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Research Interests:
Advances in high-throughput DNA sequencing and related technologies have drastically increased the quantity of information available to crop geneticists. My interests lie in the application of quantitative genetics and computational biology to associate agriculturally important phenotypes with their means and degree of inheritance. I hope to integrate these associations with molecular genetics to further unravel the pathways of development, physiology, and environmental interactions. I am also interested in developing methods to increase rates of gain in marker-assisted breeding programs based on genome-wide sequence data across entire plant populations.
I'd like to research and collaborate with others to:
(1) Further understand crop genetics & its environmental interaction (GxE)
(2) Improve prediction of phenotypes & theorization of crop ideotypes (optimal genotype for an application & environment)
(3) Develop breeding methods which most rapidly realize these ideotypes
Genetic abstractions & molecular mechanics achieved conceptual convergence nearly 100 years ago.
We now have the genomic information & computational power to apply this realization in practice.
Thesis Objectives:
Dissecting Natural Diversity in Maize Plant & Ear Height
Plant height is a primary determinant of biomass, resource allocation, and harvest index (ratio of grain: non-grain biomass). The Green revolution revealed the impact of height on shifting resources from straw to grain in wheat and rice, as well as its importance in lodging (mechanical stalk failure), and pesticide efficacy. With recent interest in stover (non-grain biomass) for lignocellulosic applications such as biopolymers and biofuels, height continues to play a pivotal role in defining crop ideotypes. Using joint-linkage and linkage disequilibrium mapping (Nested Association Mapping), across 26 diverse biparental mapping families (NAM population), we are dissecting plant height QTL (quantitative trait loci; regions of the genome responsible for variation in height) at near gene-level resolution. Given r=.84 for height and flowering time, we will compare height QTL with flowering time QTL to discern the pleiotropy (QTL affecting multiple traits) of morphology and maturity at the molecular level. To validate our methods we are fine mapping two complementary height QTL of median effect size to allow univariate discrimination of these effects and discern the molecular nature of allele series (QTL that commonly segregate in different families).
Mapping Stalk Strength QTL in Maize
As planting densities increase, standability is a critical concern for farmers . Both root and stalk lodging are traits which must be taken into consideration when breeding to maximize yield in environments plagued by high winds, and biotic stressors. In addition, when breeding for silage or biofuels and biopolymers, stalk composition is critical to easing digestibility and downstream processing. Given its importance, we are mapping QTL responsible for stalk strength in the NAM population. A rapid method to phenotype stalk hardness is rind penetrometer resistance (RPR). This assay measures the amount of force (KgF) required to "pop" a nail into the rind of a maize stalk. To increase precision and speed up data acquisition, I have modified a manual force gauge to be spring-loaded with a triggered release mechanism. Moreover, I coded a Java program which loads a field book from Excel and provides audible commands to the operator while in the field from headphones and a netbook in a pollination belt. The program relays plots remaining to be phenotyped and links phenotype outputs from the device to its respective genotype in the field book. The program also retains information regarding the time and GPS coordinates at which measurements were taken. Once phenotyping is completed across 3 states over 2 years, >30 million SNPs (single nucleotide polymorphisms; DNA variants) will be imputed and projected to the entire NAM population enabling high-resolution nested association mapping of stalk strength.
Identifying the Influence of Maize Genetics on Microbial Colonization of the Rhizosphere
In collaboration with the Ley Lab of Microbiology, we are characterizing the impact of maize genetics on the colonization patterns of bacteria within the rhizosphere. Using a combination of metagenomics (random shear sequencing of total DNA in maize roots and adhered soil) and targeted 16s rDNA sequencing, we hope to associate kinship among maize genotypes with similarities in microbial load to identify new symbiotic relationships. It is known that root exudates such as amino acids, phenolics, organic acids, sugars, and polysaccharides exudates exert significant influence on microbial colonization and are substantially polygenic. Therefore, total allelic diversity should well parallel functional allelic maize diversity influencing the microbiome. These preliminary characterizations of diverse inbreds across 5 distinct field environments will lead to future population level measurements and identification of those maize QTL influencing the microbiome of agroecosystems. Our ultimate goal is adapting maize germplasm to positively influence microbial communities enabling reduced fertilizer needs and pathogen pressures.
 Future Prospects in Molecular Breeding Optimization
We have entered a new era in the field of agricultural genetics, as we are no longer limited by the number of markers available to characterize genomes. With this advancement Genomic Selection has come to the forefront as one of the most promising methods to revolutionize breeding. Genomic selection revolves around phenotyping a small training population to build a model from the massive genotypic data now available. This model is then used to predict phenotypes across a larger panel of genotyped yet non-phenotyped individuals. This allows resources to be devoted to only those individuals with the greatest predicted promise. However, much is left to be understood in defining the best training population to build these models as well as the optimal combination of lines to be selected as parents to make future gains. In the future, I hope to collaborate with others to apply the tools of combinatorial optimization, network, and information theory to the suite of regression analyses already implemented to answer these questions and minimize the meioses required to attain the desired phenotype.
Education:
2007-Present Cornell University, College of Agriculture and Life Sciences
Ph.D. Candidate, Plant Breeding & Genetics
Minors: Genomics, Plant Cell and Molecular Biology
Advisors: Edward Buckler, Tom Brutnell, John Schimenti
2002-2007 University of Delaware, College of Agriculture and Natural Resources
B.S. Plant Biology (Honors Degree with Distinction)
Minors: Biochemical Engineering, Biochemistry
Advisor: Blake Meyers
Professional Experience:
2007-Present Graduate Research Assistant
Quantitative genetics, computational biology, fieldwork, and high-throughput genotyping
Refer to Current Thesis Objectives
2003-2007 Undergraduate Research Assistant
Genome-wide sequence survey-based approaches to Arabidopsis floral expression profiling and comparison to microarrays
Construction of promoter:GUS fusion cassettes and transformation in Arabidopsis
Construction of amiRNA constructs to characterize possible disease resistance in the TX/TN gene family
Characterization of Crocus sativus for Antirrhinium/Arabidopsis ABC model homology
2009-2010 Teaching Assistant- Genomics, Cornell University
Lectured on Quantitative Genomics and Plant Breeding
Lectured on Societal Impacts of Genomics
Paper and Exam Grading
2005-2007 Teaching Assistant- Plant & Animal Genetics Lab, University of Delaware
Drosophila cultures, media plating and Ames test analyses, Maize and Brassica Growth for Mendelian inheritance analyses
Assisted students with proper sterile technique and lab procedures
Introduced several molecular genetics labs
Paper and Exam Grading
1999-2003 Orchard Hand & Sales Associate
General Orchard Maintenance- Pruning, spraying, harvesting peaches, nectarines, apples, plums, blueberries, strawberries, black and red raspberries, currants, pumpkins, tomatoes, sunflowers, and christmas trees. Maintain irrigation system, and mow grounds
Operation of fruit store and preparation of fruit for wholesale
Publications:
Myles S., Peiffer J.A., Brown P.J., Ersoz E.S., Zhang Z., Costich D.E., Buckler E.S. 2009. Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design. The Plant Cell, 21:2194-2202.
Gore M.A., Chia Jer-Ming, Elshire R.J., Sun Qi, Ersoz E., Hurwitz B.L., Peiffer J.A., McMullen M.D. Grills G.S., Ross-Ibarra J., Ware D.H., Buckler E.S. 2009. A First-Generation Haplotype Map of Maize, Science 326:1115-1117.
Buckler E.S., Holland J.B., Bradbury P.J., Acharya C. B., Brown P.J., Browne C., Ersoz E., Flint-Garcia S., Garcia A., Glaubitz J.C., Goodman M.M., Harjes C., Guill K., Kroon D.E., Larsson S, Lepak N.K., Li H., Mitchell S.E., Pressoir G., Peiffer J. A., Rosas M.O., Rocheford T.R., Romay M.C., Romero S., Salvo S., Villeda H.S., da Silva H.S., Sun Q., Tian F., Upadyayula N., Ware D., Yates H., Yu J., Zhang Z., Kresovich S., McMullen M.D. 2009. The Genetic Architecture of Maize Flowering Time, Science 325:714-718.
Jason Peiffer, Shail Kaushik, Hajime Sakai, Mario Arteaga-Vazquez, Nidia Sanchez-Leon, Hassan Ghazal, Jean-Phillipe Vielle-Calzada, Blake Meyers. 2008. A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS. BMC Plant Biology, 8:43.
Conferences:
2010 52nd Annual Maize Meeting, Riva del Garda, Italy
2009 51st Annual Maize Meeting, St. Charles, IL
2008 6th Annual Symposium in Plant Biology: Ecological Genomics, Amherst, MA
2008 2nd Annual Plant Breeding Workshop, Des Moines, IA
2008 50th Annual Maize Meeting, Washington D.C.
2007 Mid-Atlantic Plant Molecular Biology Symposium, Patuxent, MD
2007 Plant & Animal Genome Conference XV, San Diego, CA
2007 Plant Biology Symposium- Gene Silencing: The Biology of Small RNAs & the Epigenome, UC Riverside
2006 Mid-Atlantic Plant Molecular Biology Symposium, Patuxent, MD
Presentations:
2010 Jason Peiffer, Michael Gore, Peter Bradbury, Maize Diversity Project, Edward Buckler
Dissecting Natural Allelic Diversity in Maize Plant Height: GWAS and Fine Mapping of Chr9L QTL. Presented 52nd Annual Maize Genetics Conference Riva del Garda, Italy
2010 Cinta Romay, Sara Larsson, Jason Peiffer, Moira Sheehan, Feng Tian, Peter Bradbury, Michael McMullen, James Holland,
Doreen Ware and Edward Buckler. Unraveling a flowering time QTL on chromosome 8. Presented 52nd Annual Maize Genetics Conference Riva del Garda, Italy
2009 Jason Peiffer, Michael Gore, Sherry-Flint Garcias, Maize Diversity Project and Edward Buckler
Evaluation of Stalk Strength QTL by Nested Association Mapping. Presented 51st Annual Maize Genetics Conference
St. Charles, IL
2009 Nick Lepak, Maize Diversity Project, Michael Gore, Sara Larsson, Jason Peiffer, Edward Buckler
NAM QTL for Fall Armyworm and Banvel Resistance in Maize. Presented 51st Annual Maize Genetics Conference
St. Charles, IL
2008 Jason Peiffer, M.Cinta Romay, Elhan S. Ersoz, Huihui Li, Peter Bradbury,Maize Diversity Project
Characterization of Vgt1 Allelic Series Using NAM. Presented 6th Annual Symposium on Plant Biology Amherst, MA
2008 M.Cinta Romay, Elhan S. Ersoz, Huihui Li, Peter Bradbury, Jason Peiffer, Maize Diversity Project
A Study of Vgt1 Using Joint Linkage and Association Mapping. Presented 50th Annual Maize Genetics Conference
Washington D.C.
2007 Jason Peiffer, Shail Kaushik, Hajime Sakai, Mario Arteaga-Vazquez, Nidia Sanchez-Leon, Hassan Ghazal, Blake Meyers.
A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS.Presented PAG Conference San Diego, CA.
2007 Jason Peiffer, Shail Kaushik, Hajime Sakai, Hassan Ghazal, Blake Meyers.
A Dissection of the Arabidopsis Floral Transcriptome by MPSS. Presented MAPMBS Patuxent, Maryland.
Awards:
2007 Honorary Induction into Sigma XI for Senior Thesis
2007 American Association of University Professors (AAUP) Undergraduate Award for Future Academic Leaders
2007 National Officer of the Year, Alpha Zeta Professional Agricultural Fraternity
2006 Honorary Induction Delaware Academy of Sciences
2005 Donald F. Crossan Univ. Delaware Dean's Scholarship College of Agriculture and Natural Resources
2004 F.G.Krapf Univ. of Delaware Univ. of Delaware Presidential Achievement Scholarship
2002 Eagle Scout, Boy Scouts of America, Allentown, Pennsylvania
2000 1st Place Botanical Division, Lehigh University Science and Engineering Fair
Extra-Curricular Positions:
2008-2009 President, Synapsis Cornell Plant Breeding and Genetics Graduate Student Organization
2007-2008 Treasurer, Synapsis Cornell Plant Breeding and Genetics Graduate Student Organization
2006-2007 Vice-Chancellor, Alpha Zeta Professional Agricultural Fraternity
2005-2007 Univ. of Delaware, Ag Ambassador
Fellowships:
2007-2009 USDA Training Grant - Cornell University Fellowship
2006-2007 NSF Undergraduate Research Fellowship
2005-2006 USDA Scholar Undergraduate Fellowship
2004-2005 Univ. of Del. Science & Engineering Fellowship
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