MaizeGenetics.net

Michael Gore
Ph.D. Candidate
Dept. Plant Breeding & Genetics
Cornell University
Institute for Genomic Diversity
175 Biotechnology Building
Ithaca, NY 14853-2703
E-mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Tel: (607) 255-1809
Fax: (607) 255-6249

Please click on my links:
Thesis Research Goals
Education
Professional Experiences
Teaching Experiences
Publications
Talks
Poster Presentations
Meeting Abstracts
Awards and Memberships

Research Interests

My research interests are primarily focused on the utilization of traditional and molecular breeding approaches to unlock the genetic potential of crop germplasm pools. Specifically, my dissertation research is aimed at developing molecular genetic and statistical tools for localizing quantitative effects to single genes or individual nucleotides. Ultimately, this work will lead to the identification of favorable genes and alleles and help to bridge the gap between genomics and plant breeding.

Thesis Research Goals

Thesis title: Construction and Utilization of a High-Resolution Platform for Complex Trait Dissection in Maize

Discover and Genotype SNPs to Support Complex Trait Dissection

1) Optimization of target preparation methods for detection of single feature polymorphisms (SFPs) in maize.

Gene expression microarrays consist of oligonucleotides (oligos) designed from the sequence of expressed genes and offer one potentially powerful means of genotyping thousands of recombinationally active gene regions in parallel.  The genotyping of sequence polymorphisms with an expression array is based on the concept that a perfectly matched target binds to an oligo probe or feature with greater affinity than a mismatched target (Borevitz et al., 2003; Singer et al., 2006).  If an individual oligo feature on an expression array shows a significant and reproducible difference in hybridization intensity between genotypes or strains, it can serve as a polymorphic marker or single feature polymorphism (SFP).  The goal of this study was to test the feasibility of expression arrays for use in SFP detection in maize. The goal of this study was to test the feasibility of expression arrays for use in SFP detection in maize.

To that end, we tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip Maize Genome Array (Maize GeneChip).  Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and AFLP methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Our results indicate that these particular target preparation methods offer only modest power to detect SFPs with the Maize GeneChip.  Most notably, CF and MF are comparable in power, detecting more than 10,000 SFPs at a 20% false discovery rate. This research was done in collaboration with Keygene N.V., Wageningen, The Netherlands.

2) Next-generation sequencing of gene-enriched genomic libraries with Roche’s 454 and Illumina’s Solexa to discover and score SNPs in maize.

Roche's 454 Genome Sequencing FLX system (GS-FLX) is based on massively parallel pyrosequencing of thousands to millions of short emulsion PCR fragments.  The GS-FLX system involves high-throughput sample preparation, emulsion PCR amplification, sequence detection, data processing and assembly.  An 8 hour run on the GS-FLX generates an average of greater than 400,000 high quality reads.  This produces around 100 million bases (12.5 Mb/hr) with average read lengths between 200-300 bases, depending on the application and the organism.

Illumina’s Solexa sequencing-by-synthesis technology uses four proprietary fluorescently labeled modified nucleotides and a proprietary Clonal Single Molecule Array Technology to sequence millions of DNA fragments in parallel, a single base at a time.  These modified nucleotides allow for reversible termination, which permits each sequencing reaction cycle to occur simultaneously in the presence of all four nucleotides (A, C, T, G). The Solexa platform currently yields on average 35 bases per read. However, the Solexa single-molecule sequencing approach has some advantages to the 454 technologies as it will have no problems with single base resolution in homopolymer tracts. Moreover, Solexa provides rapid, accurate, and cost-effective sequence data at an anticipated scale of over one billion bases per run, a 10-fold increase over the current 454 technology.

In our ongoing efforts to bridge the gap between plant genome studies and improved breeding strategies, association approaches offer the most direct means of identifying genes and alleles of agronomic importance. With high levels of naturally occurring genetic diversity and low levels of linkage disequilibrium (LD), diverse maize inbred lines are tremendous resources for association mapping of quantitative traits down to the gene level.  An estimated 1 million SNP markers, however, are required to capture most of the LD structure in maize.  This project seeks to: (1) identify 1 to 2 million sequence polymorphisms focused in areas of active recombination in the maize genome, and (2) score these polymorphisms against 27 diverse lines that capture 80% of the common variation in maize.  The same 27 diverse maize lines are parents of a 5,000 recombinant inbred line nested-association mapping (NAM) population that is in the process of being phenotyped for more than 35 traits at 6 field locations.  In NAM, only the founder lines need to be genotyped at high resolution; then lower resolution markers track the chromosomal segments in their offspring. The maize NAM system (27 parents with 5000 progeny lines) results in a 185-fold savings (5000/27=185) in genotyping costs as high resolution genotyping is only required of the parents.

To accomplish these SNP genotyping goals, we developed a library preparation method built on the differential cytosine methylation patterns of genes and retrotransposons, which are discriminated by the methylation-sensitive restriction enzyme HpaII.  This gene-biased HpaII library construction approach, in conjunction with 454 and Solexa sequencing, is being used for high-throughput SNP discovery and genotyping via library oversampling.  Preliminary sequence data from B73 and Mo17 HpaII libraries have been generated using a 454 GS-FLX instrument.

This project is supported by grant DBI-06638566, High Density Scoreable Markers for Maize Trait Dissection, awarded to Drs. Ed Buckler (PI), Doreen Ware (Co-PI) and George Grills (Co-PI) from the NSF-Plant Genome Comparative Sequencing Program (PGCSP).

Dissection of Complex Traits with Molecular and Statistical Genetics Methodologies

3) Joint Linkage and Association Mapping of Vitamin E Types and Levels in the Maize Kernel

Tocochromanols are a group of four tocopherols (α, β, δ, γ) and four tocotrienols (α, β, δ, γ)  that are commonly referred to as vitamin E.  These eight isomers are naturally occurring lipid-soluble antioxidants and vary widely in their vitamin E biological activities.  Vitamin E is an essential component of mammalian diets and when consumed at a safe elevated level is reported to reduce the incidence and severity of human diseases, such as heart disease, some cancers, and cataracts.  Tocochromanols are exclusively synthesized by photosynthetic organisms (i.e., all green plants and several cyanobacteria) where their functionary roles are only now beginning to be elucidated.  In the past decade, molecular genetic and biochemical-based approaches have nearly identified the complete suite of genes necessary for the biosynthesis of tocochromanols in photosynthetic tissues.  Considerable insight into the regulation and function of structural and non-structural enzymes has come from mutant analysis and transgenic studies in primarily model organisms.  We are now poised to begin leveraging this broad knowledge base via QTL and association mapping strategies for understanding the genetics underpinning the types and levels of tocochromanols compounds in the maize kernel.

Education

•    Ph.D. Candidate. Plant Breeding. August 2004-Present. Cornell University, Ithaca, New York. Minor: Plant Physiology. Advisor: Dr. Edward S. Buckler

•    M.S. Molecular Genetics. August 2000. Virginia Tech, Blacksburg, Virginia.  Concentration: Molecular Cell Biology and Biotechnology. Thesis title: High-resolution mapping of the region around the soybean virus resistance genes, Rsv1 and Rpv1. Advisor: Dr. M.A. Saghai Maroof

•    B.S. Crop and Soil Environmental Sciences. December 1997. Virginia Tech, Blacksburg, Virginia. Concentration: Biotechnology. Minors: Chemistry and Biology.

Professional Experiences

•    Graduate Research Assistant. Department of Plant Breeding and Genetics. Cornell University, Ithaca, NY. August 2004-July 2006, January 2007-Present.

•    Graduate Teaching Assistant. Department of Plant Breeding and Genetics. Cornell University, Ithaca, NY. August 2006-December 2006.

•    Senior Biologist. Lancaster Labs, 2425 New Holland Pike, Lancaster PA. September 2003-August 2004.

•    Senior Research Associate. Pioneer Hi-Bred Intl., Inc., Johnston, IA. March 2002-September 2003.

•    Research Associate. Pioneer Hi-Bred Intl., Inc., Johnston, IA. August 2001-March 2002.

•    Research Scientist. Rohm and Haas Company, Spring House, PA. July 2000-July 2001.

•    Graduate Research Assistant. Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA. January-August 1998, May-August 1999, and May-July 2000.

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Teaching Experiences

•    Graduate Teaching Assistant. Department of Plant Breeding and Genetics. Cornell University, Ithaca, NY. August 2006- December 2006. Genetic improvement of Crop Plants. (PLBR 404).

•    Guest Lecturer. Department of Plant Breeding and Genetics. Cornell University, Ithaca, NY. November 2006. Plants, Genes, and Global Food. (PLBR 201).

•    Graduate Teaching Assistant. Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA. August 1998-May 1999, August 1999-May 2000. Soils (CSES 3114) and Soils Laboratory (CSES 3124).

•    E. Buckler and M. Gore.  2007.  An Arabidopsis haplotype map takes root. Nature Genetics 39: 1056-1057. (N & V for article by Kim et al.)

•    M. Gore, P. Bradbury, R. Hogers, M. Kirst, E. Verstege, J. van Oeveren, J. Peleman, E. Buckler, and M. van Eijk. 2007. Evaluation of Target Preparation Methods for Single Feature Polymorphism Detection in Large Complex Plant Genomes. The Plant Genome S2: S-135-S-148.

M. Gore and P. Bradbury contributed equally to this work.

•    A. J. Hayes, S. C. Jeong, M. A. Gore, Y. G. Yue, G. R. Buss, S. A. Tolin, and M. A. Saghai Maroof.  2004.  Recombination within an NBS/LRR gene family produces new phenotypic variants conditioning resistance to soybean mosaic virus in soybean. Genetics 166: 493-503.

•    M. Padidam, M. Gore, D. L. Lu, and O. Smirnova.  2003.  Chemical-inducible, ecdysone receptor-based gene expression system for plants. Transgenic Research 12: 101-109.

•   M. A. Gore,  A. J. Hayes, S. C. Jeong, Y. G. Yue, G. R. Buss, and M. A. Saghai Maroof.  2002.  Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean. Genome 45: 592-599.

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Talks

•    SNP Genotyping on Next-Generation Sequencing Platforms for Complex Trait Dissection in Maize. Plant Breeding and Genetics Graduate Student Symposium. Cornell University. Ithaca, NY. September 2007.

•    SNP Genotyping for Complex Trait Dissection in Maize. USDA-ARS Plant Genetic Resources Unit (PGRU). Geneva, NY. September 2007.

•    Optimized Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes. Plant Breeding and Genetics Graduate Student Symposium. Cornell University. Ithaca, NY. October 2006.

•    QTL analysis and candidate gene association to dissect tocopherol accumulation in the maize kernel. Plant Breeding and Genetics Graduate Student Symposium. Cornell University. Ithaca, NY. September 2005.

•    High-resolution mapping of the region around the soybean virus resistance genes, Rsv1 and Rpv1. Thesis Defense Seminar. Crop and Soil Environmental Sciences. Virginia Tech. Blacksburg, VA. July 2000.

•    High-resolution mapping of the region around the soybean virus resistance genes, Rsv1 and Rpv1. Crop and Soil Environmental Sciences. Virginia Tech. Blacksburg, VA. April 2000.

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Poster Presentations

•    M. Gore, E. Ersoz, B. Hurwitz, A. Narechania, M. Wright, G. Grills, D. Ware, T. Harkins, B. Taillon, and E. Buckler. High density SNP markers for complex trait dissection in maize. Poster# 30 presented at the 71st Annual Meeting of the Northeast section of the American Society of Plant Biologists in Syracuse, New York. June 1-2, 2007.

•    M. Gore, E. Ersoz, B. Hurwitz, A. Narechania, M. Wright, G. Grills, D. Ware, T. Harkins, B. Taillon, and E. Buckler. Gene and SNP discovery using 454 sequencing of methylation-filtered HpaII libraries. Poster# 137 presented at the 49th Annual Maize Genetics Conference in St. Charles, Illinois. March 22-25, 2007.

•   M. Gore, P. Bradbury, R. Hogers, M. Kirst, E. Verstege, J. van Oeveren, E. Buckler, and M. van Eijk. Optimized target preparation method for single-feature polymorphism detection in maize. Poster# 191 presented at the 48th Annual Maize Genetics Conference in Pacific Grove, California. March 9-12, 2006.

•    M. Gore, M. Kirst, K. Howe, and E. Buckler 2005. Genome-wide scan for structural polymorphisms in diverse maize germplasm. Poster# 141 presented at the 47th Annual Maize Genetics Conference in Lake Geneva, Wisconsin. March 10-13, 2005.

•    M. A. Gore, A. J. Hayes, S. C. Jeong, G. R. Buss, S. A. Tolin, and M. A. Saghai Maroof.  Differential reaction of soybean lines to soybean mosaic virus strains as a result of recombination within an NBS-LRR gene family. Poster# 544 presented at the Plant and Animal Genome International Conference XII in San Diego, California. January 10-14, 2004.

•    M. A. Gore, A. J. Hayes, S. C. Jeong, G. R. Buss, and M. A. Saghai Maroof.  High resolution mapping of the tightly linked Rsv1 and Rpv1 potyvirus resistance genes in soybean.  Poster # 483 presented at the Plant and Animal Genome International Conference IX in San Diego, California. January 13-17, 2001.

Meeting Abstracts

•    E. Ersoz, M. Gore, B. Hurwitz, A. Narechania, M. Wright, G. Grills, D. Ware, and E. Buckler. SNP discovery with HpaII-filtered genomic libraries of maize using next-generation sequencing technologies. Poster# 44008 presented at the Plant Biology & Botany 2007 Joint Congress in Chicago, Illinois. July 7-11, 2007.

•    D. Costich, M. Gore, M. E. Denton, E. S. Ersoz, M. H. Wright, and E. S. Buckler. Developing markers for association mapping in biofuel grasses. Poster# 175 presented at the 49th Annual Maize Genetics Conference in St. Charles, Illinois. March 22-25, 2007.

•    J. Yan, M. Sawkins, T. Setter, E. Buckler, Y. Xu, M. Gore, H. Yates, P. Grudloyma, J. Gethi, E. Khosa, W. Li, C. Magorokosho, E. Huerta, C. Martinez, J. S. Pastrana, and M. Warburton. Development of informative markers through association mapping in maize to improve drought tolerance in cereals. Poster# 176 presented at the 49th Annual Maize Genetics Conference in St. Charles, Illinois. March 22-25, 2007.

•    M. van Eijk, P. Bradbury, M. Gore, R. Hogers, M. Kirst, E. Verstege, J. van Oeveren, and E. Buckler. Optimized target preparation method for single-feature polymorphism detection in maize. Poster# 90 presented at the Plant and Animal Genome International Conference XIV in San Diego, California. January 14-18, 2006.

•    R. Obendorf and M. Gore. Physiology of maize kernel quality development. C-2 Symposium. Talk 54-5 given at the ASA-CSSA-SSSA Annual Meeting. Salt Lake City, UT. November 6-10, 2005.

•    F. Rostami, L.-E. Burnley, I. Gunduz, M. Gore, L. Rossi, C. Opperman, S. Lommel, and A. Hayes. Determining Gene Expression Using Orion Methyl-Filtered Sequences. Poster# 77 presented at the Plant and Animal Genome International Conference XIII in San Diego, California. January 15-19, 2005.

•    J. A. Mammadov, S.  B. Cannon, A. J. Hayes, M. A. Gore, S. C. Jeong, and M. A. Saghai Maroof. Sequence analysis and evolutionary implications of Non-Tir-NBS-LRR genes from the soybean Rsv1 cluster.  Poster# 442 presented at the Plant and Animal Genome International Conference XIII in San Diego, California. January 15-19, 2005.

•    D. A. Vaske, D. Bhattramakki, C. Abban, J. C. Register III, S. J. Wall, O. S. Smith, A. Rafalski, W. Chu, and M. A. Gore. Linkage Disequilibrium in elite maize populations. Poster presented at the 5th International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis in Reykjavik, Iceland. October 11-14, 2002.

Awards, Honors, and Professional Memberships

•    Secretary of Synapsis- Plant Breeding & Genetics Graduate Student Association. 2006-2007

•    Awarded Scholarship to attend 18th National Agricultural Biotechnology Council. 2006

•    Hasbrouck Volunteer Award. 2006

•    Nominated for Conference of Southern Graduate Schools Master's Thesis Award. Virginia Tech. 2000

•    Awarded The William Preston Society Master’s Thesis Award. Virginia Tech. 2000

•    W. R. Winslow Trust Scholarship. Virginia Tech. 1997

•    Phytochemical Society of North America

•    American Society of Agronomy

•    Crop Science Society of America

•    American Society of Plant Biology

•    Phi Sigma Alpha Psi Chapter Biological Service Honor Society