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As DNA sequencing costs plummet and throughput rapidly increases, the question is no longer whether we can sequence large and complex plant genomes, but how soon can we sequence them? Plants as model organisms for biological investigations such as domestication, genome evolution, developmental physiology, epigenetics, pest resistance, heterosis, quantitative inheritance, and comparative genomics, allow the relationship and understanding of genotype to phenotype correlations. Nevertheless, the challenge remains of how to convert this mass of data into knowledge that can be applied in crop breeding programs.

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Wednesday, March 16 

7:30 am Conference Registration

8:00 Java and Jive Breakfast Breakout Discussion Groups

These focused groups are designed for conference attendees to discuss important and interesting topics related to sequencing and genomic tools. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse areas to exchange ideas, experiences, and develop future collaborations around a focused topic. Complimentary coffee is included.

Please click here for a complete listing of Breakout Discussion Groups.


9:00 Close of Breakout Discussion Groups


ArrowPlenary Keynote Session: The Personal Impact of Sequencing from Patient to Population 

Podcast9:25 It Takes a Village

Hugh RienhoffHugh Rienhoff, M.D., Director, - Biography 

Next-generation sequencing has made possible the study of rare genetic disease where traditional linkage analysis is not possible because of the rarity of the disorder. This description fits more than 2000 familial diseases. But the discovery of the genetic cause of rare disease remains a formidable challenge demanding the talents of many to generate the necessary data that rises to the level of proof of causality.

10:05 Data-Driven Personalized Medicine

Atul ButteAtul Butte, M.D., Ph.D., Assistant Professor, Pediatrics, Medicine, Computer Science, Stanford University, Lucille Packard Children’s Hospital - Biography 

Dr. Butte builds and applies tools that convert more than 15 billion points of molecular, clinical, and epidemiological data measured by researchers and clinicians over the past decade into insights into diagnostic and therapeutic potential. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his recent work on the first clinical evaluation of a patient presenting with a personal genome.

10:45 Networking Coffee Break in Exhibit Hall with Poster Viewing

11:15 Clinical Significance of Indigenous Genome Sequencing

Vanessa HayesVanessa Hayes, Ph.D., Professor, Human Genomics, J. Craig Venter Institute - Biography 

The African continent, birthplace of all modern man, home to a third of the world’s ethnic diversity, and epicenter for many globally significant diseases, has been poorly characterized in genetic terms. With a focus on recently diverged populations, non-migrant Africans have largely been excluded from the era of genomics and therefore disease association studies. Data will be presented from the first indigenous genome sequencing and how defining indigenous genome diversity will advance genotype-phenotype correlations of global significance.

11:55 Close of Session

Sponsored by
Agilent Technologies 
12:15 pm Luncheon Presentation
Understanding Glaucoma through Genome-Wide Targeted Exome Re-Sequencing
Terry Gaasterland, Ph.D., Professor, University of San Diego, California
Primary open angle glaucoma is a complex disease with genetic foundations, but to date, with no clear causal gene variants. We are sequencing exomes from ~300 cases to compare with 500+ random controls. This talk will present results from Phase 1 in which we evaluated alternative methods for capture, library preparation, and analysis, and established standards for the full project.    

Sponsored byBGI12:50 Luncheon Presentation
Partnering for Multi-omics Excellence
Joyce Peng, Ph.D., Marketing Director, BGI AmericasWith the diverse analytical technologies now available, we can focus the full spectrum of multi-omics methods on the important research questions that impact agriculture and human health. BGI is deeply committed to supporting multi-omics research by providing our deep sequencing, analytical, and cloud computing resources to our collaborators and clients. Here we present projects that make use of leading-edge genomic, transcriptomic, epigenomic, proteomic, metagenomic, and single-cell sequencing methods, with special focus on research relevant to human disease and agriculture.


Genotype to Phenotype Correlations 


2:15 Chairperson's Remarks: Matthew Hudson, Ph.D., Associate Professor, Department of Crop Sciences, Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana 

ArrowFeatured Speaker 

2:20 Comparative Genomics of Plant-Pathogen Interactions

Richard Michelmore, Ph.D., Professor and Director, The Genome Center, University of California, Davis

Next-gen sequencing and comparative genomics are providing unprecedented analysis of both host and pathogen genomes. Our emerging understanding of the molecules that determine specificity in plant disease and their co-evolution provides new opportunities for resistance gene deployment. These should result in strategies for more durable disease resistance driven by information on pathogen variation.

2:50 Using Sequencing for Biofuel Crop Improvement

Matthew Hudson, Ph.D., Associate Professor, Department of Crop Sciences, Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana

The latest sequencing technologies provide the necessary throughput, cost and turnaround time to apply genomic techniques to improvement of biofuel crops. Whole genome sequencing, transcriptome sequencing, genotyping by sequencing and small RNA profiling will be discussed with reference to biofuel grasses and other species.

3:20 RNA-Seq Atlas of Glycine Max: A Guide to the Soybean Transcriptome

Gregory May, President, National Center for Genome Resources


3:50 Refreshment Break in Exhibit Hall

4:30 Use of High-Throughput Sequencing to Identify Transposon Insertions Underlying Mutant Phenotypes in High-Copy Mutator Lines of Maize

Alice Barkan, Ph.D., Professor, Biology, Institute of Molecular Biology, University of Oregon

High-copy transposons have been effectively exploited as mutagens in a variety of organisms; however, their utility for phenotype-driven forward genetics has been hampered by the difficulty of identifying the specific insertions responsible for phenotypes of interest. Our method dramatically increases the throughput of linking a disrupted gene to a known phenotype in high-copy Mutator transposon lines in maize. This method is well-suited for use with large mutant collections, and could be adapted for use with other transposon systems.

5:00 SNP Discovery by High Throughput Sequencing in Soybean

Trupti Joshi, Plant Sciences, University of Missouri, Columbia

This presentation demonstrates how to quickly identify large numbers of SNPs for genetic mapping and fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques.

5:30 Evening Reception

6:30 Close of Day

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