram negative bacteria, improves BW during the first 7 days, and decreases SE recovery in broiler chickens.
Marek's disease (MD) is an important neoplastic disease of chickens caused by Marek's dis... more Marek's disease (MD) is an important neoplastic disease of chickens caused by Marek's disease virus (MDV), a highly oncogenic alphaherpesvirus. In this study using two chicken lines, one resistant and another susceptible to MD, splenic T cells and cecal microbiome were profiled to gain a better understanding of primary differences in these lines. The percent of splenic CD4(+) T cells were similar regardless of MDV challenge status in both bird lines. In contrast, CD8αα profiles were different (P < 0.005) between chicken lines under naïve status and under MDV challenge, suggesting that CD8αα T cells play a key role in mediating MDV infection. Microbiome composition was different between naïve resistant (Bluatia spp.) and susceptible birds (Streptococcus spp.) (P < 0.05) during initial colonization. With MDV-challenge, both chicken lines showed lower numbers of beneficial Faecalibacterium spp. and increased number of Lactobacillus spp. Metabolic profiles between naïve ch...
Microsatellites are tandem duplications with a simple motif of one to six bases as the repeat uni... more Microsatellites are tandem duplications with a simple motif of one to six bases as the repeat unit. Microsatellites provide an excellent opportunity for developing genetic markers of high utility because the number of repeats is highly polymorphic, and the assay to score microsatellite polymorphisms is quick and reliable because the procedure is based on the polymerase chain reaction (PCR). We have identified 404 microsatellite-containing clones of which 219 were suitable as microsatellite markers. Primers for 151 of these microsatellites were developed and used to detect polymorphisms in DNA samples extracted from the parents of two reference populations and three resource populations. Sixty, 39,46,49, and 61% of the microsatellites exhibited length polymorphisms in the East Lansing reference population, the Compton reference population, resource population No. 1 (developed to identify resistance genes to Marek's disease), resource population No. 2 (developed to identify genes involved in abdominal fat), and resource population No. 3 (developed to identify genes involved in production traits), respectively. The 91 microsatellites that were polymorphic in the East Lansing reference population were genotyped and 86 genetic markers were eventually mapped. In addition, 11 new random amplified polymorphic DNA (RAPD) markers and 24 new markers based on the chicken CR1 element were mapped. The addition of these markers increases the total number of markers on the East Lansing genetic map to 273, of which 243 markers are resolved into 32 linkage groups. The map coverage within linkage groups is 1,402 cM with an average spacing of 6.7 cM between loci. The utility of the genetic map is greatly enhanced by adding 86 microsatellite markers. Based on our current map,-2,550 cM of the chicken genome is within 20 cM of at least one microsatellite marker.
Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and p... more Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P < 0.05) were identified across the three lines. With GS, 70 selected regions were identified. Empirical thresholds for local allele frequency changes were de...
While rearing birds in confinement and at high density are very successful practices for producin... more While rearing birds in confinement and at high density are very successful practices for producing poultry meat and eggs, these conditions may promote the spread of infectious diseases. Consequently, the poultry industry places great emphasis on disease control measures, primarily at the animal husbandry level. The field of genomics offers great promise to complement these current control measures by providing information on the molecular basis for disease, disease resistance, and vaccinal immunity. This briefly summarizes some of our efforts to apply several genomic and functional genomics approaches to identify genes and pathways that confer genetic resistance to Marek's disease (MD), a herpesvirus-induced T cell lymphoma of chickens. By utilizing the "top-down" approach of QTL to identify genomics regions, and integrating it with "bottom-up" approaches of transcript profiling and Marek's disease virus (MDV)-chicken proteinprotein interactions, three genes that confer resistance to MD are revealed, plus a number of other positional candidate genes of high confidence. These genes can be further evaluated in poultry breeding programmes to determine if they confer genetic resistance to MD. This integrative genomics strategy can be applied to other infectious diseases. The impact of the genome sequence and other technological advancements are also discussed.
Three main aspects of chicken biodiversity are dealt within this report: (a) cluster analysis bas... more Three main aspects of chicken biodiversity are dealt within this report: (a) cluster analysis based on autosomal microsatellites, (b) microsatellites on the sex chromosomes, and (c) SNP-based biodiversity.(a) Cluster analysis of autosomal microsatellites: We used 29 microsatellites to genotype 2000 chickens randomly selected from 65 different populations representing various chicken types and various geographical regions. The computer program Structure placed the 65 populations into clusters that are in agreement with their geographic origin and breed history. Only at two predefined clusters, there is little admixture between non-commercial populations originating from Asia and those from Europe. In contrast, commercial broilers and brown egg layers appeared as admixed populations of these two main gene pools. Increasing the number of clusters resulted in generation of specific clusters of commercial lines, having very low admixture with other clusters. In addition, we identified se...
The resolution of genes that determine resistance to disease is described using chicken lines mai... more The resolution of genes that determine resistance to disease is described using chicken lines maintained at the Avian Disease and Oncology Laboratory (ADOL). This description includes a summary 1) of existing selected and inbred lines differing for resistance to viral-induced tumors, i.e., Marek's disease (MD) and lymphoid leukosis (LL), and of the use of inbred and line crosses to define relevant disease-resistant genes, e.g., TV, ALVE, B, R, LY4, TH1, BU1, and IGG1; 2) of the development of TVB*/ALVE congenic lines to establish the affects of endogenous virus (EV) expression on resis
Since the sequencing of the genome and the development of high-throughput tools for the explorati... more Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection (∼600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of ∼20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken.
The ChickenGTEx atlas: the genetic regulation of multi-tissue and single-cell transcriptome signatures in chickens
Chicken is a valuable model for understanding fundamental biology and vertebrate evolution, as we... more Chicken is a valuable model for understanding fundamental biology and vertebrate evolution, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional variation. Here, through integrating bulk RNA-Seq of 7,015 samples, single-cell RNA-Seq of 127,598 cells and 2,869 whole-genome sequences, we presented an atlas of regulatory variants across 28 chicken tissues and 43 cell types, including millions of regulatory effects on primary expression (protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3’ untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants and their context dependence and utility in interpreting genome-wide associations of 108 chicken complex traits. Finally, we illustrated linea...
Identification and evaluation of SNPs at the 3’ end of the tva gene segregating among ALSV resistance and susceptible lines of chickens
Avian leukosis and sarcoma virus (ALSV) is an oncogenic retrovirus consisting of six subgroups (A... more Avian leukosis and sarcoma virus (ALSV) is an oncogenic retrovirus consisting of six subgroups (A, B, C, D, E, and J). ALSV(A) is the second most common subgroup infecting commercial poultry. Molecular tools to identify the ALSV(A) receptor (tva) positive and negative chickens could be useful to the poultry industry in tracking genetically resistant chickens. Previously, no chicken tva cDNA clones had been found, but using a partial quail tva sequence (L22753), a homologous chicken EST sequence (BM488087) was identified. Primers were designed, and a segment of 1,636 bp of the chicken tva gene was isolated from each of three previously identified tva-positive BAC clones (http://poultry.mph.msu.edu/resources/Resources.htm#bacdata). New primers were then designed, and the sequence was extended at the 3’ end up to 3,155 bp. This region covers a 1,607 bp sequence gap in the draft chicken genome sequence at chr28:819894-821500. Using the original primers, fifteen SNPs were identified amon...
In order to generate an atlas of the functional elements driving genome expression in domestic an... more In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can...
Additional file 1: Table S1. of Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek's disease
Summary of identified CNVs and CNVRs in the two chicken lines. For CNVs reported by CNVnator, the... more Summary of identified CNVs and CNVRs in the two chicken lines. For CNVs reported by CNVnator, the copy number denoted the absolute copy number estimated by CNVnator, and for those predicted by Pindel, the absolute copy number was not available and represented by ratio of the total number of uniquely mapped reads in the population supporting the CNV to that supporting the reference. Besides, Pindel can detected some not pure deletions (some fragments are inserted in the deletion region), and the inserted fragments were listed in the "Note" column. (XLSX 1591 kb)
Additional file 4: Table S6-S7. of Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marekâ s disease
List of ASE genes used for comparison (Table S6) and Overlap between line-specific CNVRs of high ... more List of ASE genes used for comparison (Table S6) and Overlap between line-specific CNVRs of high frequency with ASE genes (Table S7). ASE: allele-specific expression. (XLSX 45 kb)
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Papers by Hans Cheng