University of Nebraska researchers identify genes that help corn adapt to new environments

Corn plays a key role in Nebraska’s economy and identity. Yet, this was not always the case.

Corn was first domesticated in the tropical latitudes of central Mexico. Over thousands of years, corn learned to thrive in the very different growing conditions found in temperate North America. Corn made a breakthrough in figuring out how to thrive in temperate climates that now enables the crop to play a key role in ensuring both farmer prosperity and food security across six continents.

The root system of a three-week-old corn plant processed through a computer vision pipeline used to automatically measure different root system architecture traits.

A team of University of Nebraska–Lincoln researchers have made a critical step forward in figuring out what changes allowed corn to make that breakthrough. In research published recently in the journal Genome Biology, the Nebraska-based team measured the expression of 10,000s of genes in the roots of hundreds of different kinds of corn including temperate adapted varieties that grow and thrive here in Nebraska, and tropical varieties which can only complete their lifecycle farther south — or in advanced greenhouses such as those found on Nebraska’s Innovation Campus.

The Nebraska team identified a set of genes whose expression levels were variable and genetically controlled across different tropical corn varieties, but had very consistent expression in temperate corn varieties. They were able to link these genes first to regions of the corn genome targeted by selection as the crop adapted to temperate climates and then to specific changes in the properties of corn, including when corn flowers, that would help it thrive in new environments.

″One of the most exciting things we found was that measuring gene expression in roots let us identify genes controlling properties of any part of the corn plant,″ said James Schnable, the Gardner Professor of Agronomy and the corresponding author of this study. ″The process of measuring gene expression in hundreds of different plants is expensive and time-consuming. Researchers usually think that gene expression must be measured in the right tissue and at the right stage of development to be accurate. However, our research has found that measuring gene expression in the roots of young plants can identify genes that control flowering time in adult plants. We even identified a gene controlling whether corn kernels are white or yellow using our measurements of root gene expression. This means that the data we collected can be used over and over again by different scientists asking different questions instead of starting the measurement process anew each time.″

By identifying the genes that helped corn adapt to new environments in the past, the research team hopes to be able to speed the development of new corn varieties for the future that can tolerate changes in extreme weather conditions from droughts to derechos as well as changes in management practices as Nebraska farmers adapt to growing water restrictions and ever higher fertilizer prices.

The study was led by Guangchao Sun, a research scientist and affiliate, and Huihui Yu, of the Center for Plant Science Innovation. This was a joint effort of four research groups including Karin van Dijk, Daniel Schachtman, Chi Zhang and James C. Schnable, representing three University of Nebraska–Lincoln departments — the Department of Agronomy and Horticulture, the Department of Biochemistry, and the School of Biological Sciences. The team came together to tackle this challenge as part of a large National Science Foundation project organized by the university’s Center for Plant Science Innovation.