UD team finalist in 2011 Illumina Data Excellence Award Challenge

June 15, 2011 under CANR News

A team from the University of Delaware College of Agriculture and Natural Resources (CANR) and Delaware Biotechnology Institute (DBI) has been selected as a finalist in the 2011 Illumina Data Excellence Award (iDEA) Challenge, taking place June 14-15 in San Diego. The team was selected for a project that focuses on developing user-friendly tools for the processing, analysis and visualization of DNA and RNA sequence data.

The iDEA Challenge is designed to inspire the scientific community to develop new and creative visualization and data analysis techniques. Hosted by Illumina, a San Diego-based company with technologies used for the study of genetic variation and function, the program is interested in empowering and accelerating the analysis, visualization and interpretation of data being generated by Illumina technologies.

The project on which researchers from UD and DBI have been working dates back nearly 10 years and, during that time, more than 20 laboratory members have contributed in various ways to the development and improvement of the software, whose database and web tools were arguably the first visualization system and database specifically for next generation sequence data.

Blake Meyers, the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences and chair of the Department of Plant and Soil Sciences, has been working on the project since the outset and said that though the team did not set out to work on the project specifically to enter it in the iDEA Challenge, the contest has helped them to improve their software.

“We have been working on cleaning up and organizing our software code to make it more streamlined, professional, and universally applicable — that is, to make it useful in many other organisms other than those which we study — thus this has been a useful and encouraging project for those other efforts,” Meyers said.

The UD team has developed a series of websites based on a common set of scripts and tools, specialized for different species’ genomes. The websites enable users to analyze, visualize and download various types of Illumina data, and are built on a common set of web interfaces equipped with user-customizable graphical and analytical tools that allow the user to retrieve and analyze the data.

Speaking to biologists who have very complex datasets, Meyers said he has founded that they generally “emphasize the importance of user-friendliness to methods for interacting with their data, and in my opinion, this is something that we have really developed well. Although ten years of development has meant that our website and web-based tools are quite complex, for the biologist that takes the time to learn the power of our options, there are many ways to interpret their data.”

The UD websites have received thousands of hits per day from users all over the globe and the sites and their informatics tools have been integral to numerous manuscripts that have been published in journals such as Science, Nature, Nature Genetics, Nature Biotechnology, PNAS, The Plant Cell, Nucleic Acids Research, and others.

Meyers said that as a biologist, one of the things he enjoys most about the project is “making new insights and discoveries into biological processes. But related to this is the pleasure of seeing the broad utility of the tools we’ve developed, and knowing the deeper understanding of the data that comes from visualization that allows the user to make the discoveries.”

Those currently involved with the project include:

Mayumi Nakano, a staff research associate in the lab, who has done nearly all the programming to develop the visualization tools and web interface.

Kevin McCormick, a doctoral student in the Department of Computer and Information Sciences (CIS), who has led the development of the primary database structure and database loading scripts.

Caghan Demirci, a CIS doctoral student, who has been working on streamlining and standardizing the systems.

Feray Demirci, a CIS doctoral student, who has worked on application development for specialized analyses.

Recent but former members of the lab who worked on the project include:

Gayathri Mahalingam, a CIS doctoral student, who has worked on parts of the database that stores information on DNA methylation.

Guna Gurazada, a former CIS master’s student who now works at DuPont, and who was involved in many aspects of the data handling pipeline.

The UD team attending the iDEA Challenge includes both Caghan and Feray Demirci and Nakano, and they will present from 10:30-11 a.m., Wednesday, June 15.

Article by Adam Thomas

Photo by Danielle Quigley

The original posting of this article can be viewed on UDaily

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CANR Hosts 2011 Northeastern Corn Improvement Conference

March 21, 2011 under CANR News, Events

The 65th Northeastern Corn Improvement Conference (NEC-029), co-organized by scientists at the University of Delaware, was held February 17 and 18 at the Embassy Suites in Newark, DE.

NEC-029 is one of three regional scientific groups that focus on corn improvement. The group has met annually since 1945, with participants from public and private sectors engaged in research and extension work on corn breeding and genetics, agronomy, plant pathology, and others in the Northeastern U.S. and Eastern Canada. The annual meetings have provided a forum for sharing and discussing research results related to corn improvement and public policy issues affecting corn research.

The NEC-029 conference has directed the focus of several research initiatives including one initiative to combat gray leaf spot, a disease that threatens Northeastern U.S. corn production. As a result, researchers at University of Delaware, Cornell University, Pennsylvania State University, and Virginia Polytechnic and State University have collaborated to develop new gray leaf spot resistant corn lines.

Teclemariam Weldekidan, scientist in the Department of Plant and Soil Sciences, has previously served as secretary and president of the NEC-029 and organized this year’s conference. There were 45 attendees at the conference from northeast and mid-west states and Ottawa, Canada. Twenty-one scientific papers on corn improvement were presented by invited and volunteered speakers, including graduate students. Attendees were thrilled with all aspects of this year’s conference. Several noted the meeting as the best in recent history in terms of the attendance, agenda, and venue.

Blake Meyers, the Edward F. and Elizabeth Goodman Rosenberg Professor and Chairperson of the Department of Plant and Soil Sciences, opened the meeting with remarks about UD’s College of Agriculture and Natural Resources structure, mission, and philosophy and its academic, research, and cooperative extension programs. Meyers discussed the value of agriculture in Delaware and contributions from UD’s corn breeding program including a productive UD-Pioneer Hi-Bred (a DuPont company) collaboration that led to the identification of a gene for corn disease resistance. This was followed by sessions on a range of topics including breeding and genetics, corn grain and silage composition management, new product development, crop management/ protection, and disease and insect resistance.

A special report was presented by Erick Erickson, the special assistant for planning and evaluation for the U.S. Grains Council, who discussed “World and U.S. Corn Supply and Demand Outlook.” Erickson reported the USDA’s long term projection for U.S. corn area planted to rise from 86.5 to 92 million acres, yields to climb from 164.7 to 180 bushels per acre, production to rise from 13.1 to 15.3 billion bushels, and ethanol use to rise from 4.57 to 5.53 billion bushels by the year 2020.

The new biotechnology events combined with advanced breeding and crop production techniques may push U.S. corn yields to more than 200 bushels per acre. Since the world must double food production while using less water and land, this requires progress in increasing genetic potential, increasing water use efficiency, and reducing losses due to disease and pests and post-harvest. 

For more information on Weldekidan’s work with corn, visit [http://www.udel.edu/PR/UDaily/2007/aug/corn080906.html].


CANR researchers team up to combat lima bean disease

February 3, 2011 under CANR News, Cooperative Extension

When battling downy mildew, a potentially devastating disease that strikes lima beans (Phaseolus lunatus), one of Delaware’s most important vegetable crops, assembling a team of experts to attack the problem from all angles is a must. That’s why a diverse group of plant scientists in the University of Delaware’s College of Agriculture and Natural Resources has joined together to battle this important plant disease.

Tom Evans, professor of plant pathology in the Department of Plant and Soil Sciences, and many graduate students have studied downy mildew over the past 15 years.

Evans said lima beans are vital to agriculture in Delaware and are “the cornerstone of the state’s processing vegetable industry.” Approximately 6,000 hectares of baby lima beans are grown annually, with a farm value of over $6 million. If lima bean cannot be grown profitably in the state, then many other processing vegetables would not be grown due to the economics of processing.

Downy mildew, caused by the fungus-like organism Phytophthora phaseoli, is prevalent in Delaware because it thrives in humid conditions, and lima beans are grown on small, dense acreage. Evans said that most lima bean growers are concentrated in close proximity from Dover to Georgetown and from the Delaware Bay west into Maryland, so wind-driven rain makes it easier for the pathogen’s sporangia to move from one lima bean field to another.

That was the case in 2000, when downy mildew caused $3 million damage in what Evans called “the largest downy mildew of lima bean epidemic ever recorded.” Two factors contributing to this epidemic were the emergence of a new race of the pathogen, Race F, which overcame the genetic resistance of lima cultivars being grown, and frequent wind-driven rain that spread the pathogen’s sporangia.

With the emergence of Race F, growers could no longer rely on downy mildew resistant lima bean cultivars to prevent the disease, as they had in the past. New cultivars with resistance to Race F need to be developed and in the meantime growers have relied upon fungicides to manage the disease.

Bob Mulrooney, extension specialist in plant pathology, has tested fungicides for effectiveness against downy mildew for a number of years and has identified new more environmentally-friendly chemicals which offer good control. Mulrooney’s research results are the basis for growers’ current downy mildew management practices.

Evans and his group have been responsible for studying the biology of the pathogen, monitoring the evolution of new races of the pathogen and the epidemiology of the disease.

Extension associate Nancy Gregory diagnoses the disease on samples sent in by growers, maintains the pathogen in culture for field and greenhouse experiments, and determines their races.

Emmalea Ernest, an extension associate at the Carvel Research and Education Center in Georgetown, Del., breeds lima bean for desirable traits, such as disease and drought resistance, and is developing cultivars for Delaware farmers. Ernest and Evans work together screening lima bean germplasm from around the world for resistance to races E and F of P. phaseoli. Ernest has conducted experiments to determine how the resistance genes are inherited. After making crosses between resistant parents followed by several years of field screening, Evans and Ernest are testing lima bean lines with resistance to both races this summer.

Nicole Donofrio, assistant professor of plant and soil sciences, is responsible for the pathogen side of the study, trying to understand the pathogen’s virulence mechanisms, and how it evolves to attack certain aspects of the plant. Donofrio said, “In order to fight the disease, you have to know your enemy, and the more you know your enemy, the more equipped you are to tackle it when things like a new race emerge.”

Knowing exactly how to fight against the disease from a pathogen standpoint is difficult. Donofrio points out that P. phaseoli has over 500 effector genes, molecules that bind to a protein altering its activity and enabling infection. To study effectors, Donofrio and doctoral student Sridhara Kunjeti took a two-pronged approach. First, they took what they knew about P. infestans, the pathogen responsible for the Irish potato famine and a close relative of P. phaseoli, and searched for similar genes in P. phaseoli to determine if it used similar mechanisms in its attack on lima bean.

Next, they looked at lima beans that had been infected for three and six days to see which effectors were active during those time-points of infection. Donofrio said this could lead to a breakthrough because if they are able to characterize the effector genes, they can look for traits that could be a countermeasure to pathogen attack and thereby block pathogenesis.

Randy Wisser, assistant professor of plant and soil sciences, works on aspects of quantitative genetics and plant breeding and Blake Meyers, Edward F. and Elizabeth Goodman Rosenberg Professor and chair of the Department of Plant and Soil Sciences, works on genomics of lima bean-downy mildew interactions.

In various combinations, the research team has received over $200,000 from various CANR seed grants and Delaware state grants to more fully explore P. phaseoli and downy mildew.

Article by Adam Thomas

This article can also be viewed online on UDaily by clicking here.


Blake Meyers appointed Rosenberg Professor of Plant and Soil Sciences

December 1, 2010 under CANR News, Events

Blake C. Meyers, a faculty member in the University of Delaware’s Department of Plant and Soil Sciences since 2002, has been named the Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences, UD Provost Tom Apple has announced.

“Named professorships honor faculty members who have achieved distinction in their disciplines, both on this campus and in the greater world of academia,” Apple said. “It is a pleasure to add Dr. Meyers’ name to this select and important group of UD faculty.”

Meyers, who is currently serving as the chairperson of the department, also holds a joint appointment in the Department of Computer and Information Sciences.

He will present his inaugural lecture as Edward F. and Elizabeth Goodman Rosenberg Professor of Plant and Soil Sciences at 3:30 p.m., Tuesday, Dec. 7, in Room 102 of the Delaware Biotechnology Institute. His topic will be “Plant Genomes and Their RNA Products: Insights from Advances in DNA Sequencing.” Those planning to attend are asked to RSVP by calling (302) 831-2502.

The full article with photo can be viewed online on UDaily by clicking here.