Molecular method promises to speed development of food crops

January 26, 2016 by Claudia Lutz
Plant breeding efforts, like the Illinois field trial shown here, will benefit from fast and precise technologies to evaluate transgenics. Credit: Haley Ahlers, University of Illinois.

The first human farmers needed hundreds of years and a lot of good luck to shape the first domesticated crops. Modern plant breeders wait weeks or months, not centuries, to discover what the literal fruits of their labors might be; now, a study led at Illinois and supported by the Bill & Melinda Gates Foundation has explored the strengths of a molecular method that reduces this wait time to a few days.

The new study, published in Plant, Cell and Environment, addresses a central challenge of transgenic plant development: how to reliably evaluate whether genetic material has been successfully introduced. Researchers at the University of Illinois, the Polish Academy of Sciences, the University of Nebraska-Lincoln and the University of California, Berkeley compared the traditional method to several new ones that have emerged from advances in genomic technology and identified one that is much faster than the standard approach, yet equally reliable. The study was led by Illinois postdoctoral fellows Kasia Glowacka and Johannes Kromdijk.

"For plants with long life cycles, such as our food crops, this will greatly speed the time between genetic transformation or DNA editing, and development of pure breeding lines," said Long, Gutgsell Endowed Professor of Crop Sciences and Plant Biology and the principal investigator for the study. Long is also a member of the Genomic Ecology of Global Change and Biosystems Design research themes and the Energy Biosciences Institute at the Carl R. Woese Institute for Genomic Biology.

To meet the food and fuel needs of an ever-growing global population, researchers benefit from transgenic technologies to develop crops with higher yields and greater resiliency to environmental challenges. None of the technologies used to introduce new genetic material into plants work with 100 percent efficiency. Plants and their offspring must be screened to identify those in which gene transfer was successful.

Traditionally, this was done in part by testing successive generations of plants to see if the desired traits are present and breed true over time. In addition, plant scientists can use one of several molecular methods to determine if a gene or genes have actually been successfully introduced into the plant genome. The "tried and true" method, the Southern blot, yields precise data but is slow and unwieldy. It requires isolating relatively large amounts of plant DNA, using fluorescent or radioactive dye to detect the gene of interest, and performing a week's worth of lab work for results from just a few samples at a time.

The team compared the Southern blot technique with several that use variations of a chemical process called polymerase chain reaction (PCR). This process allows researchers to quantify specific pieces of the introduced DNA sequences by making many additional copies of them, and then estimating the number of copies—somewhat like estimating the amount of bacteria present in a sample by spreading it on a petri dish and letting colonies grow until they are visible. These methods are much faster than Southern blotting, but if the DNA in each sample does not "grow" at exactly the same rate, the resulting data will be imprecise—size won't be a perfect indicator of the starting quantity.

One method examined by Long's group, digital drop PCR (ddPCR), is designed to overcome this weakness. Rather than using the PCR process to amplify all the DNA in a sample, this method first separates each individual fragment of DNA into its own tiny reaction, much like giving each bacterium its own tiny petri dish to grow in. PCR then amplifies each fragment until there are enough copies to be easily detected, and the total number of tiny reactions are counted. Because this method, unlike others, separates the growth-like step from the quantification step, it can be very precise even when the reaction isn't perfect. Results can be obtained in less than two days, and many samples can be processed simultaneously.

Long hopes that his group's demonstration that ddPCR is a "reliable, fast and high throughput" technique will help it to become the new standard for those developing transgenic crops. "I believe it will become widely adopted," he said. Although ddPCR is currently more expensive than the other methods, Long said the cost would likely drop quickly, as have the costs of other genomic technologies.

Explore further: Improving DNA amplification from problematic plants

More information: Plant, Cell and Environment, DOI: 10.1111/pce.12693

Related Stories

Improving DNA amplification from problematic plants

January 3, 2013

The polymerase chain reaction (PCR) is a common technique used to amplify, or copy, pieces of DNA. Amplified DNA is then used in genetic analyses for everything from medicine to forensics. In plant research, PCR is a vital ...

Breaking down DNA by genome

October 31, 2014

New DNA sequencing technologies have greatly advanced genomic and metagenomic studies in plant biology. Scientists can readily obtain extensive genetic information for any plant species of interest, at a relatively low cost, ...

How many organisms do live in this aquatic habitat?

April 6, 2015

The aim of this new measurement method is to estimate the distribution of aquatic animals using droplet digital polymerase chain reaction (ddPCR) in order to quantify the number of target DNA copies present. This method focuses ...

Scientists learn how to predict plant size

September 11, 2015

VIB and UGent scientists have developed a new method which allows them to predict the final size of a plant while it is still a seedling. Thanks to this method, which is based on the knowledge that a set of genes is associated ...

Nanoparticles simplify DNA identification and quantification

November 25, 2015

In an article published in Small, researchers successfully applied a new qualitative and quantitative method for the detection of a DNA sequence characteristic of Leishmania infantum kinetoplast, a frequent parasite in veterinary ...

Scientists use CRISPR technology to edit crop genes

November 30, 2015

CRISPR gene-editing is allowing rapid scientific advances in many fields, including human health and now it has been shown that crop research can also benefit from this latest exciting technology.

Recommended for you

How Lyme disease bacteria spread through the body

August 25, 2016

Researchers have developed a live-cell-imaging-based system that provides molecular and biomechanical insights into how Lyme disease bacteria latch onto and move along the inside surface of blood vessels to reach key destinations ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.