Progress 02/15/06 to 02/14/10
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?The data generated from this research has been integrated into the database maintained by the USDA/AIPL for inclusion in national genetic evaluations of Holstein cattle. This data is transparent to the dairly cattle breeder and is delivered as enhanhed breeding values within the national genetic evaluation program. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The major impact of this project was the creation of the BovineSNP50 Beadchip which fundamentally changed the way research and genetic selection is performed, not only in Holstein cattle but in all agricultural species both animals and plants. Because this produced a true paradigm shift in how genetic selection and genetic progress is achieved, the individual goals of this project became obsolete. The data generated by this project (nearly 1000 foundation bulls genotyped with the SNP50) allowed genomic selection to be implemented. Rather than delivering a few diagnostic assays to the dairy industry, the project results delivered increased accuracies for all traits genomewide allowing producers to make better selection decisions and accelerate genetic progress within the global dairy population.
Publications
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Progress 02/15/08 to 02/14/09
Outputs
Target Audience:The development of the BovineSNP50 Beadchip became the foundation for implementing genomic selection within the dairy industry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?Numerous journal articles have been published based on the data generated from thsi project. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The creation of the BovineSNP50 Beadchip fundamentally changed the way research and genetic selection is performed. The creation of the SNP50 and genotyping of nearly 1000 foundation bulls allowed genomic selection to be implemented.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2009
Citation:
Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, Kim J-J, Kim K-S, Sonstegard TS, Van Tassell CP, Neibergs HL, Chen K, Cooper A, McEwan JC, Brauning R, Coutinho LL, Babar ME, Wilson GA, McClure MC, Rolf MM, Kim J-W, Schnabel RD and Taylor JF. 2009. High?throughput phylogenomics: From ancient DNA to signatures of human animal husbandry. Proceedings of the National Academy of Sciences USA 106:18644-18649.
- Type:
Journal Articles
Status:
Published
Year Published:
2007
Citation:
Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G and Zhao S. 2007. A physical map of the bovine genome. Genome Biology 8:R165.
- Type:
Journal Articles
Status:
Published
Year Published:
2008
Citation:
Khatkar MS, Nicholas FW, Collins A, Zenger KR, Cavanagh JAL, Barris W, Schnabel RD, Taylor JF and Raadsma HW. 2008. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9:187.
- Type:
Journal Articles
Status:
Published
Year Published:
2009
Citation:
VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF and Schenkel F. 2009. INVITED REVIEW: Reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science 92:16-24.
- Type:
Journal Articles
Status:
Published
Year Published:
2009
Citation:
Cole JB, VanRaden PM, O'Connell JR, Van Tassell CP, Sonstegard TS, Schnabel RD, Taylor JF and Wiggans GR. 2009. Distribution and location of genetic effects for dairy traits. Journal of Dairy Science 92:2931-2946.
- Type:
Journal Articles
Status:
Published
Year Published:
2009
Citation:
Wiggans GR, Sonstegard TS, VanRaden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS and Van Tassell CP. 2009 Selection of single nucleotide polymorphisms and genotype quality for genomic prediction of genetic merit of dairy cattle. Journal of Dairy Science 92:3431-3436.
- Type:
Journal Articles
Status:
Published
Year Published:
2009
Citation:
Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan M, Heaton MP, O Connell JR, Sonstegard TS, Smith TPL, Moore SS and Van Tassell CP. 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4:e5350.
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Progress 02/15/07 to 02/14/08
Outputs
OUTPUTS: In the past year we have designed and built a high density SNP genotyping assay as part of a separate CSREES funded project which has been commercialized by Illumina as the BovineSNP50 genotyping assay. We have now genotyped 995 Holstein bulls for this assay producing approximately 53.7 million genotypes. We have also developed the analysis pipeline necessary to manage and analyze this volume of data.
PARTICIPANTS: Stephanie McKay (Postdoctoral Fellow) has been trained on the Illumina Infinium platform and has used the Illumina Bov50SNP assay to genotype >7,000 samples at the University of Missouri. She has published two manuscripts on the radiation hybrid mapping of high-density SNP panels and on the characterization of linkage disequilibrium among breeds. She is currently learning linkage and linkage disequilibrium mapping methods for QTL detection. PI Schnabel has trained collaborators both nationally and internationally on the genotyping and data analysis of genotypes produced using the BovineSNP50 assay. Collaborations: 1. USDA/BARC: Drs. Curt Van Tassell, Tad Sonstegard and Lakshmi Matukumalli (iBMC Consortium). 2. USDA/USMARC: Drs. Tim Smith, Mark Allan and Warren Snelling (iBMC Consortium). 3. Washington State University: Dr. Holly Neibergs (Genetics of resistance to Johne's disease in Holsteins). 4. MTT Agrifood Research Finland: Dr. Johanna Vilkki (Finish Ayrshire QTL
mapping). 5. University of Helsinki: Hannes Lohi, Kari Elo and Magnus Andersson (Fertility abnormalities in Finnish Ayrshire). 6. University of Missouri: Dr. Jane Armer (Human SNP association mapping for lymphoedema). 7. University of Missouri: Dr. Gary Johnson (Dog SNP mapping for neurological diseases).
TARGET AUDIENCES: This project has impacted both scientists and dairy industry producers. We have trained collaborators both nationally and internationally for using the SNP chip such that they can now analyze high density SNP data for their own research projects. We have also made the genotypes from this project available to collaborators who will use the data for whole genome enabled animal selection which will directly benefit the dairy industry. We have made several presentations at both national and international conferences detailing the progress of our work.
PROJECT MODIFICATIONS: This project initially sought to fine-map milk production and fertility QTL on only chromosomes 2 and 14 by microsatellite genotyping followed by small-scale SNP genotyping (1,536 SNPs). However, advances in SNP genotyping technology since the beginning of this project have drastically increased the numbers of SNPs that can be tested. This has arisen due to the ability to pool data produced by three NRI funded projects (PIs: Taylor, Van Tassell and Schnabel) and due to the assay pricing provided to the iBMC Consortium for the BovineSNP50 assay. Therefore, the scope of this project has increased to encompass the entire bovine genome which has already been genotyped at high density. Additionally, collaboration with Dr. Van Tassell has more than doubled the number of samples that will be included in the project, which will increase the power of the analyses. While development of the SNP assay affected progress in Year 1, it has also eliminated the need to do
fine-mapping. Thus, the project is on schedule but most importantly will produce many times more data than originally intended for the same budget.
Impacts
This project was one of several funded by CSREES aimed at using high density SNP genotyping to improve animal agriculture, specifically cattle. We have leveraged the resources of all these projects to produce more genotypic data than any of the projects alone could have produced. Specifically, Dr. Curt Van Tassell has contributed genotypes on an additional 2000+ Holstein bulls from his project (2006-35205-16888) to be included in this project. Likewise, we have made the genotypes for our 995 Holstein bulls available to be included in his project. To date, a preliminary analysis of BTA14 has been conducted and was presented at the Plant and Animal Genome Meetings on January 13, 2008. Using joint linkage/linkage disequilibrium analysis we were able to demonstrate that it is now possible to map QTL to sub-megabase intervals accurately. We also demonstrated that there are still deficiencies in the current Btau4.0 genome assembly that will impact any form of analysis
dependent on correct marker order. In collaboration with Dr. Van Tassell, the genotypes produced for the bulls in this project will also be included in the first release of sire evaluations based on genomic predictions, which will be released to cooperators in early 2008. This represents the first step in delivering immediately applicable results to the cattle industry.
Publications
- 1)McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, GillCA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF and Moore SS. 2007. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC-Genetics Accepted.
- 2)Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenchild CD, Moore SS, Warren WC and Sonstegard TS. 2008. Simultaneous SNP discovery and allele frequency estimation by high throughput sequencing of reduced representation genomic libraries. Nature Methods. 5:247-252 cover article.
- 3)McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Neto ED, Georges M, Gill CA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF and Moore SS. 2007. Whole genome linkage disequilibrium maps in multiple breeds of cattle. BMC Genet. 8:74.
- 4)Sellner EM, Kim J-W, McClure MC, Taylor KH, Schnabel RD and Taylor JF. 2007. BOARD-INVITED REVIEW: Applications of genomic information in livestock. J. Anim. Sci. 85:3148-3158.
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Progress 02/15/06 to 02/15/07
Outputs
This project initially sought to fine-map milk production and fertility QTL on only chromosomes 2 and 14 by microsatellite genotyping followed by small-scale SNP genotyping (1,536 SNPs). However, advances in SNP genotyping technology since the beginning of this project have drastically increased the numbers of SNPs that can be tested as well as reduced the cost of genotyping. Therefore, the scope of this project has changed to reflect current technology. As part of a separate CSREES funded project we are developing a high density SNP assay that will produce greater than 48,000 SNP genotypes per animal. This new assay will allow us to fine-map the entire genome rather than just the two chromosomes initially targeted by this proposal. Rather than proceed with the initial course of action outlined in the proposal, we have elected to wait until this new assay becomes available. Suitable animals for the mapping phase of the project have been identified and their DNA
extracted but no genotyping has been performed in year 1.
Impacts
This project will produce diagnostic assays that can be used by the dairy industry to alter milk production and/or fertility in Holstein cattle. The magnitude of economic impact cannot be determined at this time since selection based on a large number of genetic markers has never been possible to date. However, results from this research have the ability to fundamentally change the dairy cattle breeding industry and significantly increase the rate of genetic gain within dairy cattle.
Publications
- No publications reported this period
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