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 methods with HASCh-seq methods can be a powerful way to identify candidate targets for genome editing to improve crop traits.

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