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Plants exhibit enormous variation in traits relevant to breeding, such as plant height, yield, and resistance to insect pests. One of the greatest challenges in modern plant research is determining which differences in genetic information cause such changes.

 

Recently, researchers at the University of Düsseldorf in Germany and the Carnegie Institution of Science in the United States have developed a method to precisely identify these specific differences in genetic information. Using maize as an example, they demonstrate in the journal Genome Biology the great potential of this approach, noting regions of the maize genome that may contribute to improved yield and insect resistance.

 

The blueprint for all living organisms is encoded in their DNA, including genes which code for proteins and determine an organism's inherent characteristics. In addition, DNA includes other important parts, especially the regions responsible for gene regulation, that is, controlling when, under what conditions and to what extent genes are activated.

 

Compared to genes, these regulatory regions, also known as "cis-elements", are difficult to find. However, it is variations in these DNA elements that are largely responsible for the differences between organisms and therefore between different plant species.

 

Over the past few decades, researchers have discovered that regulatory regions are binding sites for specific proteins. These proteins, called transcription factors, determine when genes are activated and for how long.

 

According to co-corresponding author Thomas Hartwig, Ph.D., from the Institute of Molecular Physiology at the University of Düsseldorf, looking for the few variants that are critical to changing traits, such as insect resistance, among millions of non-causal genomic differences is tantamount to finding a needle in a haystack.

 

"Unlike protein-coding genes, regulatory sites often cannot be identified based on sequence alone. This makes them difficult to pinpoint. Our method uses hybrid plants to determine the direct effect of changes in DNA sequence on transcription factor binding," Carnegie Scientific Research Professor Zhi-Yong Wang of the institute said.

 

Using hybrids, the research team can compare which regulatory regions differ across the genome. They used hybrid allele-specific chromatin-associated sequencing (HASCh-seq) to identify differential binding sites for the transcription factor ZmBZR1 in maize in response to brassinosteroid signaling. Brassinolide is a hormone associated with growth and disease.

 

The researchers identified thousands of target genes for ZmBZR1 and observed allele-specific binding of ZmBZR1 in nearly 20 percent of the target genes, explaining why a variety of maize may behave differently in terms of yield or disease resistance. In addition, they found that these differences are the result of a combination of genetic and epigenetic factors.

 

Dr Hartwig said: "Understanding where the genome modern breeding methods can be applied in and transfer traits from some breeds to others is very important for biotechnology. Our research can serve as a guide for how to find these interesting genomic regions.”

 

The researchers believe that combining classical GWAS methodswith HASCh-seq methods can be a powerful way to identify candidate targets for genome editing to improve crop traits.

 

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Plant growth is driven by light and is powered by photosynthesis of green leaves. The same is true for roots that grow in the dark—they receive the products of photosynthesis, specifically sucrose, or sugar, through a central transport pathway in the phloem. Dr. Stefan Kircher and Prof. Peter Schopfer from the Faculty of Biology at the University of Freiburg have shown in experiments using the model plant Arabidopsis thaliana that sucrose not only ensures the supply of carbohydrates to the roots, but also acts as a signal transmitter for the formation of light-dependent root structures. It does this in two ways: First, sucrose directly directs the elongation of the taproot. Second, sucrose is transported to the root tip, which then regulates the production of the plant hormoneauxin. This hormone drives the rate of new lateral root formation, synchronized with the elongation of the main root by joint signal transmitters. "This allows root growth to adapt to changes in light and other environmental conditions, such as a change from day to night, to the current photosynthetic performance of the leaf," Kircher said.

 

To demonstrate that sucrose, produced through photosynthesis, was the decisive signal transmitter, Kircher and Schopfer placed plants in a room with light but no carbon dioxide (CO2) in the air, rendering photosynthesis impossible. The result is that no more lateral roots are formed. This result was confirmed in another experiment in which the two biologists treated leaves or roots with a sucrose solution in the dark. In both methods, lateral root development was the same as in light-exposed control plants. "These results show that sucrose production in leaves is necessary for lateral root formation. It confirms the hypothesis of sucrose as a signal transmitter for light stimulation," says Kircher.

 

In earlier studies, the researchers had shown that auxin, produced in roots from the amino acid tryptophan, drives the rate at which new lateral roots develop. Kircher and Schopfer now show how sucrose triggers this process. To do this, they kept the plants in a dark room for two days and performed various experiments to discover their effect on lateral root formation. Applying tryptophan to the roots at the same time as treating the leaves with sucrose worked best. In contrast, if tryptophan was applied to leaves or roots without sucrose, it had little effect. "These observations confirm that auxin synthesis can be triggered by sucrose produced through photosynthesis," Kircher said.

 

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