Progress 05/01/05 to 04/30/08
Outputs
OUTPUTS: The objectives of the proposal, as originally written, were to fine-map twinning rate QTL on chromosomes 5 and 19 within the Holstein population. However, development of high throughput genotyping tools near the onset of the project made it logical to revise the experimental plan and employ these tools for far more extensive genotyping at a comparable cost. Objectives of this project were changed to include a comprehensive genome screening for twinning rate QTL and validation of marker associations. The experimental design involved testing marker association with twinning rate in two phases; a comprehensive genome-wide scan initially followed by genotyping putatively significant markers in a second, validation phase. Initially 200 Holstein bulls with high reliability twinning rate predicted transmitting abilities (PTAs) were chosen for genotyping. These 200 bulls were sires and sons from 19 paternal-half sib families and were chosen for high reliability PTA values in the upper and lower tails of the within-family distribution. In addition, sons were selected for balanced representation of maternal grandsires within family to lessen likelihood of false positive results. Phenotypic data for the preliminary phase of the study was twinning rate predicted transmitting ability calculated based on U.S. Holstein calving records obtained from 1994-1998. Association between genetic markers and twinning rate PTA was evaluated with two, separate analyses. The first was a single marker association analysis which included effects of sire family and marker genotype in the model. The second approach was a combined linkage-linkage disequilibrium (LLD) analysis. An additional 740 Holstein bulls with high reliability twinning rate PTAs were chosen for genotyping in the validation phase of the study. Phenotypic data for the validation phase of the study was twinning rate PTA calculated based on U.S. Holstein calving records obtained from 1999-2006. PARTICIPANTS: Participants in the project included Eui-Soo Kim, Dr. Xianwei Shi, Dr. Mary Cooke, Dr. P. Jeffrey Berger, Dr. Kent Weigel and Dr. Brian Kirkpatrick. Eui-Soo Kim did most of the data analysis for the project, and much of the project was the basis for his PhD Dissertation. Drs. Shi and Cooke were postdoctoral research associates who conducted lab work for the project (preparation of DNA samples and SNP discovery). Drs. Berger and Weigel contributed to the project by analyzing calving records to produce twinning rate predicted transmitting abilities used in the mapping analyses. Dr. Kirkpatrick contributed to project design, data analysis and results reporting. Dr. Berger is a faculty member at Iowa State University; all others are affiliated with the University of Wisconsin-Madison. TARGET AUDIENCES: Target audiences include the dairy genetics industry and dairy producers. The dairy genetics industry includes dairy cattle breeders, artificial insemination studs and genetic service providers. Results are being reported in the scientific literature and relevant SNP association information is the subject of a patent application by the Wisconsin Alumni Research Foundation (WARF). WARF will be pursuing licensing of this technology with the dairy genetics industry. PROJECT MODIFICATIONS: The initial objectives of the project were fine-mapping of twinning rate QTL on bovine chromosomes 5 and 19. Between the time of proposal submission and the onset of the project, great advances were made in the bovine genome sequencing project. One result was the initial development of high throughput SNP genotyping tools, specifically a 10,000 SNP genotyping array. In recognition of the new ability to generate much greater amounts of genotype information at lesser cost, the project was revised to include a genome-wide scan with subsequent marker validation in a second, independent sample of animals.
Impacts
Single marker analyses produced 95 positive associations at a suggestive linkage threshold (p < 0.0007). Of these 95 SNPs associated with twinning rate, thirteen loci were associated at the significant linkage threshold level of p < 2.3 x 10-5. The LLD analysis detected 26 suggestive QTL (p < 0.0007). These suggestive QTL effects were detected on fifteen chromosomes. Results from association and LLD analyses were complementary. In the validation phase a total of 174 of the individually most significant markers (nominal P<0.001) were chosen for genotyping along with approximately 10 SNPs each for 14 of the most significant LLD regions. SNPs or clusters of SNPs with effects of the same sign as observed in the preliminary analysis and a nominal P<0.01 or greater were considered validated. 160 of the 174 SNPs selected for single marker association validation were successfully genotyped and of these 49 (31%) were validated with these criteria. Nine of the 14 LLD regions genotyped in the validation phase (64%) were validated by the above criteria. A stepwise regression approach was used to identify a subset of the validated markers that would be useful together as predictors of twinning rate PTA. The final set of 24 SNPs explained 57% of the variation in twinning rate PTA. Association of these SNPs with lactation and production traits was also examined, and relatively few SNPs had significant association with these, meaning selection against alleles conferring increased twinning rate could occur with little impact of this selection on lactation or production traits. Results are being reported through the scientific literature and a patent application is being prepared for the application of these markers in selection for or against twinning rate.
Publications
- Kim, E.-S. 2008. Linkage disequilibrium mapping of bovine twinning rate QTL. PhD dissertation. University of Wisconsin-Madison
- Kim, E.-S. and B.W. Kirkpatrick, 2008. Linkage disequilibrium in the North American Holstein population. Animal Genetics (submitted)
- Kim, E.-S., P.J. Berger, and B.W. Kirkpatrick. 2008. Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium. Animal Genetics (submitted)
- Kim, E.-S., X. Shi, O. Cobanoglu, K. Weigel, P.J. Berger and B.W. Kirkpatrick. 2008. Refined Mapping of Twinning Rate QTL on Bovine Chromosome 5. Journal of Animal Science (submitted)
- Bierman, C., X. Shi, K. Weigel, P.J. Berger and B.W. Kirkpatrick. 2008. Validation of twinning rate whole genome association study results. Animal Genetics (in preparation)
|
Progress 05/01/06 to 05/01/07
Outputs
Efforts to fine-map previously identified QTL continued. As an initial step in this effort 200 Holstein sires with high reliability twinning rate PTAs were genotyped using the ParAllele 10K SNP typing tool. Combined linkage/linkage disequilibrium analysis of this data has lead to the identification of regions on 12 chromosomes which are potentially associated with twinning rate in cattle. These associations are currently being validated in an independent sample of Holstein sires of more recent vintage. Fine-mapping of twinning rate QTL on BTA5 was initiated by typing 380 Holstein sires with 120 markers over an 80 Mb region. Strong evidence and narrowed locations for two QTL on BTA5 were identified and candidate gene analyses have begun.
Impacts
Identification of SNPs in tight linkage disequilibrium with QTL are expected to be identified. These markers will be useful tools for animal selection.
Publications
- E.S. Kim, P.J. Berger and B.W. Kirkpatrick. 2007. Fine Mapping Of A Bovine Twinning Rate QTL on Chromosome 5. PAG-XV, abstract P522.
- Kirkpatrick, B.W., P.J. Berger and E.S. Kim. 2006. Genome-wide Association Test for Bovine Twinning Rate QTL. International Society for Animal Genetics, abstract D544.
- Cobanoglu, O., E.S. Kim, P.J. Berger and B.W. Kirkpatrick. 2006. Fine-mapping of twinning rate QTL on bovine chromosome 14. International Society for Animal Genetics, abstract D545.
|
Progress 05/01/05 to 04/30/06
Outputs
Efforts to fine-map previously identified QTL were initiated. As an initial step in this effort 200 Holstein sires with high reliability twinning rate PTAs were genotyped using the ParAllele 10K SNP typing tool. Linkage disequilibrium analysis of this data is ongoing and should aid in both fine mapping QTL and replicating QTL identified in previous within-family linkage analyses. SNP discovery work is ongoing to identify SNPs which will fill gaps in coverage from the 10K SNP chip.
Impacts
Identification of SNPs in tight linkage disequilibrium with QTL are expected to be identified. These markers will be useful tools for animal selection.
Publications
- No publications reported this period
|
|