UD researchers identify novel regulatory network within legumes

January 26, 2012 under CANR News

Three collaborating laboratories in the Department of Plant and Soil Sciences at the University of Delaware — those of professors Blake Meyers, Janine Sherrier and Pamela J. Green — recently identified a novel regulatory network within legumes, including in alfalfa and soybean plants.

The work was performed predominantly by Jixian Zhai, a doctoral student in the department and was published in the December issue of the prestigious journal Genes & Development, one of the top journals in molecular biology and genetics. The genomics project was funded by a grant from the U.S. Department of Agriculture.

Conducting their research at the Delaware Biotechnology Institute (DBI), the investigators set out to get a comprehensive view of how small RNAs function in legumes and how they might be important to these plant species. They focused their work on the chromosomal sequences (genome) of Medicago, a legume genus that includes both the crop plant alfalfa and the species that was recently sequenced, Medicago truncatula.

The researchers sequenced libraries containing millions of small RNAs, important gene regulatory molecules, as well as the genes targeted by these small RNAs. Using advanced computational techniques to categorize the RNA sequences, they identified a novel function for a handful of “microRNAs” — special small RNAs that direct the targeted destruction of specific protein-coding messenger RNAs.

Among these plant microRNAs, the team determined that many target genes encode NBS-LRRs, or “guard proteins” that function in defense against pathogenic microbe infiltration. These NBS-LRRs function as an immune system to battle pathogens but presumably must be suppressed to allow the interactions with beneficial microbes for which legumes are particularly well known. The result of this microRNA targeting is a complex network of co-regulated small RNAs that Zhai characterized using a set of computational and statistical algorithms and analyses.

“The NBS-LRRs keep pathogens out, but these plant cells are still allowing beneficial microbes to enter,” says Sherrier. “The regulation of genes encoding NBS-LRR proteins has been largely unknown until now.”

Over time, these mechanisms have evolved into a more elaborate system in legumes to take advantage of this defense-suppressing system and facilitate the development of nodules, the specialized root structures of legumes in which the beneficial plant-microbe interactions take place.

“We may have found the ‘switch’ that recognizes good versus bad microbes,” adds Meyers, Edward F. and Elizabeth Goodman Rosenberg Professor and chair of the Department of Plant and Soil Sciences. “These guard proteins usually trigger cell death when a pathogen is recognized, but the plant cell is triggering cell death when it encounters a ‘good’ microbe. The circuit we identified may play a role in preventing cell death when the microbe is a friend.”

This discovery could ultimately prove important to the improvement of plant-microbe interactions in other crop plants by allowing plants to become healthier by letting in the good microbes, but keeping the pathogens out.

“We didn’t expect to find something as exciting as this,” says Sherrier. “It’s exciting because no one knows about this kind of gene control and also because it is showing us the diverse interaction between plants and bacterium as well as plants and fungi that could help us develop better mechanisms in other plants, like Arabidopsis.”

“Beyond the applied significance, the finding that NBS-LRR genes are key targets opens up a new frontier for basic research,” says Green, Crawford H. Greenewalt Professor of Plant and Soil Sciences.

If this diverse regulation of beneficial microbes could be added to other crop plants, it could mean scientists could program the plants to grow stronger and taller with less water, and even fertilize themselves.

Article by Blake Meyers and Laura Crozier

Photos by Evan Krape and Kathy F. Atkinson

This article was originally published on UDaily

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UD doctoral student in soil science receives Dixon Award

December 5, 2011 under CANR News

Chunmei Chen, a University of Delaware doctoral student in the Department of Plant and Soil Sciences, was chosen to receive the Dixon Award for best graduate student presentation in soil mineralogy at the recent 2011 Soil Science Society of America meeting in San Antonio.

Chen received a $500 award for being recognized as having the best Division S-9 student presentation, with the selection based on quality of presentation and contribution of the research to advancing the state of knowledge of soil mineralogy.

“I feel very happy and honored to receive the award,” Chen said. “It is encouraging and helpful for me because I would like to continue my career in research.”

Chen presented her research on the Christina River Basin Critical Zone Observatory (CRB-CZO), which specifically reports on the interaction of soil organic matter with soil minerals at the molecular scale along landscape redox gradients.

“The research will lead to better soil management strategies that maintain and enhance levels of soil organic matter, which has important implications in addressing soil carbon sequestration and climate change,” Chen said.

Division S-9 of the Soil Science Society of America established the Joe B. and Martha J. Dixon Soil Mineralogy Endowment to honor Joe Dixon’s career and contributions to soil mineralogy. Each year, two graduate students with projects relating to soil mineralogy are awarded the funding.

Chen earned a bachelor’s degree in agricultural resources and environment from the Nanjing Agricultural University and a master’s degree in environmental science from the Institute of Soil Science, Chinese Academy of Sciences.

Chen plans to submit a manuscript based on her presentation for publication. She hopes to finish her doctorate and eventually become a university faculty member.

Article by Brittany Barkes

This article was originally published on UDaily

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UD’s Wisser receives USDA grant to study genetic barriers in corn

November 15, 2011 under CANR News

When it comes to crops in the U.S., corn is king. Just because it is king, however, does not mean that breeders and in turn growers are using corn to its fullest potential.

With this in mind, the University of Delaware’s Randall Wisser and a group of six fellow researchers have received a five-year $4.2 million grant from the U.S. Department of Agriculture’s National Institute of Food and Agriculture (USDA-NIFA) to study the genetics of adaptation and crop improvement.

Wisser, assistant professor in the Department of Plant and Soil Sciences, said that “there is a great deal of diversity in corn, or maize, particularly in the tropics, which has generally been underutilized in the U.S.” This is because tropical sources of maize are unadapted to North American environments.

Wisser added, “It is virtually impossible to realize the potential breeding value of maladapted materials; finding ways to efficiently adapt crops to new environments is a frontier of agricultural genetics research.”

Populations that lack genetic diversity can fall prey to climate change or other stressors by not having an array of genes on which to draw from. Breeding-based solutions to addressing abiotic and biotic challenges require access to genetic diversity. “If you’re drawing from a limited sample of diversity, the likelihood that you’ve got the necessary genes is less,” Wisser said.

Through its research, the team aims to help plant breeders increase breeding efficiency and access more genetic diversity, increasing their capability of responding to current and future challenges in food production.

Wide-ranging study

The research team is conducting a range of studies that combine field and controlled environment testing with genome sequence analysis and analytics.

In one avenue of research, they are working to better understand the genetics underlying how environment variables such as temperature and day lengths influence plant maturity, a primary barrier to adaptation.

When tropical maize is grown in a North American environment, like Delaware, where summer day lengths can reach up to 15 hours (compared to 10-12 hour days in the tropics), the plants are not receiving the appropriate signals that tell them to flower. They just keep growing, getting very tall and producing lots of leaves, flowering very late or not at all. The plants are out of synch with the growing season and get damaged by frosts or produce no seeds.

Maize that now grows in the U.S. has been adapted over hundreds of years with increasing selection intensities. Through many generations of breeding, an elite pool of maize plants have been developed for North American farmers that are insensitive to long days and flourish in these climates.

“In the process of intense selection, there’s been a big loss in potentially valuable genetic diversity,” Wisser said. “We are thinking about ways to recoup some of what has been lost to help deal with the complex problems of the future”

In another study of the project, the team will test if there are common regions in which the corn genome is associated with broad environmental adaptation or in which genetic barriers are created.

The group will track the flow of genes across generations of selection in the same tropical population adapted to a broad range of environments from Wisconsin to Puerto Rico.

“If adaptation is achieved through one or a few genetic tracks, then existing methods can be used to more quickly adapt tropical maize to different environments,” Wisser said. “If, on the other hand, there are multiple independent genetic tracks to adaptation then a different set of solutions will be needed.”

Wisser said he is hopeful that by studying the adaptation process researchers can pinpoint the barriers that limit use of tropical genetic diversity for North American maize improvement and “open the flood gates” for accessing maize diversity.

The research team

Other investigators in the study are Sherry Flint-Garcia from the USDA-Agricultural Research Services (ARS) and University of Missouri; James B. Holland from the USDA-ARS and North Carolina State University; Nick Lauter from the USDA-ARS and Iowa State University; Natalia deLeon from the University of Wisconsin-Madison; and Seth Murray and Wenwei Xu from Texas A&M University.

Further information about the Maize ATLAS (Adaptation Through Latitudinal Artificial Selection) project can be found at this website.

The study is funded by the USDA Climate Change Mitigation and Adaptation in Agriculture program, which also funded research by Carl Schmidt, associate professor of animal and food sciences and biological sciences at the University of Delaware, concerning heat stress in poultry. For more on that story, see the earlier UDaily article.

Article by Adam Thomas

Photo by Danielle Quigley

This article can also be viewed on UDaily > >

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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.

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Students battle rice blast disease with underground microbes

November 30, 2010 under CANR News

Rice is the most important grain consumed by humans, providing more than one-fifth of the calories sustaining the world’s population. By some estimates, however, global production of rice could feed an additional 60 million people, if it weren’t for rice blast disease, caused by the fungus Magnaporthe grisea.

This past summer, four students from the University of Delaware and two of its partner institutions in Delaware’s National Science Foundation EPSCoR program, Delaware State University and Delaware Technical and Community College, found themselves on the front lines of the battle to defeat rice blast.

Those battle lines have been drawn on opposite coasts of the United States, through a collaboration between scientists in Delaware and at the University of California at Davis, the land-grant institution of the UC system. The students therefore split their summer internship between laboratories in both states.

The project is led by Harsh Bais, professor in UD’s Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, and is funded by the National Science Foundation.

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

Article courtesy of Beth Chajes, DENIN

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