3rd Annual Plant Sciences Symposium

The UW-Madison Plant Sciences Graduate Student Council hosted the 3rd Annual Plant Sciences Symposium Symposium titled Transforming Innovation into New Resources for Plant Science on Friday, September 13, 2013. There were several distinguished speakers, opportunities for discussion with colleagues, and catered food. The event was held in the Varsity room at Union South at UW-Madison. The symposium was also available via online streaming for the second year for those unable to attend in person. The symposium featured talks from six accomplished and dynamic scientists.

Dr. Nathan Springer
“Epigenomic variation in maize”

Nathan Springer received his B.S. at Southeast Missouri State University in 1997 and his Ph.D. in Plant Biology at University of Minnesota, where he worked in Ronald Phillips’ lab. Following his Ph.D., he completed a post-doctoral position with Shawn Kaeppler at University of Wisconsin-Madison. He has since served as a faculty member in the Department of Plant Biology at University of Minnesota for the past ten years. Dr. Springer’s research involves studies of maize genetics and genomics.

Abstract: Plant breeding attempts to harness variation in plant populations to produce high-yielding genotypes. In many cases, breeders are not aware of the molecular variation that underlies the selected traits. Genome-enabled tools and resources now allow for a much greater understanding of the variation present in crop plants and how it is affected by breeding practices. There is substantial interest in understanding the contribution of epigenetic variation in plant breeding and improvement. Genome-wide profiling of 50 diverse maize lines identified several thousand differentially methylated regions that are influenced by both genetic and epigenetic differences. In some cases, these DNA methylation differences may contribute to functional variation in gene expression. DNA methylation patterns are often inherited faithfully but there are some examples of unstable inheritance. There is evidence that DNA methylation patterns may be influenced by some breeding practices such as tissue culture.

Dr. Jim Myers
“Breeding for organic systems: Motivation, models, and implications”

Jim Myers develops improved vegetable varieties for organic systems as a professor in the Department of Horticulture at Oregon State University. He focused on breeding for disease resistance from 1990-2007 as part of the Bean/Cowpea CRSP, which supports research to develop improved dry bean cultivars for Eastern and Southern Africa. He is currently the project director for the Northern Organic Vegetable Improvement Collaborative (NOVIC), an USDA-NIFA-OREI funded project which aims to breed and trial vegetable varieties adapted to organic production systems across the northern U.S. Dr. Myer has developed and released 13 dry bean, one green bean, and two tomato cultivars.

Abstract: The rationale for breeding crops for organic production in organic systems is based on the observation of genotype by production system interaction in organic – conventional paired trials. With an emphasis on soil building and restriction on synthetic inputs, organic production systems present a different environment in terms of nutrient availability, weed competition, and pest and disease defense. Nearly all contemporary crop cultivars developed to date having been bred in conventional systems, and as a result, may be less than optimally adapted to organic environments. Research comparing genotypic performance under conventional and organic production is now available for several field and horticultural crops. While some studies have found significant genotype by production system interactions, others have found less evidence for difference in performance between the two systems. Researchers are more likely to find significant interaction when long-term organic plots are compared to conventional farms and less likely when organic production resembles conventional production (recently established organic plots and/or “input substitution” approaches). One surprising finding in several studies is that while organic environments are usually more variable than similar conventional environments, heritabilities in organic are comparable to conventional environments. Under organic production, genotypes exhibit a wider range of phenotypic expression compared to conventional. Some commercial companies are exploiting this property to select early generation materials under organic conditions with subsequent testing and deployment in both organic and conventional systems. Such an approach may produce greater gain from selection and more stable cultivars for both systems. New research on what traits might provide specific adaptation to organic production includes those associated with roots and soil, and weed competitiveness. Genomics and bioinformatics, and epigenetics have potential, but have yet to be applied to understanding genotypic performance in organic systems. Organic plant breeding efforts around the U.S. and in Europe are expanding in both field and horticultural crops. The expansion has been greatest in the public sector with the private sector hesitant to engage in this effort. The majority of funds to support breeding efforts in the public sector have come from Sustainable Agriculture Research and Education Program and USDA-NIFA-Organic Research and Extension Intiatitve and through philanthropic organizations such as Organic Farming Research Foundation, and Clif Bar Family Foundation Seed Matters Initiative. Commercial plant breeding has taken over much of the role of cultivar development for the major crops, but this shift has been associated with a decline in public plant breeders, which in turn has created concern about the supply of future plant breeders for the private sector. Organic plant breeding provides a niche where public plant breeders can contribute and engage in training the next generation of applied plant breeders. With overall consumer demand for organic produce continuing to increase, there will be strong incentive for plant breeders to develop cultivars that are productive under organic growing conditions.

Dr. Sherry Flint-Garcia
“Using genetics, genomics, and breeding to understand diverse maize germplasm”

Sherry Flint-Garcia earned her B.S. at Saint Mary’s University of Minnesota and completed her Ph.D. in Genetics at University of Missouri.  She is now a research geneticist at USDA-ARS and an adjunct assistant professor at University of Missouri.

Dr. Flint-Garcia’s research focuses on the genetic diversity of maize. She utilizes various methods to improve agronomic traits by examining and expanding the germplasm base, including identifying variation within genes that have been artificially selected during the teosinte domestication process.

Abstract: Genetic analysis and improvement of crops relies on variation in genes controlling agronomic traits.  My research program focuses on understanding genetic diversity in maize (Zea mays ssp. mays), so that we may mine beneficial alleles from the appropriate germplasm sources.  Careful choice of germplasm is critical to genetic analysis and the successful utilization of the wide array of germplasm available to us:  elite (expired PVP) inbred lines, diverse inbred lines, landraces, and teosinte, the wild ancestor of maize. A very important issue is genetic diversity in the germplasm pools.  In maize, artificial selection during domestication starting 9000 years ago and modern plant breeding over the last century has diminished this critical genetic variation relative to teosinte.  This is especially true for key genes responsible for traits that define differences between maize and teosinte. Among the traits targeted during domestication and breeding are many yield component traits, including number of ears, kernel row number, seed size, and kernel composition.  Therefore, we must reintroduce variation from teosinte if we hope to learn how domestication has impacted modern maize and continue maize improvement using these genes. Successful implementation of association analysis depends on several factors related to the population under study:  linkage disequilibrium (LD), population structure, and allele frequencies.  Each of these factors can limit the effectiveness of association analysis if ignored during experimental planning.  Highly elite populations have much more extensive LD which limits mapping resolution, whereas highly diverse germplasm can low allele frequencies which limits statistical power.  Careful choice of germplasm can curb the negative effects of these three factors.

Dr. Edgar Spalding
“Machine vision for quantifying dynamic phenotypes in mutant and naturally varying populations”

Edgar Spalding received his B.S. with honours at Acadia University in Nova Scotia, Canada. From Acadia, he moved to Penn State University for graduate work on the biophysical aspects of seedling growth with Dr. Daniel Cosgrove. After a post-doctoral position studying membrane transport and electrophysiology at Yale University with Dr. Mary Helen Goldsmith, he joined the Department of Botany as faculty at University of Wisconsin-Madison in 1994, where he has remained ever since.

Dr. Spalding researches seedling growth and development via cellular, physiological, and developmental studies on Arabidopsis thaliana and maize. The goal of his research is to increase measurement throughput in order to leverage the genetic resources built up around these model systems. His lab also develops the computational tools required to make automated image-based studies of plant growth and development.

Abstract: Most often, genotype information exceeds its phenotypic counterpart in all dimensions and manners. Our Phytomorph project is motivated by the belief that improved technologies for quantifying growth and development will reduce this mismatch by producing more reliable and detailed phenotype data sets, resulting in more efficient functional genomics research. The Phytomorph approach utilizes parallelized and automated image capture and computational analysis to extract phenotype information from time lapse images. The primary roots of Arabidopsis and maize seedling are good subjects with which to develop this approach because their simple cylindrical shape facilitates the image processing step and their responses to environmental perturbations such as reorientation with respect to gravity are rapid enough to be studied in a few hours. One study to be described in this talk utilized a bank of CCD cameras to monitor Arabidopsis seedling roots every 2 min for 8 h. Because of the high-degree of automation it was feasible to measure the responses of a population of recombinant inbred lines in order to perform quantitative trait locus (QTL) mapping. This approach added a time axis to the phenotype data and therefore to the resulting QTL map. When particular loci start and stop to influence variation in the response of roots to gravity was shown by this analysis because machines acquired the phenotype data precisely and automatically with high time resolution. Essentially the same studies are being performed with mapping populations of maize, tomato, and carrot. A major goal of the Phytomorph project is to find predictive relationships between highly quantified phenotypes. Proof of the concept has been achieved with seed features measured very accurately from images and near-infrared spectra then combined with root growth behavior data to reveal relationships between pre- and post-germination events. If some phenotypic features in seeds and seedling roots grown in a lab can be mathematically linked, will it be possible to link lab-grown root features to an important field-expressed trait? How far can predictive relationships between phenotypes be pushed? The easier we can make the process of acquiring large sets of accurate phenotype measurements, the greater the chances of finding useful predictive models. These are future directions for the Phytomorph project.

Dr. Richard Vierstra
“Phytochromes: From 3D structures to engineering photomorphogenesis”

Richard Vierstra is a Professor in the Department of Genetics at the University of Wisconsin-Madison.  He received his B.S. in Biology with a minor in Chemistry at University of Connecticut and his Ph.D. in Botany and Plant Pathology at Michigan State University.

Dr. Vierstra’a lab is attempting to elucidate the molecular mechanisms used by eukaryotes to selectively degrade intracellular proteins. Protein degradation has an integral role in cell maintenance, growth, and development and is an important component in the ability to genetically engineer organisms. He is also interested in ubiquitin pathways in addition to studying the form-dependent degradation of the morphogenic photoreceptor, phytochrome.

Abstract not available.

Dr. Andy Baumgarten
“From discovery to product deployment: Pioneer’s Boreas Standability Program”

Andy Baumgarten received his Ph.D. from University of Minnesota in 2004 and began working with Pioneer in 2005 at the Mankato, Minnesota location. Andy currently leads the Applied Technologies and Genomics group within Pioneer’s Breeding Technologies department.

Abstract: Pioneer’s Boreas wind-machines provide high-throughput, precise phenotyping for standability traits such as brittlesnap and root lodging. Furthermore, a comprehensive molecular breeding strategy has been developed to increase the impact of this phenotyping within Pioneer’s maize breeding programs. I will discuss the development of the Boreas machines, how they have increased Pioneer’s general stanability resistance, and how we have used molecular breeding concepts to increase the impact of Boreas. I will end with some brief discussion on how we are applying similar approaches to integrate genomic technologies into breeding programs.

Although the Plant Sciences Symposium is a student-run event, we would not be able to accomplish it without help from many others. Funding was graciously provided by DuPoint Pioneer, the Associated Students of Madison, and the Departments of Agronomy and Plant Breeding and Plant Genetics. We would also like to acknowledge the support of the faculty in our various departments.