A guide through the genome

Plants show enormous variety in traits relevant to breeding, such as plant height, yield and resistance to pests. One of the greatest challenges in modern plant research is to identify the differences in genetic information that are responsible for this variation. A research team led by the “Crop Yield” working group at the Institute for Molecular Physiology at Heinrich Heine University Düsseldorf (HHU) and the Carnegie Institution of Science at Stanford has now developed a method to identify precisely these special differences in genetic information. Using the example of maize, they demonstrate the great potential of their method in the journal Genome Biology and present regions in the maize genome that may help to increase yields and resistance to pests during breeding.

The blueprint of all organisms is encoded in their DNA. This includes the genes that encode the proteins and determine an organism’s inherent characteristics. In addition, there are other important sections of the DNA, in particular the regions that control the regulation of genes, i.e. when, under which conditions and to what extent the genes are activated.

Compared to the genes, however, these regulatory regions – also known as “cis elements” – are difficult to find. It is changes in precisely these DNA elements that are largely responsible for the differences between organisms, though – and thus also between different plant varieties.

In the past few decades, researchers have discovered that the regulatory regions are the binding sites of specific proteins. Known as transcription factors, it is these that determine when and for how long genes are activated.

Co-corresponding author Dr Thomas Hartwig, who heads the Crop Yield research group at HHU’s Institute for Molecular Physiology and the Max Planck Institute for Plant Breeding Research (MPIPZ) in Cologne: “Finding the few variations that are key to changing traits such as pest resistance among the millions and millions of non-causative genome differences is the ultimate search for a needle in a haystack.” 

“Unlike protein-coding genes, regulatory sites usually cannot be identified based on the sequence alone. This makes them very difficult to pinpoint. Our method uses hybrid plants to measure the direct effects of variation in DNA sequence on transcription factor binding,” says lead author Professor Dr Zhi-Yong Wang from the Carnegie Institution for Science.

The study was developed in a cooperation with researchers from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben as well as the University of Nebraska-Lincoln and Iowa State University in the USA.

Using hybrids, i.e. the first generation of plants created by crossbreeding two varieties, the research team can compare which regulatory regions differ across the entire genome. Co-author Dr Julia Engelhorn: “Our analytical method allows us to measure precisely whether transcription factors bind more to the maternal or paternal genome.” This procedure has also enabled the team to identify thousands of differences associated with traits, such as yield and pest resistance in maize.

The technology was demonstrated for a transcription factor in the brassinosteroid pathway, a hormone related to growth and disease. Institute director Professor Dr Wolf B. Frommer: “The team has identified thousands of genomic variations that can explain why one variety of maize behaves differently in terms of its yield or resistance to disease. Moreover, the team was able to show that these differences are almost equally genetic and epigenetic.” The latter describes processes that influence gene activity without being encoded in the DNA sequence itself.

One central result of the study is a list of more than 6,000 genome regions that can be targeted for plant breeding. These may include, regions through which positive traits are expressed in certain maize varieties that others plants lack.

Hartwig: “Knowing where in the genome modern breeding methods can be applied to transfer characteristics from certain varieties to others is of great importance to biotechnology. Our study may serve as a guide on how to find these interesting genome regions.” Professor Frommer adds: “The study findings lay the foundation for using modern techniques to cultivate new varieties of maize by skilfully combining the optimal variants.” 

The study received funding through the CEPLAS Cluster of Excellence at HHU, the German Research Foundation (DFG), the Carnegie Institution for Science, the Alexander von Humboldt Professor Wolf B. Frommer, the US National Institutes of Health, and the Ministry of Economic Affairs, Tourism, Agriculture and Forestry of Saxony-Anhalt.

Original publication

Thomas Hartwig, Michael Banf, Gisele Passaia Prietsch, Jia-Ying Zhu, Isabel Mora-Ramírez, Jos H.M. Schippers, Samantha, J. Snodgrass, Arun S. Seetharam, Bruno Huettel, Judith, Kolkman, Jinliang Yang, Julia Engelhorn, Zhi-Yong Wang: Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize. Genome Biology 2023.

DOI: 10.1186/s13059-023-02909-w