Progress 10/01/04 to 09/30/10
Outputs
OUTPUTS: To support studies in genetics of animal health, pedigreed populations of novel chickens were maintained and reproduced. At the initiation of the project, 23 lines existed. Due to economic constraints, the number was reduced to 12 lines. The Iowa State University chicken genetic lines are of two basic genetic types: (a) highly inbred lines or (b) advanced intercross lines (AIL). The highly inbred lines (50 - 100 generations of sib matings) are of defined MHC type, with the inbreeding of the earliest lines starting in 1925. Lines are primarily of egg-type origin, but also include the non-commercial Fayoumi and Spanish lines. A non-inbred broiler line was also maintained. Birds of the MHC-defined lines were serologically typed each generation with line-specific anti-erythrocyte antisera to verify line purity (approximately 900 birds each generation); all birds as chicks and the potential breeders, a second time before mating. A resource population for in-depth characterization of the host genetics of response to Salmonella (Iowa Salmonella Response Resource Population, ISRRP) was developed over the years by crossing outbred broiler males with females of two distinct, highly inbred lines (Leghorn and Fayoumi). The ISRRP was maintained in AILs, with the F17 generation being hatched in the past years. The continued production of AIL facilitates the opportunities to narrow the confidence intervals (fine-map) around quantitative trait loci (QTL) and to conduct detailed studies on gene expression. Birds of the AILs were used to map heterophil functions in heterophils isolated from the peripheral blood of birds that were fed immunomodulators. Genomic DNA samples were isolated from 341 birds, and genotyped with the 60K chicken SNP chip. Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. Genetic lines were distributed to collaborators, as numbers allowed. Fayoumi chicks were shipped to collaborator H. Zhou (Texas A and M University) to study response to avian influenza virus and to H. Lillehoj (USDA-ARS, Beltsville) to study response to Eimeria challenge. Chicks were transported to the University of Wisconsin (M. Barre) to establish a flock there. Samples were collected and shipped to B. Voy (University of Tennessee - Knoxville) to study obesity-related genetics. Multiple graduate students, and undergraduate interns, received instruction and research experience through participation in the project. PARTICIPANTS: Project director is Susan J. Lamont. Participants from Iowa State University were: Jack Dekkers (Professor); Claire Andreasen (Professor); Dusan Palic (Assistant Professor); Michael Kaiser (Research Associate II); Sarah Redmond (Ph.D. student in Interdepartmental Genetics); Derrick Coble (Ph.D. student in Interdepartmental Genetics); Ceren Ciraci (Ph.D. student in Interdepartmental Genetics); Erin Beach (Ph.D. student in Interdepartmental Genetics); P. Chuammitri (PhD student in Veterinary Microbiology). Academic collaborators included: Texas A and M University (Huaijun Zhou), USDA-ARS (Hyun Lillehoj), University of Wisconsin (Mark Barre), and University of Tennessee - Knoxville (Brynn Voy). TARGET AUDIENCES: Animal and poultry health professionals, veterinarians, researchers in animal and poultry breeding and genetics, commercial breeders of poultry. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Identification of single-nucleotide polymorphisms in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease will provide practical tools for chicken breeders to enhance innate resistance in their commercial egg-producing and meat-producing lines. The information on genetic variation will also enable fine-mapping and eventual identification of the specific genes in the disease-resistance pathways. The high level of genetic polymorphisms in the Iowa State University Salmonella Response resource population demonstrated the efficacy of the use of this advanced intercross line in mapping genetic control of host resistance to Salmonella colonization. Studies fine-mapped the genetic control of heterophil function, and helped to define the pathways of resistance used by these cells. Maintenance of unique genetic material helps to ensure that natural variation to meet future needs is available. Sharing genetic resources with other researchers enabled a larger portfolio of studies to be initiated at the collaborators' institutions.
Publications
- Redmond, S.B., Lamont, S.J., Andreasen, C.B., and Palić, D. 2010. Genome-wide analysis of chicken heterophil function reveals associations with known disease resistance loci and a likely mechanism for cell death through extracellular trap production. One Health Symposium: People, Plants and Animals. Iowa State University, Ames IA. September 15, 2010. Abstract 38.
- Peiris, L., Ralph, J., Lamont, S.J. and Dekkers, J.C. 2010. Predicting allele frequencies in DNA pools using high density SNP genotyping data. Animal Genetics 18 May 2010 epub ahead of print.
- Redmond, S.B., Tell, R.M., Coble, D., Mueller, C., Palic, D., Andreasen, C.B., and Lamont, S.J. 2010. Differential splenic cytokine responses to dietary immune modulation by diverse chicken lines. Poultry Sci. 89:1635-1641.
- Lamont, S. J. 2010. Genetics of Disease Resistance. In: Estany J, Nogaredo C, and Rothschild M. (eds): Adapting Animal Production to Changes for a Growing Human Population. International Conference, Lleida, Spain, May 19-21, 2010, pp 83-92
- Coble, D. Redmond, S.B., Hale, B., and Lamont, S.J. 2010. Distinct lines of chicken use different immune mechanisms in response to Salmonella enteritidis. One Health Symposium: People, Plants and Animals. Iowa State University, Ames IA. September 15, 2010. Abstract 39.
- Redmond, S.B. and Lamont, S.J. 2010. SNP association analysis of two chicken advanced intercross lines for growth. P588. Proc. Plant & Animal Genome XVIII, San Diego, CA.
- Sandford, E., Ciraci, C., Abasht, B., Dekkers, J.C.M., Lamont, S.J. 2010. SNPs in region of NF-kappa-B gene associated with expression of immune-related genes. Iowa State University Animal Industry Report, 2010, A.S. Leaflet-R2483
|
Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: To support studies in genetics of animal health, pedigreed populations of novel chickens (inbred or advanced intercross lines) were maintained and reproduced. Twenty Iowa State University chicken genetic lines were reproduced and maintained. The lines are of two basic genetic types: (a) highly inbred lines or (b) advanced intercross lines (AIL). Seventeen highly inbred lines (50 - 100 generations of sib matings) of defined MHC type were maintained, with the inbreeding of the earliest lines starting in 1925. Lines are primarily of egg-type origin, but also include the non-commercial Fayoumi and Spanish lines. Fayoumi chicks were shipped to collaborator H. Lillehoj (USDA-ARS, Beltsville) to study response to Eimeria challenge. A non-inbred broiler line is also maintained. Birds of the MHC-defined lines were serologically typed each generation with line-specific anti-erythrocyte antisera to verify line purity (about 1400 birds each generation); all birds are typed as chicks and the potential breeders are typed a second time before mating takes place. A resource population for in-depth characterization of the host genetics of response to Salmonella (Iowa Salmonella Response Resource Population, ISRRP) has been developed over the years by crossing outbred broiler males with females of two distinct, highly inbred lines (Leghorn and Fayoumi). The ISRRP is now maintained in AILs, with the F15 generation being hatched in the past year. The continued production of AIL facilitates the opportunities to narrow the confidence intervals (fine-map) around quantitative trait loci (QTL) and to conduct detailed studies on gene expression. Birds of the F15 generation of the Iowa Salmonella Response Resource Population, ISRRP) were fed the dietary immunomodulator β-glucans or basal diet for 3 weeks from ages 5-8 wk. Several heterophil functions were measured on isolated heterophils from individual birds. Analysis of phenotypes by line and diet treatment showed significant effect of genetic line-cross on phagocytosis and bacterial killing (Broiler X Fayoumi significantly higher for both) and significant interaction of cross and diet on NET production and oxidative burst. Genomic DNA samples were isolated from the same 341 birds, and genotyped with the 60Kchicken SNP chip. Statistical analysis is underway to identifiy QTL or gene SNPs associated with heterophil function and response to Salmonella. The use of the advanced intercross populations is expected to greatly facilitate fine-mapping of the genetic control of heterophil function. Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. Two graduate students received instruction and research experience through participation in the project. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Identification of single-nucleotide polymorphisms in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease will provide practical tools for chicken breeders to enhance innate resistance in their lines. They will also enable fine-mapping and eventual identification of the specific genes in the resistance pathways. The high polymorphism in SNP in the Iowa State University Salmonella Response resource population demonstrated the efficacy of the use of this advanced intercross line in mapping genetic control of host resistance to Salmonella colonization. Unique genetic material helps to ensure that natural variation to meet future needs is available.
Publications
- Beach, E., Ciraci, C., Abasht, B., Dekkers, J.C.M, and Lamont, S.J. 2009. SNPs in region of NF-kappa-B gene associated with expression of immune-related genes. Proc Poultry Science Association Annual Meeting, July 2009, Raleigh NC
- Izadi, F., Lamont, S.J., Ritland, K., and Cheng, K.M. 2009. Genetic diversity of free-run/free-range chicken flocks estimated by neutral and adaptive molecular markers. P515. Proc. Plant & Animal Genome XVII, San Diego, CA.
|
Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: To support studies in genetics of animal health, pedigreed populations of chickens (inbred and advanced intercross lines) were maintained and reproduced. Sequencing of genomic DNA, after amplification of specific fragments of the several genes related to immune function, showed allelic variation in free-run and free-range chicken lines. Application of a recently developed 3k single-nucleotide polymorphism (SNP) panel on genomic DNA from over 100 chickens infected with Salmonella enteritidis characterized the SNP variation in the line. The SNP data of the advanced intercross, founder lines, and early intercross generations were used to assess the actual decay of linkage disequilbrium in a living population of animals. Methods and results were disseminated through publication of peer-reviewed papers, abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. Two graduate students received instruction and research experience through participation in the project. PARTICIPANTS: Project director is Susan J. Lamont. Participants from Iowa State University were: Michael Kaiser (Research Associate II, who assisted with conduct of experiments and protocols associated with generation and maintenance of genetic lines) and Jason Hasenstein, (Ph.D. student in Interdepartmental Genetics, who conducted the LD analysis and the QTL mapping in the F8 intercross lines, graduated and is currently employed at the University of Wisconsin). Cooperators include the laboratory of Dr. Kim Cheng at the University of British Columbia and his graduate student, Fariba Izadi, in the assessment of SNP variation in free-run and free-range chickens. TARGET AUDIENCES: Scientists in animal and poultry breeding and genetics; commercial breeders of meat and egg poultry; animal health professionals, graduate students. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Identification of single-nucleotide polymorphisms in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease will provide practical tools for chicken breeders to enhance innate resistance in their lines. They will also enable fine-mapping and eventual identification of the specific genes in the resistance pathways. The high polymorphism in SNP in the Iowa State University Salmonella Response resource population demonstrated the efficacy of the use of this advanced intercross line in mapping genetic control of host resistance to Salmonella colonization, and its use to define the decay of linkage disequilibrium throughout the generations revealed the important finding that the actual reduction is less than that predicted by theory. This information will lead to the refinement of future experimental designs. Characterizing the natural genetic variation in immune-related genes in free-range and free-run birds established the feasibility of use of these genetic resources in future studies of host resistance to various diseases, and helped define the potential effects of varied environmental conditions on the allelic diversity in the population.
Publications
- Davison P., Kaiser, M.G. and Susan J. Lamont, S.J. 2008. Genetic diversity of the antiviral Mx gene in 14 chicken lines. Iowa State University Animal Industry Report, 2008, A.S. Leaflet R2330
- Ghebremichael, S.B., J. R. Hasenstein, J.R., and S. J. Lamont, S.J. 2008. Association of interleukin-10 cluster genes and Salmonella response in the chicken. Poultry Sci. 87: 22-26.
- Hasenstein, J.R., Hassen, A.T., Dekkers, J.C.M., and Lamont, S.J. 2008. High resolution, advanced intercross mapping of host resistance to Salmonella colonization. In : Pinard M-H, Gay C, Pastoret P-P, Dodet B (eds): Animal Genomics for Animal Health. Dev Biol (Basel). Basel, Karger, 2008, vol 132, p 213-218.
- Hasenstein, J.R., Hassen, A., Dekkers, J.C.M., and Lamont, S.J. 2008. Whole-genome QTL analysis of response to Salmonella in advanced intercross line chicks. Proc. Plant & Animal Genome XVI, San Diego, CA.
- Izadi, F., Lamont, S.J., Kaiser, M.J., and Cheng, K.M. 2008. Genetic variations in immune-related genes in free-run and free-range chicken flocks. Proc. Poultry Sci Assoc Meeting, Niagara Falls, Ontario, Canada
|
Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: To support studies in genetics of animal health, pedigreed populations of chickens (inbred and advanced intercross lines) were maintained and reproduced. Sequencing of genomic DNA, after amplification of specific fragments of the Mx gene, showed allelic variation in the Iowa State University chicken lines in the single-nucleotide polymorphism (SNP) that determines resistance to influenza virus in mice. Application of a recently developed 3k SNP panel on genomic DNA from over 100 chickens infected with Salmonella enteritidis characterized the SNP variation in the line. Twenty-one SNP, identifying19 genes, were found to be statistically associated with host resistance to Salmonella, as measured by bacterial colony count in spleen tissue or contents of the cecal lumen. Methods and results were disseminated through publication of abstracts and on-line industry reports, and presentations at scientific meetings and to individual stakeholders. One graduate student and one summer
undergraduate intern received instruction and research experience through participation in the project.
PARTICIPANTS: Project director is Susan J. Lamont. Participants from Iowa State University were: Michael Kaiser (Research Associate II) and Jason Hasenstein, (Ph.D. student in Interdepartmental Genetics, currently employed at Cincinnati Children's Hospital), and a summer intern, Patricia Davison. Academic collaborators were Sandra Ewald and Emily Livant from Auburn University.
TARGET AUDIENCES: Scientists in animal and poultry breeding and genetics ; commercial breeders of meat and egg poultry ; animal health professionals.
Impacts
Significant progress was made in identification of single-nucleotide polymorphisms (single points of genetic variation) in important genes and genomic regions that are associated with the natural ability of chickens to resist viral and bacterial disease. The high polymorphism in SNP in the Iowa State University Salmonella Response resource population demonstrated the efficacy of the use of this advanced intercross line in mapping genetic control of host resistance to Salmonella colonization. Identification of QTL markers for host response to Salmonella in this line will enable genetic selection for enhanced innate health in poultry, and will enable fine-mapping and eventual identification of the specific genes in the resistance pathways. The identified candidate genes near the QTL markers helped to reveal the important biological pathways involved in host resistance to bacterial colonization. These may aid the development of effective vaccines. Characterizing the
natural genetic variation in Mx alleles in ISU genetic populations of chickens at Iowa State University established the feasibility of use of these well-characterized genetic resources in future studies of host resistance to avian influenza. The severe pathology and high infectivity rate among chickens, and the passage of this virus from chickens to humans, makes it essential to find methods to effectively control its spread.
Publications
- Hasenstein. J.R., and Lamont, S.J. 2007. Chicken Gallinacin gene cluster associated with Salmonella response in advanced intercross line. Avian Dis. 51:561-567.
- Hasenstein, J. R. and Lamont, S.J. 2007. Chicken Gallinacin gene cluster associated with Salmonella colonization in two advanced intercross lines. Iowa State University Animal Industry Report A.S. Leaflet R2215.
- Hasenstein, J., Hassen, A., Dekkers, J.C.M, and Lamont, S.J. 2007 High-density SNP analysis of chromosome 3 associations with Salmonella burden in two advanced intercross chicken lines P563. Proc. Plant and Animal Genome XV, San Diego, CA.
- Hasenstein, J.R., Hassen, A.T., Dekkers, J.C.M., and Lamont, S.J. 2007. High resolution, advanced intercross mapping of host resistance to Salmonella colonization. Proc. Animal Genomic for Animal Health Symp., October 23-25, 2007, Paris, OIE
|
Progress 01/01/06 to 12/31/06
Outputs
High-density SNP analysis of QTL on GGA3 associated with host response to Salmonella infection in advanced intercross lines was conducted. One outbred broiler sire was crossed with dams from two distinct and highly inbred lines: Fayoumi and Leghorn. The F8 advanced AIL progeny were phenotyped for bacterial colonization in the spleen or cecum after pathogenic SE inoculation. Progeny were genotyped for 3072 SNPs using an Illumina BeadArray platform. This report covers the analysis of the 209 SNPs genotyped on GGA 3. A linear mixed model was used to analyze associations with SE burden of 105 SNPs that were polymorphic in the F8 and spanned the chromosome with a mean interval of 60 kb. The model included hatch, sex, room, necropsy period, line, and the additive effect of SNP within line as fixed effects, and sire and dam as random effects. At a false discovery rate of 0.25, seven SNPs in four regions were significantly associated with SE burden in the cecum, and four SNPs
in four regions with SE burden in the spleen. One significant SNP in the cecum was in close proximity to genes (Gallinacins) identified in a previous generation of the same crosses as being associated with SE response. Linkage disequilibrium (LD) can accumulate as a result of drift, migration, mutation, and selection; and LD is eroded by recombination. Low LD can greatly reduce the effectiveness of marker-assisted selection, quantitative trait locus mapping, and candidate gene selection. This study evaluated LD between 2733 SNP markers in an F2 population and two F8 advanced intercross line (AIL) populations and considering three subgroups of chromosomes by size. LD in the F2 and F8 populations were observed at high levels (D' and r2 values of ≥ 0.5) at less than 6 cM, and dropped off rapidly with increasing distance between markers, with moderate D' and r2 values (≤ 0.3) between markers at distances as high as 20-30 cM. The majority of differences in LD between SNPs were
explained by genetic distance (p-value < 0.0001) and population (p-value < 0.0001). The global pattern of LD was similar between the F8 AILs, and a much higher level of LD was seen in the F2 population. The decline of LD with distance was more rapid in both of the F8 populations than in the F2. Results show that biallelic SNPs are useful markers for measuring levels of LD using D' and r2. This year, we analyzed SNPs in each of the 13 chicken Gallinacin genes in the F8 generation. Many eukaryotes use antimicrobial peptides in innate immune responses to fight bacterial infections. Poultry gallinacins are the functional equivalents of mammalian β-defensins. Genes of the chicken β-defensin cluster (GAL 1-13) were sequenced from three representative individuals of each AIL and a mean of 14.8 single nucleotide polymorphisms per kilobase was identified. One allele-specific SNP per gene was genotyped using SNaPshot to test for statistical associations with SE colonization after
challenge. Among the thirteen Gallinacin genes evaluated, five were associated with bacterial load in the cecal content and one with SE load in the spleen.
Impacts
This is one of the first completed studies to utilize high-density SNP genotyping to identifiy SNP associations with disease-related traits, and demonstrated the utility of those platforms to fine-map QTL. This fine-mapping will facilitate the identification of causal genes and mutations, and provide molecular markers that can be used in breeding to enhance commercial populations. The availability of advanced intercross lines allowed investigation of LD over generations and the demonstration of reduction of LD over long distances in the genome. Demonstration of association of chicken defensin genes with response to Salmonella provides a candidate gene region to validate for marker-assisted selection to improve pre-harvest food safety, as well as to use to increase fundamental understanding of host defense mechanisms.
Publications
- Hasenstein, J. R. and S.J. Lamont. 2006. Four Gallinacin Genes and Salmonella Response in Chickens. In: Proc. 8th World Congr. Genet. Appl. Livestock Prod. Belo Horizonte, Brazil, August 13-18, 2006, published on CD.
- Hasenstein, J.R., Dekkers, J.C.M., and Lamont, S.J. 2006. Chromosomal Linkage Disequilibrium in Two Advanced Intercross Lines of Poultry Designed for Disease Resistance Genetic Studies. In: Proc Stadler Genetics Symposium, Columbia, MO. Oct. 2-4, 2006.
- Hasenstein, J.R., Zhang, G., and Lamont, S.J. 2006. Analyses of five gallinacin genes and the Salmonella enterica serovar enteritidis response in poultry. Infection & Immunity 74:3375-3380.
|
Progress 01/01/05 to 12/31/05
Outputs
Genomic DNA was isolated from erythrocytes from chickens of the F8 generation of the Iowa Salmonella Response Resource Population (ISRRP). These birds had been inoculated with pathogenic Salmonella enteritidis (SE), and the bacterial load in the spleen or content of the cecal lumen was quantified one week later. These bacterial counts will serve as the phenotypes in the subsequent analysis of associations of genetic variation (single-nucleotide polymorphisms, SNP) and host response to Salmonella. We participated in the design of SNPs included in the Illumina chicken SNP genotyping panel of over 3000 SNPs widely spaced in the chicken genome. Our contribution was to add SNPs in specific candidate genes for immune response, based upon our prior research with these genes and SNPs. Samples of genomic DNA from many Iowa State University chicken research lines were isolated, checked for quality and concentration, and then sent to Illumina for typing. These lines included the
ISRRP F8 SE inoculation trials, 17 highly inbred lines (including several sets of MHC-congenic lines), and the S1 lines (consisting of four sublines that represent the possible combinations of two MHC types and two Ir-GAT genotypes high and low). Genotyping data have been received from Illumina. Initial inspection indicated very high success rate on both the individual DNA samples typed (indicated high quality sample prep) and on SNPs typed (indicating high quality design of SNP primers and assays). Data bases are being set up to facilitate the statistical analyses of these data over the next year. Antimicrobial peptides (AMPs) are components of the innate defense system and Gallinacin genes in poultry are proposed to be the functional equivalents of mammalian beta-defensin AMP genes. One allele-defining SNP in Gallinacin 7 was used to test statistical associations of sire allele SNP with SE response, using a linear mixed model. The Gal7 broiler sire SNP was associated (P = 0.02) with
anti-SE vaccine antibody response of F1 progeny.
Impacts
Demonstration of association of a chicken defensin gene with response to Salmonella provides a candidate gene region to validate for marker assisted selection to improve pre-harvest food safety, as well as to use to increase fundamental understanding of host defense mechanisms. Preparing biological materials for genotyping and receiving high-quality genotype data on over 3,000 SNPs provide the foundation for comprehensive analysis of SNP associations with host response to Salmonella. This will lead to the identification of genomic regions that control host immunity and the ability to continue to identify candidate genes, as well as identifying molecular markers to be applied in genetic improvement programs.
Publications
- Hasenstein, J.R., Zhang, G., and Lamont, S.J. 2005. Analysis of five Gallinacin genes in a salmonella enteritidis resource population in poultry. Page 107 In: Proc. Plant and Animal Genome XIII, San Diego, CA, January 15-19.
- Hasenstein, J.R., Zhang, G. and Lamont, S.J. 2005. Small Peptide, Sizable Effects: Gallinacin 7 and Salmonella Resistance in Chickens, pp. 118 in Proc Third International Symposium on Genetics of Animal Health, ed. S. J. Lamont, M. Rothschild and D. L. Harris. Iowa State University, Ames, IA.
- Rothschild, M.F., Lamont, S.J., and Reecy, J.M. 2005. Current status of animal genomics. In: Proc. Annual AAAS Meeting, Washington, DC, February 17-19.
|
|