The biological clock and extra gene pairs control important plant functions

A popular food crop’s biological clock controls nearly three-quarters of its genes, according to research from Dartmouth College.

Genetic research shows how the crop uses internal responses to the day-night cycle – known as circadian rhythms – to regulate processes such as reproduction, photosynthesis and reactions to stressful conditions.

The study, published in the journal eLife, can help researchers identify genes to improve growth and resistance to stress when a plant is moved to a new region or encounters changing climatic conditions.

“As plants are grown in new geographic areas, they have to select traits that allow them to survive under different conditions,” said C. Robertson McClung, professor of biology at Dartmouth and senior researcher on the study. “Many of these traits are in the genes of the circadian clock.”

Like animals, plants have biological clocks that allow them to adapt to predictable changes, such as day-night cycles or changing seasons. While animals can relocate to adapt to such environmental changes, plants are locked in place. To survive, plants must turn genes on and off to alter their biological functions.

The research team used RNA sequencing to identify how the genes of the popular Brassica rapa crop are controlled by the plant’s internal timing mechanism. The B. rapa species includes varieties such as turnips, oilseeds, Chinese cabbage and leafy vegetables.

In the study, the plants were exposed to normal conditions characterized by warm days and cool nights. They were then removed from this environment and sampled over a two-day period to reveal which genes were active in response to the plant’s internal clock signals.

The research found that over 16,000 genes, about three-quarters of all plant genes, are regulated by circadian rhythms in the absence of changes in light and temperature.

“We were surprised to find that so many genes are regulated by the biological clock. This underscores the importance of controlling the circadian clock of many functions within the plant,” said McClung.

Many cultivated plants, such as wheat, potatoes and brassica, have doubled or tripled their complete genetic complement. This has led the researchers to question what effect the additional gene pairs have on the plant’s biological clock or survival processes such as drought resilience.

The research team found that the extra gene copies are often active at different times of the day than their gene pairs.

Furthermore, the researchers found that often only one member of a duplicate gene pair responded to drought. In both of these cases, the differences in the timing of gene activation, or in reactivity to drought, must have occurred after the genes duplicated.

The results lead to the conclusion that the same gene duplication responsible for a more sensitive biological clock also creates greater resistance to drought.

“During the evolution of terrestrial plants, the number of gene pairs expanded,” said Kathleen Greenham, assistant professor of plant and microbial biology at the University of Minnesota, who co-led the study as a post-graduate researcher. doctorate in Dartmouth. “One set of copies can maintain critical growth processes while the others are free to develop new functions that researchers can use to produce stress-resistant crops.”

Identifying differences within gene pairs that make them sensitive or non-responsive to drought conditions could provide researchers with a way to help plants increase resilience to climate-induced change.

“Time of day is important for gene expression when it comes to tackling drought,” said Ryan Sartor, a postdoctoral researcher at North Carolina State University who co-led the study. “This is a first step to help understand basic relationships. A more complete understanding of this complex system could lead to the development of more stress-resistant crops.”

According to the research team, the circadian rhythms that regulate much of plant biology are likely to be affected by climate change as environmental signals become less reliable. This makes it harder for plants to adapt and survive, but it also serves as a clue for researchers looking for ways to build plant resilience.