Abstract Detail

Advances in Plant Systematics and Population Genomics: Applications of Next Generation Techniques

Cronn, Richard [1], Knaus, Brian [1], Liston, Aaron [2], Maughan, Jeff [3], Parks, Matthew [4], Syring, John [5], Udall, Joshua [6].

Simplifying the complex: Targeted sequencing strategies for population, phylogenetic, and genomic studies in plants.

The recent and dramatic advances offered by modern DNA sequencers annually re-define the amount of sequence data that can be gathered for comparative genetic analysis. Even with the achievements in sequencing to date, plant genomes present formidable obstacles that can make it difficult to execute large-scale population and evolutionary genetic studies. Many factors - wide genome size variation (from ~100 Mbp to well over 100Gbp), extensive variation in the contribution of organellar DNA to total DNA, polyploidy, and gene number/redundancy - contribute to these challenges, and they demand powerful and customizable genome reduction strategies to achieve the desired goals.
In this talk, we summarize the many available genome reduction strategies that can be used to target partial-to-complete organelle genomes, and known and anonymous nuclear targets. These methods fall under four general categories; PCR-based enrichment, hybridization-based enrichment, restriction enzyme-based enrichment, and physical enrichment of sub-genomic partitions. Central to all methods is multiplex DNA sequencing, a process that enables simultaneous sequencing of multiple target pools. We provide examples of how these strategies have been successfully used in three specific applications: (1) enriching and sequencing partial-to-complete chloroplast genomes for phylogenetic analysis; (2) enriching and sequencing nuclear loci to identify population- and taxon-specific polymorphism; and (3) enriching transcriptomes for gene discovery, polymorphism identification, and gene expression analysis. While the benefits of targeted sequencing are greatest in plants with large genomes, most comparative projects can benefit from the improved throughput offered by targeted multiplex DNA sequencing, particularly as the amount of data produced from a single instrument far exceeds 100 billion bases per run.

Broader Impacts:

1 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA
2 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA
3 - Brigham Young University, Plant and Wildlife Science Dept, 285 Widstoe Building, Provo, UT, 84602
4 - Oregon State University, Department of Botany & Plant Pathology, Cordley Hall, Corvallis, OR, 97331-2092, USA
5 - Linfield College, 900 SE Baker St, McMinnville, OR, 97128, USA
6 - Brigham Young University, Plant and Wildlife Science Dept, 292 Widstoe Building, Provo, UT, 84602, USA

Keywords:
Next Generation Sequencing
target enrichment
multiplex PCR
hybridization
transcriptomes
multiplex sequencing.

Presentation Type: Symposium or Colloquium Presentation
Session: SY03
Location: Lenox Room/Chase Park Plaza
Date: Monday, July 11th, 2011
Time: 4:45 PM
Number: SY03008
Abstract ID:504