June 28, 2017

2013 University of Minnesota Plant Breeding Symposium

Innovative Phenotyping: Catching up to the Genomics Era

 

Jesse Poland (PowerpointVideo recording)

Jim Bradeen (PowerpointVideo recording)

Kathleen Brown (PowerpointVideo recording)

Glenn Howe (PowerpointVideo recording)

Patrick Schnable (PowerpointVideo recording)

Roundtable Discussion

Speakers

This year’s welcome address from DuPont Pioneer will be given by:

 verde Luis Verde, Head of Breeding Technologies

 

We are pleased to announce the  speakers for this year’s symposium:

 poland Jesse Poland, USDA-ARS and Kansas State University: “Connecting (High-Throughput) Genotype to (High-Throughput) Phenotype”
 Jim Bradeen Jim Bradeen, University of Minnesota: “From Genotype to Phenotype: Turning Plant Disease Resistance Research Inside Out”
 KBrown Kathleen Brown, Penn State University: “Phenotyping root traits for abiotic stress tolerance”
 renee Renee Lafitte, DuPont Pioneer: “High-Throughput Field Phenotyping in Maize Drought Experiments”
 howe Glenn Howe, Oregon State University: “High-Throughput Phenotyping in Forest Trees: The Promise and The Peril”
 
 schnable Patrick Schnable, Iowa State University: “Next Generation Phenotyping and Breeding”

 

 

Program Schedule

 2013 schedule

 

Jesse Poland

Abstract

The essence of plant genetics is to understand the link between genetic variation and observed phenotypes.  The association of DNA polymorphisms with phenotypes on a genome-wide scale and dissection of the genetic architecture of complex traits on a species-wide level requires accurate phenotyping of large populations along with genome-wide molecular markers.  Genotyping can now be accomplished with low-cost, high-throughput assays and sequencing.  We have developed genotyping-by-sequencing as a rapid low-cost platform for high-throughput whole-genome profiling.  This approach can be used for de novo characterization of elite breeding germplasm and diverse collections.  Phenotyping, on the other hand, is labor intensive and has become the limiting factor in plant biology studies and crop improvement programs.  Platforms for high-throughput phenotyping (HTP), particularly in field environments, are needed to compliment the wealth of available genomic information.  We are developing field-based HTP platforms for rapid assessment of multiple quantitative traits through integration of proximal sensing tools and GPS referencing.  Geo-referenced proximal sensing data can be used in connection with forward and reverse modeling to rapidly quantify a range of physiological traits.  The advancements in high-throughput genotyping and HTP are starting to converge with the power to expand our functional understanding of plant genomes while increasing and accelerating the breeding cycle.

Bio

Dr. Jesse Poland is a Research Geneticist with USDA-ARS and holds and adjunct appointment in the Department of Agronomy at Kansas State University.  Dr. Poland’s research group is located on the KSU campus with field research across the state.  Dr. Poland currently supervises three graduate students, a post-doctoral scholar and sits on the graduate committees of 5 other students at Kansas State University and Colorado State University, where he holds affiliate faculty status.

Research in Dr. Poland’s group is focused on wheat genetics and germplasm improvement.  They are currently developing new marker technologies for use in breeding, diversity studies, and association genetics.  In collaboration with public breeding programs, Dr. Poland is exploring the use of genomic selection methods in wheat breeding.  In the area of germplasm development, Dr. Poland’s group is focused on developing new breeding lines with resistance to the major pests of wheat including stem rust, strip rust, leaf rust and Hessian Fly.  Dr. Poland’s lab is developing high-throughput phenotyping approaches for field-based evaluation of breeding lines with the primary focus being genetic characterization of heat and drought tolerance and development of improved germplasm.

Lab website: www.wheatgenetics.org

 

Jim Bradeen

Abstract

Wild relatives are rich sources of genes for crop improvement.  This is especially true for disease resistance (R) genes.  Recent advances in high throughput DNA sequencing technologies have made genotyping faster and cheaper than phenotyping, in many cases. This project aims to capitalize upon molecular functional knowledge of disease resistance and technological advancements to facilitate comparative genomics approaches for identifying and accessing R-genes harbored in crop wild relatives.

An ongoing effort, this project first yielded user-friendly tools for visualizing patterns of R-gene distribution and allelic diversification both within and across the genomes of related species.  Working in the Solanaceae and Rosaceae, we developed the SolaR80 and RosaR80 systems, respectively. These systems employ a curated analytical pipeline and a controlled terminology for defining R-gene lineages.  We are now populating these conceptual frameworks through ultra-deep sequencing approaches targeting the R-gene space of individual genotypes, populations, and species.  Through collaborations, we are also developing on-line tools for the broader research community.  In the future, our R-gene frameworks will incorporate information about the genome context of R-genes and metadata including historical knowledge of plant and pathogen species distributions and climatic conditions. 

We predict that our analyses will facilitate resource efficient R-gene discovery by using knowledge of R-gene molecular diversity to prioritize populations or species for more costly phenotyping efforts. We also anticipate that linking R-gene content and patterns of allelic diversification with knowledge of R-gene genome context and pertinent metadata will yield testable hypotheses to link specific R-gene lineages to putative resistance function.

Bio

A native of Kalamazoo, Michigan, Jim Bradeen earned a BS degree in Horticulture at Michigan State University and MS and PhD degrees in Plant Breeding & Plant Genetics from the University of Wisconsin—Madison.  His postdoctoral experience included study of epigenetic regulatory mechanisms in maize and geminivirus evolution at the Waksman Institute of Microbiology at Rutgers University and fine mapping and cloning of a late blight resistance gene from a wild potato species at the USDA-ARS/University of Wisconsin.  He joined the University of Minnesota faculty in 2002 and is currently an Associate Professor in the Department of Plant Pathology.  Jim is an expert on the functional and structural genomics of plant disease resistance.  He teaches keystone graduate Plant Pathology courses including “Molecular Plant-Microbe Interactions”, “Current Topics in Molecular Plant Pathology”, and a course on scientific professional speaking.  In 2012 Jim was awarded a Distinguished Teaching Faculty Award from the UM College of Food, Agricultural and Natural Resource Sciences.  Jim’s research emphasizes the application of genomics approaches to identify, characterize, access, and deploy disease resistance genes from wild crop relatives in the Solanaceae and Rosaceae.

 

Kathleen Brown

Abstract

Root traits are important for crop adaptation to soil stresses such as drought and nutrient deficiencies. Using trait-based selection for root traits is particularly challenging. Roots in realistic systems are not easily accessible, they have strong responses to the environment, and our knowledge of which traits are important for which stresses is very limited. We have developed phenotyping methods for root architectural, morphological, and anatomical traits, and used these methods to investigate the importance of various traits for soil exploration and root metabolic efficiency.

Bio

Dr. Kathleen Brown received a B.A. in Biology from the State University of New York at Potsdam, M.S. in Genetics from the University of New Hampshire, and Ph.D. in Horticulture/ Plant Physiology from the University of Florida. After completing a postdoctoral position at the University of Missouri, she was appointed to the faculty in Horticulture (now Plant Science) at Penn State University in 1980. She teaches courses for undergraduate students in the horticulture major and for graduate students in the Intercollege Program in Plant Biology. Her research is on the physiology, genetics, and agro-ecological impact of root traits for to adaptation to poor soils, with a focus on crops such as common bean, maize, and rice. More information can be found on the laboratory website: http://roots.psu.edu

 

Renee Lafitte

Abstract

Field phenotyping for tolerance to drought stress has benefitted from improvements in experiment designs, analysis, management, and data types that can be collected. Careful selection and characterization of fields allows better use of within-field variation, and precision irrigation enables the application of informative drought treatments. Analytical approaches now enable better separation of spatial and genetic effects. Technologies that increase the amount of information that can be collected per plot make the most of expensive field experiments, while more thorough environmental characterization allows the interpretation of observed genotype-by-location interactions. These tools and approaches can increase the rate of improvement realized in breeding programs targeting drought-prone environments.

Bio

Dr. H. Renee Lafitte received a B.Sc. in Botany from Duke University followed by a M.Sc. in Agronomy and Ph.D in Crop Physiology from the University of California, Davis. Renee began field phenotyping for stress tolerance in 1985 at the International Center for Maize and Wheat Improvement (CIMMYT) in Mexico. There, she supported drought breeding activities using managed selection environments. She also established screening systems for improving tolerance to low nitrogen in maize, and developed and delivered courses in on-farm research for breeders and agronomists from partner countries in Latin America, Africa, and Asia. In 1995, she was employed at the International Rice Research Institute (IRRI) in the Philippines. There, she was responsible for field-based phenotyping to assess genetic variation in drought response in rice, including projects incorporating QTL analysis, gene expression profiling, controlled environment screening for seedling responses, and studies of inheritance. She also served as team leader for IRRI’s project on genetic enhancement for improving productivity and human nutrition in fragile environments. Renee joined Pioneer Hi-Bred International in 2005. She is a Research Fellow with responsibility for managing the field evaluation group that tests new transgenic corn lines for improved yield stability under drought and nutrient stress. Renee is based at Pioneer’s North American managed stress site in Woodland, California.

 

Glenn Howe

Abstract

In forest trees, accurate and efficient phenotyping is important for making breeding decisions and understanding patterns of genetic variation in natural populations.  Although fast and inexpensive approaches are exceedingly valuable, high-throughput phenotyping is difficult in trees because they are large, rotations are long, and trees are typically grown as genetically diverse populations in highly heterogeneous environments.  I will present an overview of forest tree breeding, and then discuss tree phenotyping from a conceptual standpoint, including challenges imposed by low heritabilities for many important traits, large genotype by environmental interactions, and modest juvenile-mature correlations.  Second, I will discuss proven and proposed methods of ‘high-throughput’ phenotyping in forest trees—including methods for assessing dormancy, cold hardiness, drought hardiness, disease resistance, and wood properties—and the potential for using remote sensing to measure phenotypes in the field.  Finally, I will discuss genomic selection and its potential to influence how we approach phenotyping in tree breeding programs, and ways to address the problem of climate change.

Bio

Dr. Glenn Howe is Associate Professor and Director of the Pacific Northwest Tree Improvement Research Cooperative in the Department of Forest Ecosystems and Society at Oregon State University (OSU).  He earned his B.S. in forestry at The Pennsylvania State University, M.S. in forest genetics and tree improvement at Michigan State University, and Ph.D. in genetics at Oregon State University.  He did post-doctoral research in the Department of Forest Resources at the University of Minnesota, and was Assistant Professor in the School of Natural Resources at Ohio State University before joining the faculty at OSU.  He is the OSU Site Director for the Center for Advanced Forestry Systems (CAFS), a national cooperative research program funded through the National Science Foundation’s Industry/University Cooperative Research Center Program, and directs the Western Conifer Climate Change Consortium, whose goal is to “enhance the ability of western forests to mitigate and adapt to climate change by providing forest owners, managers, policy-makers, and other stakeholders the information needed to respond to climate change by adopting new management strategies.”  Dr. Howe’s research has mostly focused on tree breeding and the physiological and ecological genetics of adaptation to climate, including a focus on the genetics of dormancy, photoperiodism, cold hardiness, drought hardiness, and wood properties using quantitative, molecular, and genomic approaches.

 

Patrick Schnable

Abstract

Agriculture faces enormous challenges driven by growing populations, changing diets, the globalization of markets and new uses for agricultural products, ecological concerns, increased costs and reduced availabilities of agricultural inputs, and the impacts of global climate change.  The R&D cost per unit of genetic gain is increasing annually in maize and yields have plateaued in some crops.

As a consequence of public-sector investments in the human genome project the cost of DNA sequencing has plummeted faster than Moore’s Law for computers.  The Next Generation Sequencing (NGS) revolution, in combination with advances in robots and computing have laid the groundwork for “next generation breeding”. 

Methods by which NGS technologies can be used to efficiently and cost-effectively assay genetic diversity (e.g., SNPs), identify markers associated with qualitative traits (BSR-Seq), and genotype breeding populations (tGBS) to map quantitative traits will be described.  As well, two “Next Generation Phenotyping” platforms will be introduced.

Bio

Patrick S. Schnable holds an endowed professorship at Iowa State University where he serves as the founding director of the Center for Plant Genomics.  He is also a ChangJiang Scholar Professor at China Agriculture University in Beijing. Schnable received his BS from Cornell University and was awarded a PhD in Plant Breeding and Genetics from Iowa State University. Prior to his faculty appointment Schnable conducted post-doctoral research at the Max Planck Institute for Plant Breeding in Köln, Germany.

Schnable’s scientific investigations of the maize genome have been wide-ranging and he has developed and/or deployed important genomic tools and resources.  He is the author of ~120 peer-reviewed publications, served as the co-lead author of the maize genome sequencing paper (2009, Science) and has an h-index of 47 (Google Scholar).  Reflecting his interest in computational approaches to data analysis he has an Erdös number of 4.

Schnable was elected a fellow of the American Association for the Advancement of Science in 2010.  He serves as an associate editor for PLoS Genetics (Impact Factor 8.7) and as the chair of the American Society of Plant Biology’s Science Policy Committee.  He is a past chair of the Maize Genetics Executive Committee.

Schnable is also the managing partner for Data2Bio LLC, which designs, conducts, analyzes and interprets Next Generation Sequencing projects.

 

Luis Verde

Bio

Dr. Luis Verde is Senior Research Manager in charge of Breeding Technologies (BT) at the Crop Genetics Research and Development (CGR&D) group. The BT team goal is to develop and incorporate new technologies into breeding systems to create new and improved commercial products.

Luis began his career at Pioneer Hi-Bred, in 2003 as a corn breeder in Johnston Iowa for the CRM’s 108-113 breeding program. In 2005, all breeding efforts were moved to Dallas Center where he became station manager. In 2010, he was named lead of the Breeding Innovation team and member of the Global Molecular Breeding Initiative. In 2011 Luis was named BT lead the role that he currently holds.

 Luis was born in Uruguay but moved at an early age to Argentina where he earned his B.S. in Agronomy at UNMdelP.  In 1998, Luis moved to Iowa to study with Mike Lee and holds M.S and Ph.D. degrees in Plant Breeding from Iowa State University.

 

Thanks to generous sponsorship from DuPont Pioneer, the graduate students of the Applied Plant Sciences graduate program have put on a plant breeding symposium each spring since 2008.

 

Student Organizing Committee:

  • Co-Chairs: Celeste Falcon and Liana Nice
  • Addie Thompson, Yong Bao, Hannah Swegarden, Justin Anderson, Kathryn Turner, Amy Jacobson, JoAnn Kirsch, Prabin Bajgain, Ahmad Sallam,