Progress 01/01/10 to 12/31/14
Outputs
Target Audience: Out target audiences comprise: 1) Researchers in quantitative and molecular genetics interested in performing genomewide association and genomic breeding value prediction in pig populations. 2) Pig breeders interested in using SNP chip technology for improving economically important traits. Changes/Problems: No main challenges that required major changes What opportunities for training and professional development has the project provided? Several students and professionals were trained over the course of this project: 1) Yvonne Badke, PhD graduated in 2014. MSU. Currntly working at Bayer Crop Science. 2) Pablo Reeb, PhD Student graduating in Summer 2015. MSU. 3) Yeni Liliana Bernal Rubio, PhD Student graduating in July 2015. UBA 4) Jose Luis Guandron Duarte, PhD Student graduating in August 2015. UBA 5) Chelsea Pike, Undergraduate Animal Science MSU. 6) William Ratledge, Undergraduate Animal Science MSU. 7) Yijian Huang, Postdoctoral researcher (2013). MSU. Currently working at SPG. How have the results been disseminated to communities of interest? Our group presented results at scientific meetings to reach researchers in quantitative genetics. We also gave talks at breeder groups and companies (NSR, GENUS PIC) What do you plan to do during the next reporting period to accomplish the goals? This is a final project. there will be no next reporting period
Impacts
What was accomplished under these goals?
We accomplished all proposed goals over the course of the project. 1a) We published estimates of LD in 4 breeds of pigs used in the USA. The resulting paper (Badke et al 2012) has been widely cited. 1b and 3) We performed tagSNP selection and we also validated selected tags for a low density chip. Our group played a very important role in the verification of the tagset selected in the GGP chip and it is reflected in one publication (Badke et al 2013). 2a and 3) We assessed the merit of the GGP for imputation and for prediction of breeding values under differnt genotyping scenarios (Badke et al 2014, Gualdron Duarte 2013) 2b) We generated methodology for GWA and we applied it to pork quality data (Gualdron Duarte 2013) Our methods will be incorporated in a routine genomic evaluation performed by the National Swine Registry.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Steibel, J.P.; Wang, H. and Shou, P.Z. A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium. BMC Bioinformatics 16 (1), 61.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
LG Duarte, RJC Cantet, RO Bates, CW Ernst, NE Raney, JP Steibel. Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations. BMC bioinformatics 15 (1), 246.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Y Huang, RO Bates, CW Ernst, JS Fix, JP Steibel. Estimation of US Yorkshire breed composition using genomic data. Journal of animal science 92 (4), 1395-1404.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
YM Badke, RO Bates, CW Ernst, J Fix, JP Steibel. Accuracy of estimation of genomic breeding values in pigs using low-density genotypes and imputation. G3: Genes| Genomes| Genetics 4 (4), 623-631
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
J Steibel, P Reeb, CW Ernst, RO Bates. Cis and Trans-acting eQTL Mapping from RNAseq Data in Swine Populations.
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Progress 01/01/13 to 12/31/13
Outputs
Target Audience: Pig Breeding Industry Academic Quantitative Geneticists with interest in animal and plant breeding Graduate and Undergraduate students with potential interest in anima and plant breeding Changes/Problems: There were no major changes implemented What opportunities for training and professional development has the project provided? We trained several students in the context of this project. 1) Yvonne Badke's PhD dissertation was 100% dedicated to this project. She completed her PhD dissertation on September 2013 and she is now employed by the crop breeding industry. Yvonne has obtained numerous awards in the context of the research developed for this project. The most recent one is the National Swine Improvement Federation Graduate Student award for her contributions to the pig breeding industry. 2) Jose Luis Gualdron completed training as a vissiting graduate students from University of Buenos Aires, Argentina. He presented one abstract and published one paper. Jose Luis continues to be coadviced by me and he is working with data generated under this project from his home university. 3) Yeni Liliana Bernal Rubio is currently avissiting graduate students from University of Buenos Aires, Argentina and she is working using data and tools generated under this projects (but with external funds). Yeni has already submitted an abstract to the midwest ASAS meetings and she is preparing a paper. I estimate she will publish a total of three papers from her work related to this project. Yeni's funding is external to this grant, but she uses tools and data generated from the grant. 4) Pablo Reeb is a Phd student working under my supervision on RNAseq analysis. He received training on the use of RNAseq data for genotyping using tools and resources generated from this project. Pablo has been funded by MSU and he has not been paid from this grant, but he has contributed results and used tools and data generated from the grant. 5) Peter VandeHaar is an undergraduate student who received training on genetics programming. Peter is a biochemistry and computer science student at Calvin College, MI. He did a summer intership that consisted of taking code generated by Yvonne and re-programming it in a user friendly manner. Peter will likely return to work with us for three months in 2014. He received training in animal breeding and genetics programming and he contributed user friendly code for implementaiton of analysis published by our group in the context of this grant. 6) Kaitlin Wurtz is an incoming PhD student in animal behavior and gentics. Kaitlin is working on genotype imputation using mixed breed panels for application in genomewide association. She is supported by internal funds, but she uses data and resources generated within this grant. This grant has been instrumental in training all these students and vissiting scholars. How have the results been disseminated to communities of interest? We published papers in peer review journals and we communicated results in contributed and invited talks. In particular for 2013: 1) we published 2 papers in BMC genetics 2) we delivered contributed presentations in Joint Animal Meetings, Plant Animal Genome 3) we delievered invited presentations in National Swine Improvement Federation, Federal University of Lavras, Brazil. What do you plan to do during the next reporting period to accomplish the goals? We are wrapping up this grant. We want now to extend results on using sequence data for genotyping and imputation. We will finish and deliver an increased size reference pannel and we will publish on the use of multi breed panels for imputation. These results are absolutely essential for extending the impact of this grant to currently available technologies. We will deliver software for imputation and GEBV prediction as well as for GWA. We will train graduate and undergraduate students: Kaitling Wurtz, Pablo Reeb, Yeni Bernal and Peter VandeHaar
Impacts
What was accomplished under these goals?
An important outcome of this year is the delivery of data and tools for assessment of genotype imputation accuracy in pigs. We published two papers and made all data available for use in future imputation models. We made available annotation for the 60 K snp chip (see section on tools and data delivered) that was well received by colleagues worldwide. At this point we have already made available over 1200 genotypes and we have a database of over 10000 haplotypes that we will deliver from the same platform. This data will be an important resource for conducting further research on genomic prediction and genomewide association.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2014
Citation:
Badke, Y.M.; R.O.; Ernst, C.W.; Schwab, C.; Fix, J. and Steibel, J.P. Accuracy of estimation of genomic breeding values in pigs using low density genotypes and imputation. Under review
- Type:
Journal Articles
Status:
Accepted
Year Published:
2013
Citation:
Gualdron-Duarte, Jose L., Bates, Ronald O., Ernst, Catherine W., Ranney, Nancy, Cantet, Rodolfo J., Steibel, Juan P. 2013. Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels. BMC Genetics 14 (38)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Badke, Yvonne, Bates, Ronald O., Ernst, Catherine W., Fix, Justin, Steibel, Juan P. 2013. Accuracy of estimation of genomic breeding values in pigs using low density genotypes and imputation. ASAS/ADSA Joint Animal Meetings, Indianapolis, IN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Reeb, Pablo, Ranney, Nancy, Preeyanon, Likit, brown, Titus, Bates, Ronald O., Ernst, Catherine W., Steibel, Juan P. 2013. Assessing statistical properties of cSNP discovery and geno - typing using RNAseq and genotyping chip data. ASAS/ADSA Joint Animal Meetings, Indianapolis, IN.
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2013
Citation:
Huang, Yijian, Bates, Ronald O., Ernst, Catherine W., Fix, Justin, Steibel, Juan P. 2013. Estimation of US Yorkshire breed composition using genomic data. ASAS/ADSA Joint Animal Meetings, Indianapolis, IN.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2013
Citation:
Badke, Yvonne M., Bates, Ronald O., Ernst, Catherine W., Schwab, Clint, Fix, Justin S., Van Tassell, Curt, Steibel, Juan P. 2013. Accuracy of genotype imputation using the Geneseek Genomic Profiler for Porcine LD. PAG XXI conference. San Diego, CA.
- Type:
Other
Status:
Published
Year Published:
2013
Citation:
Steibel, J. P. Estimation and Exploitation of Linkage Disequilibrium in Pig populations. (July 2013). Department of Statistics Seminar. Federal University of Lavras. Lavras, Brazil. Invited seminar.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2012
Citation:
Steibel, J. P. Accuracy of Imputation and Potential Benefits to the pig Industry, (November 29, 2012). National Swine Improvement Federation.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Badke, Y.M.; Bates, R.O.; Ernst, C.W.; Schwab, C.; Fix, J.; Van Tasell C.V.P. and Steibel, J.P. Methods of tagSNP selection and other variables affecting imputation accuracy in swine. BMC Genetics 2013, 14:8
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: The objectives of this project are: 1) Estimate linkage disequilibrium in four breeds of pigs and select tag SNP specific to each breed. 2) Perform High Density GWA scans and GEVB prediction for economically important traits in one breed. 3) Validate tagSNP selected by comparing results of objective 2) to those obtained using tagSNP panels selected in objective 1. We completed assessment of imputation accuracy in pig populations. We also studied the design of reference panel for imputations and found that current reference panels are adequate for SNP imputation for GEVB prediction, but GWA studies could benefit from larger reference panels. These are important results when considering future applications of imputation. Two graduate students and a post doctoral fellow received training under this project. PARTICIPANTS: PD: Juan P. Steibel. CoPD Ronald O. Bates, Cahterine W. Ernst. Support personnel: Nancy O. Raney. Collaborators: Clint Schwaab; Justin Fix Justin, National Swine Registry; Rodolfo J.C. Cantet, University of Buenos Aires, Argentina; Fernando Cardoso, Embrapa, Brazil. Opportunities for training: Yvonne M. Badke, Animal Science PhD Student whose program is largely based on this grant. Jose Luis Gualdron is a PhD Student from University of Buenos Aires trained using data generated by this grant. YiJian Huang is a Postdoctoral fellow trained in the context of this researcher. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
An important outcome of this year is the delivery of the haplotype panels and a set of R tools for imputation. This adds to the tool created last year. We created a website (https://www.msu.edu/~steibelj/JP_files/Imputation.html) in September of 2012. We also continued to create a change in conditions for the application of genomics technology in swine breeding. Part of the results from this year were used by GeneSeek to design a low density chip. We participated in the validation of the chip that now is being used by the pig breeding community. We trained a post doctoral researcher that now will work with the National Swine registry. The registry payed for the training of the researcher. This was possible thanks to data and knowledge generated through the activities of this grant.
Publications
- Abstracts: Y M Badke, R O Bates, C W Ernst, and J P Steibel. (2012). Comparison of three methods for tagSNP selection, ASAS/ADSA Midwest 2012, oral presentation.
- J. L. Gualdron Duarte, R. O. Bates, C. W. Ernst, N. E. Raney, R. J. C. Cantet, J. P. Steibel. 2012. Genotype imputation accuracy in an F2 pig cross using high-density and low-density SNP panels. ADSA-AMPA-ASAS-CSAS-WSASAS Joint Annual Meeting. Phoenix (Arizona). July 15 -19.
- Y M Badke, R O Bates, C W Ernst, C Schwab, J S Fix, C P Van Tassell, J P Steibel. (2012) Accuracy of genotype imputation using the GeneSeek Genomic Profiler for Porcine LD, PAG XXI, poster presentation. Submitted.
- Papers: Badke, Y. M., Bates, R. O., Ernst, C. W., Schwab, C., Fix, J., and Steibel, J. P. (2012). TagSNP selection and imputation accuracy using a reduced size haplotype panel in swine. under review. https://www.msu.edu/~steibelj/JP_files/imputation.html
- J. L. Gualdron Duarte, R. O. Bates, C. W. Ernst, N. E. Raney, R. J. C. Cantet, J. P. Steibel. 2012. Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels. Submitted.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: The goals of this project are to develop and adapt statistical and computational methods to link phenotypic variation to genomic variation. It is articulated in three objectives: 1) to develop Bayesian hierarchical models for analysis of gene expression data; 2) to develop cost-effective experimental designs for exploitation of linkage disequilibrium (LD) in livestock breeding and 3) to develop and apply statistical models for analysis of eQTL. Objective 1: To date we continued working on comparing Empirical Bayesian models for analysis of qPCR, microarray and RNA sequencing data. Two of my students (Pablo Reeb and Maria Arceo) are pursuing graduate studies on this area working on RNAseq and microarray analyses respectively. A third student (Rodrigo Manjarin) from Dr. Trottier's laboratory, worked under my co-supervision to complete a study on selection of reference genes for use in gene expression analysis that pertains to this goal too. Objective 2: We performed analysis of first the collection of high density SNP reference haplotype panels for four breeds of pigs and we secured further funds to analyze an experimental swine cross. Selection of reduced panels of SNP is underway. A undergraduate student (Chelsea Pike) a Graduate student (Yvonne Badke) and an international visiting scholar (Jose Luis Gualdron Duarte) received training under this objective. Objective 3: We finished the eQTL in longisimun dorsi muscle samples from a pig cross using low density markers. Future plans involve the use of combined high-low density SNP genotypes and allelic specific expression to further the results from this objective. PARTICIPANTS: Principal Investigator: Juan P. Steibel Collaborators: Catherine W. Ernst, Ronald O. Bates, Robert J. Tempelman, Rodolfo J.C. Cantet, Fernando Cardoso. Graduate Students: Yvonne Badke, Maria Arceo, Pablo Reeb, Rodrigo Manjarin. Undergraduate Students: Chelsea Pike. Visiting Scholars: Jose Luis Gualdron. TARGET AUDIENCES: Researchers in quantitative and molecular genetics, in particular those working with livestock and wildlife species. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
This project is aimed at developing statistically powerful and computationally efficient methods to link phenotypic and genotypic variation. We contributed to the knowledge of genomic variation in pig breeds through making available a set of reference haplotypes from four US swine breeds. We are also inducing a change in action in genomics researchers by making available through the web a set of tools to investigate LD in livestock species using high density SNP genotypes. Since its inception in September of 2011, the website (https://www.msu.edu/~steibelj/JP_files/LD_estimate.html) received over 79 visits from 15 locations and we received testimonial evidence of use of the released package from colleagues in North Carolina and Southern Brazil. We also started to create a change in conditions for the application of genomics technology in swine breeding. Based upon communication of our results to the National Swine registry, the registry decided to hire a PhD level researcher that will work with our group to implement the use of breed-specific LD information in determining breed purity for their registered animals. Another perceived change in knowledge was in the area of qPCR control gene selection. Our work on such area was well received and we are invited to contribute a technical note that is in preparation right now.
Publications
- Gualdron Duarte, J.L., Steibel, J.P., Forneris, N.S., Bates, R.O., Ernst, C.W., Raney, N., Badke, Y., Cantet , R.J.C. 2011. Calculo de la fraccion del genoma compartida entre hermanos en cerdos. 34E Congreso Argentino de Produccion Animal, I Joint Meeting AAPA-ASAS. Ciudad de Mar del Plata (Buenos Aires, Argentina). October 4-7.
- M. Arceo, C.W. Ernst, J.K. Lunney, N.E. Raney, T. Huang, C.K. Tuggle, R.R.R. Rowland, J.P.Steibel. 2011. Differential gene expression and functional analysis of RNA from blood of PRRSV infected PHGC pigs. International PRRSV Symposium . Chicago. 12/2-3/2011
- Papers: Wysocki, M., H. Chen, J. P. Steibel, D. Kuhar, D. Petry, J. Bates, R. Johnson, C. W. Ernst, and J. K. Lunney. 2011. Identifying putative candidate genes and pathways involved in immune responses to porcine reproductive and respiratory syndrome virus (PRRSV) infection. Animal Genetics. In Press.
- Manjarin R., Trottier N.L, Weber P.S., Liesman J.S., Taylor N.P., Steibel J.P. 2011. A simple analytical and experimental procedure for selection of reference genes for reverse-transcription quantitative PCR normalization data. J. Dairy Science, 94(10):4950-61.
- Choi, I., Steibel, J.P., Bates, R.O., Raney, N.E., Rumph, J.E., Ernst, and C.W. 2011. Identification of carcass and meat quality QTL in an F2 Duroc x Pietrain pig resource population using different least-squares analysis models. Frontiers in Livestock Genomics. In press.
- Steibel, J. P., Bates, R. O., Rosa, G. J. M., Tempelman, R. J., Rilington, V. D., Ragavendran, A., Raney, N. E., Ramos, A. M., Cardoso, F. F., Edwards, D. B., and Ernst, C. W. 2011. Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in Pigs. Plos One. 2 (6).
- Abstracts: Reeb, P. D., Li, W., Brown, T., Steibel, J. P.; Experimental designs and analysis models to study the sea lamprey transcriptome using Next-Generation RNA sequencing. 6th Annual Fisheries and Wildlife GSO Research Symposium (MSU). East Lansing, MI, USA, 25th February 2011.
- C. Pike, R.O. Bates, C.W. Ernst, J.P. Steibel, D.B. Edwards. 2011. QTL mapping of coat color traits in an F2 Duroc x Pietrain pig resource population. 2011 ASAS-ADSA Midwest meeting. Des-Moines, IA, March 2011.
- J.P. Steibel and Y. M. Badke. Estimacion de Desequilibrio de Ligamiento usando Marcadores de ADN: su aplicacion en la implementacion de esquemas efectivos de seleccion genomica en porcinos. Invited Speaker at: I Simposio sobre Genomica y modelacion en los nuevos escenarios de la Ganaderia Bovina Tropical. June 2011. Palmira, Colombia.
- J. P. Steibel and P. Reeb. 2011. Sound and efficient designs and models for RNA-seq experiments with application in animal genomics. J. Anim. Sci. Vol. 89, E-Suppl. 1.
- M. E. Arceo, C. W. Ernst, M. Wysocki, J. K. Lunney, and J. P. Steibel. 2011. Evaluating statistical models to assess differential gene expression in PRRSV infected pigs using plasmode datasets. J. Anim. Sci. Vol. 89, E-Suppl. 1.
- Y. M. Badke, R. O. Bates, C. W. Ernst, C. Schwab, and J. P. Steibel. 2011. Estimation of linkage disequilibrium in four US pig breeds. J. Anim. Sci. Vol. 89, E-Suppl. 1.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: The objectives of this project are: 1) Estimate Linkage Disequilbrium in four pig breeds using high density genotyping and select tag SNPs specific to each breed. 2) Perform high density GWA scans and GEBV prediction for economically important production traits in one breed. 3) Validate tag SNP panels by comparing association tests derived from low density SNP panels to those obtained using high density SNP genotypes. We obtained and successfully genotyped samples for all three objectives of our project. Initially we obtained and genotyped 119 sire-dam-offspring trios using the Illumina SNP60 BeadChip (357 samples). After data filtering and quality control 86 of these trios (258 samples) were of acceptable quality. Matching funds from the National Swine Registry (NSR) supported genotyping to replace lost samples so that total sample size was increased to 111 trios (333 animals) which. we deemed to be an adequate quantity for objective 1. We also genotyped 931 (all available) sires of the Yorkshire breed. Genotyping rate on these animals was excellent, with over 95% of the samples exhibiting more than 90% call rate. Data verification, quality control and checking was performed as data arrived, using in-house produced software as well as public domain analysis packages. We started data analysis in the context of objective 1. We phased all trio data and started computing measures of linkage disequilibrium. This analysis continues during the first trimester of 2011. Analysis of SNP data with the purposes of breed identification which is also an area of active research was conducted and results presented to the NSR. We interacted with the NSR throughout the process and reported our results to them. PARTICIPANTS: PIs: Dr. Juan P. Steibel. Dr. Ronald O. Bates. Dr. Catherine W. Ernst. Support personnel: Nancy Ranney, MSU. Collaborators: Dr. Clint Schwab, National Swine Registry. Opportunities for training: Yvonne Badke, Animal Science, MSU. is a PhD Student whose academic program is largely based on this grant. TARGET AUDIENCES: Target Audience: Swine Breeders. Animal Breeders. Where targeted through participation in meeting or reporting to their organizations. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
An important outcome the first year of this project was the creation of a large panel of haplotypes (Hap-map). We will use such panel for estimation of linkage disequilibrium and for imputation of genotypes. As result of the first year of work, a software pipeline has been created to receive, check and store high density genotypes. A second pipeline for phasing and LD estimation was also constructed based on existing software. Results from this project are already impacting the swine breeders at the NSR who identified the potential for developing breed specific panels as a priority and decided to partner on further research in this area.
Publications
- Reduced Marker Panels: Potential for More Cost‐effective Use of Genomic Data. C.W Ernst, R.O. Bates and J.P. Steibel. National Swine Improvement Federation. Annual Meeting and Symposium. Kansas City, MO. December 2, 2010.
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