MaizeGenetics.net

	Association genetics lie at the intersection of population genetics and quantitative genetics. Broadly put, I am interested in the influences of domestication and selection on the patterns of diversity at the DNA sequence level and their influence on the phenotype. Adaptive Traits: Flowering Time Flowering time is regulated via multiple environmental and endogenous inputs. Molecular dissection of flowering time in model organism Arabidopsis thaliana indicates that the flowering time of the plants are quantitatively controlled with an integrated network of pathways that act as a developmental swich that initiates the reproductive stage of the plants' life cycle.
The correct timing of this transition is essential to maximize reproductive success given the requirement for synchronous flowering in out-crossing species and the dependence on favorable conditions for optimal seed set. Therefore, flowering time is a causative agent for the clinal adaptation of the subpopulations of species, leading to population differentiation, and even speciation. Flowering time is not only regulated by genetic but also epigenetic factors and contribute to the variation in specific and general combining ability of plants used for breeding. Some questions that instigated our research on flowering time are: What are the major regulators of flowering time in maize? What is the influence of population structure on the flowering time, and can we effectively control for the population structure in an experimental setting? Are there any indicators of influence of selection, natural or otherwise, on the patterns of diversity in genes controlling flowering time? This research is funded by Plant Genome Program (DBI-0321467) granted to John Doebley, Ed Buckler, Brandon Gaut, Major Goodman, Jim Holland, Steve Kresovich,Mike McMullen, Lincoln Stein, and Doreen Ware titled Molecular and Functional Diversity of Maize (1/1/2004-12/31/2008).
Differential Methylation In the Maize Genome In plants, 5-methylcytosine (5mC) residues are found predominantly at symmetric CpG and CpNpG sequences. DNA methylation patterns attributable to 5mC are established and maintained by DNA methyltransferases, which catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the 5th position in the pyrimidine ring of cytosine. Methylation patterns of DNA are not only correlated with gene expression but are also associated with inactivation of transposable elements, imprinting, paramutation, as well as transgene silencing in plants. Furthermore, there is some evidence suggesting several developmentally regulated quantitative traits such as flowering time are regulated through the methylation status of transcriptional regulators. In order to dissect the genetic basis of variation in differential methylation in the maize genome, we have adopted a NextGen Sequencing approach where reduced representation genomic libraries that were prepared by HpaII- methylation sensitive restriction enzyme was sequenced from 27 diverse lines and 1 methylation deficient mutant in two different backgrounds (Mo17 and B73) to investigate patterns of differential methylation between diverse lines. This project is funded by NSF-Plant Genome Comparative Sequencing Program (PGCSP) DBI-06638566 granted to Ed Buckler and Doreen Ware titled High Density Scoreable Markers for Maize Trait Dissection
Resequencing Maize Genome for the Analysis of Genome-wide Functional Diversity and Selection The recent advancements in the technology targeting ultra-high throughput DNA sequencing and genotyping presents an unmatched opportunity for complex trait dissection studies through progression of association mapping projects from candidate gene based to whole genome studies. Maize is the pioneering species for application of candidate-gene based association mapping practices in agronomically important plant species. To date, however, association mapping practices were restricted to candidate gene studies due to high levels of diversity and rapid decay of linkage disequilibrium in this genome. The nucleotide diversity estimates indicate that there is one SNP per every 70 base pairs in the maize genome, that approximates to ~ 42 million SNPs over the genome of ~3000 million base pairs. Gene space in the genome, however, is much smaller due to the rapid expansion of the maize genome via helitron type transposable elements. With a rough approximation of 10Kb/ gene, an estimated 50,000 genes in the functional genome size would be around 500 million base pairs, that is 15-20% of the whole genome. This particular genome expansion mechanism was identified to be associated with differential chromatin and DNA methylation patterns that discriminate gene space from the transposon rich intergenic sequences. The DNA methylation pattern, in particular presents an opportunity to selectively enrich for the gene space by utilizing DNA-methylation sensitive restriction enzymes such as HpaII. In conjunction with next generation sequencing technologies, this type of reduced library preparation methods can enable sequencing of the gene space of the maize genome at several fold coverage at a menial cost. We will utilize the data that will be generated through resequencing of 27 maize (Zea mays mays) and 16 teosinte (Zea mays parviglumis) inbred lines over these reduced genomic libraries to investigate patterns of diversity and selection in the maize genome. This project is funded by NSF-Plant Genome Comparative Sequencing Program (PGCSP) DBI-06638566 granted to Ed Buckler and Doreen Ware titled High Density Scoreable Markers for Maize Trait Dissection
Developing association mapping in polyploid perennial biofuel grasses   To accelerate the breeding of biofuel crops will require the genetic dissection of biomass characteristics and yield. By capitalizing on recent advances in genomics-based research, coupled with decades of fundamental whole-organism and population-based research by forage breeders, we propose an association-mapping study of two important biofuel grasses, switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.). The major motivation for applying association mapping in switchgrass and reed canarygrass, for which there are, at present, limited genetic resources, is the identification of molecular markers that are tightly linked to biomass-related trait loci, thus enabling marker assisted selection and greatly accelerating the breeding programs for enhanced biomass production. In perennial polyploid species such as these, effective marker assisted selection will be key to rapid selection for improved varieties and adaptation to environments across the US.   Research objectives: Assemble association panels of diverse populations and linkage populations for switchgrass and reed canarygrass (~1000 clones each). -completed 2008 Summer Trait evaluation for key biofeedstock characteristics in these panels.-due Summer 2009-2010 Develop high density SNP markers in switchgrass-due Spring 2009. Genotype association panels and linkage populations in switchgrass - due Fall 2009 Evaluate population structure and germplasm diversity in switchgrass - due Winter 2009 Establish association mapping and estimate marker based breeding values in switchgrass- due Winter 2009   This project is funded by a Department of Energy Grant to Drs. Edward Buckler, Mike Cassler and Jerry Churney.
Education 2006 - present Post-doctoral Research Associate Institute for Geneomic Diversity Cornell University, Ithaca, NY 2001 - 2006 PhD , Genetics Genetics Graduate Group University of California, Davis, CA 1998 - 2001 MS , Biological Sciences Graduate School of Natural and Applied Sciences Middle East Technical University, Ankara- Turkey Department of Biological Sciences, Population Biology Major 1994 - 1998 BS , Biological Sciences & Environmental Engineering (double major) Molecular Biology and Environmental Microbiology majors Middle East Technical University, Ankara- Turkey
Teaching Experience Fall, 2005 Applied Bioinformatics -Teaching Assistant ( Jorge Dubcovsky & David Neale) Fall, 2004 Transmission Genetics (John Roth & Janine LaSalle) Spring, 2002 Genes and Gene Expression BIS101 – UC-Davis- Teaching Assistant (Les Gottlieb) Spring, 1999/2000/2001 Introduction to Molecular Biology and Genetics (honors) GENE104 with lab – METU-Teaching Assistant Fall, 1999 Biostatistics - BIO400 with lab – METU-Teaching Assistant Fall, 1999/2000 Introduction to Molecular Biology and Genetics (honors) GENE103 with lab – METU-Teaching Assistant Summer, 1999/2000 High School Outreach- Summer School on Molecular Biology and Genetics-Assistant Lecturer Spring, 1999 Advanced techniques in Molecular Genetics (honors)- GENE270 –METU-Teaching Assistant Fall, 1998 Cytology-BIO203 with lab – METU-Teaching Assistant Spring, 1997 Plant Biology - BIO356 with lab –METU-Undergraduate Student Assistant Spring, 1996 Computational Biology - BIO319 with lab –METU-Undergraduate Student Assistant Fall, 1996 Biology for non-science majors- BIO106- METU-Undergraduate Student Assistant
PhD Research My Ph.D. Dissertation title is “Candidate Gene based Association Mapping of Fungal Disease Resistance In Loblolly Pine” As a part of the collaborative genome project called ADEPT, between University of California-Davis, University of Florida and University of Georgia, a candidate gene-association mapping approach was used to identify the role of natural genetic variation effecting quantitative disease resistance of loblolly pine against Fusiform Rust (FR) and Pitch Canker (PC) fungal diseases. After screening ~100 candidate genes identified by homology searches of existing loblolly pine EST libraries for the presence of Single Nucleotide Polymorphisms (SNPs), 58 candidate genes have been selected to be tested for associations between quantitative resistance phenotypes and candidate-SNP genotypes. Furthermore, 15 of these candidates were also involved in stress response (candidates for drought tolerance trait) and they have been also adopted for drought-tolerance association testing. SNP discovery have been carried out by direct sequencing of the selected regions from the haploid-genome of 32 individual trees (megagametophytes) forming our discovery panel. More than 2Mbs of resequencing data was generated. 45 SNPs selected from these candidate genes (1-2 SNPs / gene) have been genotyped over a family based association population of 960 individuals, generated by crosses between 32 trees used as the discovery panel and association tests have been carried out to reveal associations between genotypes and fungal disease resistance phenotypes.
MSc. Research My MSc. Dissertation title is “The pattern of genetic variation in Pinus brutia populations in southern Turkey determined by nuclear SSR markers” Worked as a part of multinational European Union collaborative project FORADAPT lead by INRA-France, the project was aiming for screening the populations of four dominant conifer species of Mediterranean basin (Pinus halepensis, Pinus brutia, Pinus pinaster and Cedrus libani) for global, physiological and molecular responses to climatic stresses and determining resources for conservation and improvement of these genetic resources. 32 n-SSR markers generated from Pinus halepensis libraries were tested on Pinus brutia samples and six populations of Turkish red pine (~900 individuals) was screened for genetic diversity.
Internships and Undergraduate Research Summer, 1997 Turkish Scientific and Technical Research Council, Gebze Research Center; Intern at Microbiology and Biotechnology section. Fall,1997 Special Project on tissue culture system establishment for embryogenesis and direct organogenesis of endemic chickpea (Cicer arietinum L.) cultivars.
Selected Presentations Elhan S. Ersoz, Li, H., Bradbury, P., Maize Diversity Project Fine mapping of maize flowering time QTL on Chromosome 1 - 50th Maize Genetics Meeting Feb 27th-March 2nd 2008, Washington D.C. Elhan S. Ersoz and Michael Gore SNP Genotyping for Complex Trait Dissection in Maize - Geneva, NY- September 20th, 2007 Elhan S. Ersoz, Michael Gore, Mark H. Wright, Bonnie Hurwitz, Apurva Narechania, George Grills, Doreen Ware and Edward Buckler SNP discovery with HpaII-Filtered Genomic Libraries of Maize Using Next-Generation Sequencing Technologies - July 7th-11th , 2007, Chicago, IL Elhan S. Ersoz, Karin J. Holmberg, Ted Thannhauser, Edward Buckler Linkage and Association Mapping of total DNA-5mC methylation in maize - 49th Maize Genetics Meeting -March 22nd-25th, 2007, Chicago, IL Elhan S. Ersoz Candidate Gene-Quantitative Phenotype Associations for Resistance to Fusiform Rust and Pitch Canker in Loblolly Pine - 50th Western Association of Forest Genetics Conference, July 17-21, 2005 –Oregon State University, Corvallis, OR Elhan S. Ersoz Candidate Gene-Quantitative Phenotype Associations for Resistance to Fusiform Rust and Pitch Canker in Loblolly Pine - 50th Western Association of Forest Genetics Conference, July 17-21, 2005 –Oregon State University, Corvallis, OR E. Ersoz Candidate Gene-Quantitative Phenotype Associations for Resistance to Fusiform Rust and Pitch Canker in Loblolly Pine – 28th Southern Forest Tree Improvement Conference, June 21-23, 2005 – Sheraton Capital Center Hotel, Raleigh, NC Elhan S. Ersoz, Santiago C. Gonzalez-Martinez, Geoff P. Gill, Garth R. Brown, Alison Morse, John M. Davis, David B. Neale, 2004. Nucleotide Diversity and Linkage Disequilibrium in Loblolly Pine Genome: Focus on Gene Expression Regulation. IUFRO, Population, Evolutionary and Ecological Genomics of Forest Trees, September 13-17, 2004. Asilomar, CA. http://dendrome.ucdavis.edu/asilomar/ Elhan S. Ersoz , Santiago Gonzalez-Martinez , Geoff Gill , Garth Brown , Alison Morse , John Davis , Tim White , David B. Neale, 2004. SNP Discovery in candidate genes for disease resistance (pitch canker and fusiform rust) and drought tolerance in loblolly pine. Forest Tree Workshop, Plant & Animal Genomes XII Conference. January 10-14, 2004. San Diego, CA. http://www.intl-pag.org/12/abstracts/W22_PAG12_95.html Elhan S. Ersoz , David B. Neale, 2003. Association Mapping of Fungal Disease Resistance Traits in Loblolly Pine. American Society of Plant Biology Organization Western Subsection Meeting on Plant Genomics October 10-11, 2003. Davis, CA. http://www.aspb.org/sections/western/prizes.cfm
Publications in Preparation Mixed Model Facilitation for Genome-Wide Association Syudies on Large Samples Ersoz, E.S., Zhang, Z.,Buckler, E.S.-in prep. Association Mapping of Flowering-TimeTraits on the Extended Maize Association Population Ersoz E.S., Yan, J., Warburton, M., Gore, M.A., Zhang, Z., Buckler, E.S.-in prep. Extending the Maize Association Population with Test-Cross Hybrids Ersoz E.S., Yan, J., Warburton, M., Gore, M.A., Zhang, Z., Flint-Garcia, S., Buckler, E.S.-in prep. Patterns of nucleotide diversity and selective constraint in loblolly pine: Ersoz E.S., Wright M.H., Gonzalez-Martinez, S.C., Langley, C.H., Neale D.B.- in prep. Candidate Gene Association Mapping of Loblolly Pine III. Fusiform Rust and Pitch Canker Fungal Disease Resistance in Loblolly Pine. Ersoz, E.S., Wright M.H., Gonzalez-Martinez, S.C., Kayihan G.C., Morse A.M., Davis J.M., Huber D., Neale D.B.- in prep.
Publications The Genetic Architecture of Maize Flowering Time. Edward S. Buckler*, James B. Holland*, Michael M. McMullen*, Stephen Kresovich*, Charlotte Acharya, Peter Bradbury, Patrick Brown, Chris Browne, John Doebley, Magen Eller, Elhan Ersoz, Sherry Flint-Garcia, Arturo Garcia, Jeff Glaubitz, Major Goodman, Carlos Harjes, Kate Hutchins, Dallas Kroon, Sara Larsson, Nick Lepak, Huihui Li, Sharon Mitchell, Jason Peiffer, Marco Oropeza Rosas, Torbert Rocheford, Cinta Romay, Susan Romero, Stella Salvo, Hector Sanchez Villeda, Qi Sun, Feng Tian, Narasimham Upadyayula, Doreen Ware, Heather Yates, Jianming Yu, Zhiwu Zhang Science 7 August 2009: Vol. 325. no. 5941, pp. 714 - 718 Large-Scale Discovery of Gene-Enriched SNPs Michael A. Gore, Mark H. Wright, Elhan S. Ersoz, Pascal Bouffard, Edward S. Szekeres, Thomas P. Jarvie, Bonnie L. Hurwitz, Apurva Narechania, Timothy T. Harkins, George S. Grills, Doreen H. Ware, and Edward S. Buckler Plant Gen. July 2009 2:121-133; doi:10.3835/plantgenome2009.01.0002 Applications of Linkage Disequilibrium and Assocaition Mapping in Maize Chapter 13 in Molecular Genetic Approaches to Maize Improvement, Biotechnology in Agriculture and Forestry volume 63. Ersoz, E.S., Yu, J., Buckler, ES. eds. A.L.Kriz, B.A.Larkins, Springer High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.) Eckert, A.,Pande, B., Ersoz, E.S., Wright M.H., Rashbrook, V., Nicholet, C., Neale D.B. Tree Genetics & Genomes Applications of linkage disequilibrium and association mapping in crop plants. Ersoz, E.S., Yu, J., Buckler, ES. Genomics Assisted Crop Improvement , Chapter 6. eds. R. Tuberosa and R. Varshney, Springer. Association Genetics in Pinus taeda L. II. Water-use efficiency. Gonzalez-Martinez, S.C, Huber D., Ersoz. E.S. , Davis J.M., Neale D.B.- Heredity-July 2008. Association Genetics in Pinus taeda L. I. Wood Property Traits. Gonzalez-Martinez, S.C., Wheeler N.C., Ersoz, E.S., Nelson C.D., Neale D.B., 2007; Genetics 175: 399-409 DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda. Gonzalez-Martinez, Ersoz, E.S.,Brown, G.R., Wheeler, N.C. Neale D.B., 2007; Genetics 172: 1915-1926 Isolation of a full-length CC-NBS-LRR resistance gene analog candidate from sugar pine showing low nucleotide diversity. Jermstad, K.D., Sheppard, L., Kinloch Jr., B., Delfino-Mix, A., Ersoz, E.S., Krutovsky, K., Neale, D.B., 2006- Tree Genes and Genomes 2 (2): 120