Progress 01/15/07 to 01/14/10
Outputs
OUTPUTS: This project is mid-way through the objectives; there are no outputs to report at this time. Significant DNA markers identified in objective 1 and confirmed in objective 2 will enable application of marker assisted selection to reduce susceptibility to Johne's disease in dairy cattle. The artificial breeding industry will use these markers as one among many criteria to select bulls for their semen markets. Producers will use the marker information in two ways: a) to select among AI bulls for matings in their herds and b) to select cows as dams of young bulls for the artificial breeding industry. PARTICIPANTS: INDIVIDUALS: G. E. Shook - project director, recruit cooperating dairy herds, data base management, statistical analysis, overall coordination. M. T. Collins - conducts disease testing and interpretation of test results. B. W. Kirkpatrick - DNA extraction, genotyping, analysis and interpretation of genotyping results. TRAINEES: Two post-doctoral trainees and one graduate student have assisted in conducting this research; six undergraduate students have completed the DNA extractions for objective 2. PARTNER ORGANIZATIONS: Johne's Disease Integrated Program - JDIP supported our group for analysis of association of the CARD15 locus with susceptibility to Johne's disease. JDIP is a collaboration among 21 universities, USDA, and international partners that is funded in part by NRI "to promote development and support of projects designed to enhance knowledge, promote education, develop real-world solutions, and mitigate losses associated with Johne's disease". American Jersey Cattle Association - We have submitted a proposal to AJCA to determine if DNA markers that have significant association with Johne's disease in Holsteins are also significant in the Jersey breed. COLLABORATIONS: New Zealand - Informal collaboration with Johne's disease project at AgResearch and LIC Dr. Hasan Khatib, Dairy Science Department, University of Wisconsin-Madison, has used the DNA samples from our project to study association of SNPs in candidate genes (STAT1, STAT5A, OPN, PPARGC1A, POU1F1, and FGF2) with production and fertility traits in dairy cattle. This work has resulted in six publications during the past three years. Dr. Cesar Cortez-Romero from Mexico has obtained funding for a project on Johne's disease. At this time, collaboration is in an early discussion stage. Potentially, he will investigate whether SNP markers found significant in our populations are also significant in Mexican cattle. TARGET AUDIENCES: Producers, Veterinarians, Extension specialists in animal genetics and animal health, Animal Biotechnology Industry, Animal Breeding Industry, Scientific Community PROJECT MODIFICATIONS: Two modifications have been made: 1) Subsequent to submitting our proposal, a new ELISA antibody assay with improved sensitivity (i. e., higher probability of detecting infected animals) was developed in the laboratory of co-investigator Collins. We re-tested all serum samples in our original population with this new assay. The serum samples had been collected under a previous project, and the results of this new diagnostic test were used in the current project. Another advantage for re-testing is that the same disease test has been used in both of our replicate populations. 2) Initially, we proposed using the replicate population to examine only those genomic regions that were significant in our original population. Due to the relatively low cost of the 50K SNP chip, we decided to conduct the entire genome scan in the replicate population. This enables cross-validation of the results and provides a far more powerful and comprehensive evaluation of significant marker locations.
Impacts
Objective 1: Disease test results and DNA samples were obtained from 5611 cows in 300 herds during a previous project. This resource was used in the current project. Disease tests included fecal cultures for the Mycobacterium paratubercuolsis pathogen and serum ELISA assays for antibodies against the pathogen. DNA samples from 267 cows with positive or strong positive ELISA disease test result were genotyped with a 50K SNP chip. Also, 34 sires of the cows were genotyped to aid in determining individual cows' inheritance of paternal and maternal alleles. Combined linkage and linkage disequilibrium analysis for association of SNP markers with disease status was completed. Several significant markers and chromosome regions have been identified. These are being validated with a replicate population in Objective 2. Objective 2: Resources consisting of serum ELISA disease tests and DNA samples were completed in July 2008. Samples were collected from 4,811 Holstein and 376 Jersey cows in 9 herds over an 18 month period. Disease tests and DNA extractions have been completed. Disease prevalence in these data is 100% at the herd level and 9.9% among cows. Genotyping with the 50K SNP chip was recently completed for 55 sires of cows and for 321 cows with positive or strong positive ELISA disease test results. Linkage disequilibrium analysis to determine the association of SNP alleles with disease status is in progress. This second analysis replicates the first one. SNP markers that are significant in both replicates will be considered validated. Markers that are significant in both replicates will be used to locate potential candidate genes, identify SNPs in those genes, and test their association with paratuberculosis susceptibility (Objective 3): Objective 3: Work on this objective will follow completion of the work in Objective 2.
Publications
- No publications reported this period
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Progress 01/15/07 to 01/14/08
Outputs
OUTPUTS: This project is in the early stages; there are no outputs to report at this time. Significant DNA markers identified in objective 1 and confirmed in objective 2 will enable marker assisted selection to reduce susceptibility to Johne's disease in dairy cattle. The artificial breeding industry will use these markers as one among many criteria to select bulls for their semen markets. Producers will use the marker information in two ways: a) to select among AI bulls for matings in their herds and b) to select cows as dams of young bulls for the artificial breeding industry.
PARTICIPANTS: INDIVIDUALS: G. E. Shook - project director, recruit cooperating dairy herds, data base management, statistical analysis, overall coordination. M. T. Collins - conducts disease testing and interpretation of test results. B. W. Kirkpatrick - DNA extraction, genotyping, analysis and interpretation of genotyping results. TRAINEES: Two post-doctoral trainees are conducting the work under objectives 1 and 3; one graduate student is conducting the work on objective 2; five undergraduate students are doing the DNA extractions for objective 2. PARTNER ORGANIZATIONS: Johne's Disease Integrated Program - JDIP supported our group for analysis of association of the CARD15 locus with susceptibility to Johne's disease. JDIP is a collaboration among 21 universities, USDA, and international partners that is funded in part by NRI "to promote development and support of projects designed to enhance knowledge, promote education, develop real-world solutions, and mitigate losses associated
with Johne's disease". COLLABORATIONS: ** New Zealand - Informal collaboration with Johne's disease project at AgResearch and LIC. ** Israel - Submitted two proposals to the US-Israel Bi-National Agricultural Research and Development fund to conduct joint marker discovery and replication of the discovered markers. Proposals were not funded. ** Dr. Hasan Khatib, Dairy Science Department, University of Wisconsin-Madison, has used the DNA samples from our project to study association of SNPs in candidate genes (STAT1, STAT5A, OPN, PPARGC1A) with production and fertility traits in dairy cattle. This work has resulted in four publications during the past two years.
TARGET AUDIENCES: Producers, Veterinarians, Extension Specialists in animal genetics and animal health, Animal Biotechnology Industry, Animal Breeding Industry, Scientific Community
PROJECT MODIFICATIONS: Subsequent to submitting our proposal, a new ELISA antibody assay with improved sensitivity (i. e., higher probability of detecting infected animals) was developed in the laboratory of co-investigator Collins. We have re-tested all serum samples with this new assay. The serum samples had been collected under a previous project, and the results of this new diagnostic test will be used in the current project. Subsequently, we repeated a bivariate quantitative analysis of fecal culture and ELISA antibody disease tests to estimate effects of herd, lactation number, sire, and cow. Results from this new analysis were used to select cows for genotyping.
Impacts
** Objective 1: Disease test results and DNA samples were obtained from 5611 cows in 300 herds during a previous project. This resource will be used for the current project. Disease tests included fecal cultures for the Mycobacterium paratubercuolsis pathogen and serum ELISA assays for antibodies against the pathogen. Recently, a new, more sensitive assay (i. e., higher probability of detecting diseased animals) has been developed in our collaborating laboratory. We have re-assayed all of the original serum samples with the new method. Subsequently, we performed a bivariate quantitative analysis of fecal culture and ELISA antibody disease tests to estimate effects of sire, herd, and lactation number on the test results. The effects were estimated simultaneously to account for the confounding among design factors that is inherent in field data sampling. Using results of the quantitative analysis, a susceptibility index was calculated for each animal that was the sum of
the sire effect, herd effect, and individual animal residual term for both disease tests. This effectively adjusted the susceptibility index for lactation number effects that increase with cow age. Animals with the highest susceptibility index (i. e., most highly infected) were chosen for genotyping. The most important term in the index was the individual animal residuals. Among animals with similar residual terms, those from sires and herds with higher disease prevalence were favored for genotyping by this selection process. DNA samples from 250 cows have been submitted for genotyping with a 60K SNP chip. ** Objective 2: Resources consisting of serum ELISA and fecal culture disease tests and DNA samples are being accumulated. Samples will be collected from 3,600 Holstein and 300 Jersey cows in 9 herds over a 15 month period that will end in June 2008. Disease prevalence in these data is 100% at the herd level and 10% among cows.
Publications
- No publications reported this period
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