Worldwide populations of Arabidopsis thaliana all have the same genes, but they vary in many traits, including the size of their chloroplasts. A recent study in Plant Physiology identified one of the genes, FtsZ2-2, contributing to the natural variation in Arabidopsis chloroplast size. The findings point scientists to a target gene to make larger chloroplasts, an application that may one day generate more productive crops.

Plant biologists have known for years that mutations in numerous Arabidopsis genes can experimentally change chloroplast size. But they didn’t know which of the genes, if any, were actually contributing to the trait in the wild. Laboratory mutations, while effective for experiments, can dramatically alter a plant such that it might not survive in nature, says study coauthor Katherine Osteryoung, a plant molecular and cell biologist at Michigan State University in East Lansing. Natural mutations that persist in the population tend to have much subtler effects, she explains, that don’t wreak havoc on the whole plant. Knowing which genes act in the wild therefore highlights those that can mutate without killing the plant. “If you know in nature there is a mutation, and in spite of it, the overall plant is fine—it doesn’t create a mess of the plant—that’s the advantage of knowing the gene actually affecting in nature,” says Sureshkumar Balasubramanian, a plant biologist at Monash University in Melbourne, Australia who was not involved in the study.

To find a gene that could explain natural variation in chloroplast size, Osteryoung and collaborators first looked across 22 A. thaliana varieties from around the world. They found that plants in the Polish Landsberg erecta variety, known as Ler-0, had relatively small chloroplasts, and plants from the Cape Verde Islands, known as Cvi-1, had the largest chloroplasts.

Researchers then examined 92 vials of seeds whose entire genomes were identical to the Ler-0 parent, except for one small region from Cvi-1. Among the 92 vials, the position of the Cvi-1 region varied, appearing in 92 different locations on Arabidopsis’ five chromosomes.

When Osteryoung’s team grew the seeds, most of the plants had the small chloroplasts of the Landsberg erecta parent. But a few had the large chloroplasts of the Cape Verde parent, suggesting the Cvi-1 region in their chromosomes controlled chloroplast size. Every plant with large chloroplasts turned out to have the Cvi-1 region in the same segment of chromosome 3.

Since FtsZ2-2 occurs in the same area of chromosome 3, the researchers suspected it might be responsible. They tested their suspicion in a separate experiment in a different variety of A. thaliana plants called “Columbia.” In Columbia plants mutated with disabled FtsZ2-2 genes, they inserted new FtsZ2-2 genes from Landsberg erecta or Cape Verde plants. Different FtsZ2-2 genes led to different-sized chloroplasts in adult plants. That discrepancy suggested Ftsz2-2 was the gene on chromosome 3, Osteryoung says.

Finally, Osteryoung’s group sequenced FtsZ2-2 from plants with larger and smaller chloroplasts.

In doing so, they discovered that the Cvi-1 protein is smaller than the Ler-0 protein; it’s this smaller protein that likely makes chloroplast division less efficient, explains plant scientist Paul Jarvis at the University of Oxford in England who wasn’t involved in the study. Chloroplasts “don’t divide so frequently,” he says, “so they get bigger.”

Osteryoung notes that plants actually have two FtsZ gene families, which seem to be duplicates of one ancestral gene. Perhaps having the second copy, FtsZ2, which can be mutated without killing the plant, confers the ability “to fine tune chloroplast size.” This could give plants an edge in photosynthetic performance. The same type of genetic variation that this study found in FtsZ2-2 could explain variation in chloroplast size in other plant species, notes plant developmental biologist Tammy Sage at the University of Toronto in Canada, who wasn’t involved in the study. She adds, though, that “other genes may also be playing an important role.”

Researchers would next like to know, Jarvis says, “what impacts these changes in chloroplast size have on plant fitness”; for example, how well large and small chloroplasts perform photosynthesis.

If larger chloroplasts make sugar more efficiently from sunlight, then “perhaps manipulating chloroplast size would be one of many things that a breeder could consider,” Osteryoung says. Selecting for chloroplast size could potentially lead to faster-growing, earlier-fruiting, or more productive crops, she notes. Even so, she cautions that more experiments will be necessary—for example, testing whether tweaking chloroplast size would even make plants more efficient photosynthesizers.