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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Soybeans vs. Edamame

April 6, 2011 under Cooperative Extension

“What is the difference in the soybeans that are grown in Delaware, and the kind we get from China in the grocery store (edamame). Why aren’t Delaware farmers selling them at the farm markets on the roadside?”  These questions were posted on Facebook from a curious reader.  We reached out to our faculty in the Department of Plant and Soil Sciences and this is what we have to share:

Edamame soybeans are food grade soybeans versus the typical feed grade soybean grown in Delaware.  Essentially what that means is that the helium (the eye like structure where the soybean attaches to the pod wall) is black in feed grade beans and clear in color on food grade soybeans.  Edamame soybeans are also harvested when the seed fills the pod cavity while feed grade beans which are generally a smaller seeded bean are allowed to dry to about 13.5%  moisture for harvest and storage.  Edamame beans are often picked by hand since the beans ripen from the bottom of the plant up towards the top so hand picking increases yields.  We tried mechanical harvest of edamame beans in Maryland (and maybe even Delaware) using lima bean pickers but it wasn’t a clean harvest and would need a lot of sorting and hand labor to clean them adequately.  I think Schllinger Seeds down near Queenstown, MD has a number of edible soybeans that can be used for  edamame and you can grow them successfully here in a back yard garden.

So there you have it!  Thanks to Richard Taylor, agronomy extension specialist for responding so quickly.

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Delaware agriculture is an $8 billion industry, according to new UD study

March 24, 2011 under CANR News

Agriculture is an $8 billion industry in Delaware, according to a recent study published by the Department of Food and Resource Economics in the University of Delaware’s College of Agriculture and Natural Resources.

The study — conducted by UD faculty members Titus Awokuse and Tom Ilvento, with help from graduate student Zachary Johnston — used input-output analysis, taking into account the market value of products sold from on-farm production, revenue from processing and manufacturing of agricultural products, and inter-industry linkages to determine the value added to the economy.

A study of this magnitude had not been conducted since the early 1980s. According to the authors, this new report is much more accurate in its calculations for the true impact of agriculture in Delaware.

Historically, $1.1 billion has been the most commonly cited number for the impact of agriculture in Delaware. “But this is the total market value of agricultural products sold at the farm level, just a small piece of the picture,” according to Awokuse, associate professor and director of graduate studies for food and resource economics.

The new report shows that the processing of farm products adds a previously unaccounted for $3.8 billion. Forestry production and processing add an additional $831 million, with ag-related services (i.e. crop dusting, ditch digging) adding $28 million.

The research project was commissioned by Robin Morgan, dean of the college. “This study was needed because the impact of agriculture in Delaware is much larger than farm receipts and (the impact) should account for processing of agricultural products. Agriculture is a large and vital part of Delaware’s economy, and our understanding of its impact needs to be as accurate as possible,” says Morgan.

In addition to the total industry impact, the report provides separate results by county and for several key agricultural commodities: poultry, dairy, fruits and vegetables, corn, soybeans, wheat, greenhouse, nursery and horticultural products.

With Delaware’s long history of poultry production, it was no surprise to the authors that the majority of the economic value of agriculture comes from the production and processing of poultry products, with an industry output of $3.2 billion and over 13,000 jobs.

The report also provides a summary of statistics relative to the changing face of agriculture in Delaware, noting there are fewer farms in Delaware, but the size and productivity of farming operations has increased over time.

Awokuse notes that this trend is in large part because “both technological and biological innovations within agriculture now allow a single operator to be more productive and maintain a larger operation, hence the consolidation of farms across the state.”

And, according to the authors, the state of Delaware agriculture will continue to change.

“Farmers are being asked to produce more on less and less acreage and they turn to science and technology to make that happen. Agriculture is a modern, efficient, technologically advanced industry, even if the image is still rooted in a 19th century image of farming,” says Ilvento, professor and chair of the Department of Food and Resource Economics. “Changing that image, assisting farmers to find modern solutions, and promoting the importance of agriculture — that’s what our college is all about.”

A full version of the report can be viewed online.

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

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