There's a place in West Virginia where trees grow upside-down. Branches sprout from their trunks in the ordinary fashion, but then they do an about-face, curving toward the soil. On a chilly December day, the confused trees' bare branches bob and weave in the breeze like slender snakes straining to touch the ground.

"It's really kind of mind-boggling," says plant molecular biologist Chris Dardick, waving toward the bizarro plum trees. "They're completely messed up."

I'm visiting an orchard at the Appalachian Fruit Research Station, an outpost of the U.S. Department of Agriculture nestled in the sleepy Shenandoah Valley. The disoriented plums are but one in an orchard of oddities, their outlines, seasonally stripped of leaves, standing out in stark relief.

There are trees with branches that shoot straight up, standing to attention in disciplined rows, with nary a sideways branch. There are trees with branches that elegantly arch, like woody umbrellas; others with appendages that lazily wander this way and that.

Dwarf trees crouch, sporting ball-like crowns akin to Truffula trees. Compact "trees" poke from the ground in clumps of scraggly, knee-high sticks. The topsy-turvy growth of all of these trees comes from genetic variations that cause the dialing up, dialing down, or elimination altogether of the activity of key genes controlling plant architecture.

Understanding these misfits has real-world applications: It could help grow the next generation of orchards that, densely packed with trees, produce more fruit while using less land and labor than today. But Dardick is also trying to answer a fundamental question: How do different trees get their distinctive shapes? From the towering spires of spruce and fir, the massive spreading limbs of an oak to the stately arching canopies of an elm, the skeletal shapes of trees offer signature silhouettes.

(C. HOLLENDER (LEFT), C. DARDICK (CENTER AND RIGHT)/Courtesy Knowable Magazine)

Work by breeders, biologists, and botanists have revealed sizable pockets of knowledge about the hormones, genes, and processes that yield the diverse shapes of trees and other plants, between species and within species. It has not been easy: Two of trees' most appealing attributes — their long lives and large sizes — make them intractable research subjects.

But as scientists pursue these questions, commonalities are emerging between vastly different species. The puzzle of shape diversity and adaptability turns out to be tied to the fundamentals of being a plant: grappling with gravity, fighting for sunlight, all while anchored in one place for a lifetime.

"Plants are stuck. The best they can do is grow toward something," says Courtney Hollender, a former postdoc of Dardick's who now runs her own lab in the Department of Horticulture at Michigan State University in East Lansing. "That's all they've got; they can't run, they have to adapt to their environment. And they've developed brilliant ways to do it."

When genes defy gravity

Much of the knowledge about the architecture of plants is rooted in millennia of human efforts to alter plant shapes to make them more suitable for cultivation. It is hard to overstate the importance to human history of some of these changes, says plant molecular geneticist Jiayang Li, who details some of their genetic underpinnings in the Annual Review of Plant Biology. A classic example is the transformation of the ancestor of corn (maize) into a key staple crop for much of the world. It arose from a species of the Central American grasses called teosintes — bushy plants with many branches. Domestication, among other things, abolished that branching, yielding the single-stalked upright corn we plant today.

Much of Li's own research has focused on architectural variation in rice, although the work turns out to have implications for the architecture of plants in general, from lowly mosses to towering trees. Like other grasses, rice grows shoots called tillers — specialized, grain-bearing branches that emerge from the base. In cultivated rice, the angle at which these tillers grow varies widely: Some varieties are squat and wide-spreading, others have shoots that are more upright. Breeders are interested in altering tiller angle because upright plants can be grown more densely, giving farmers more bang for their acreage.

In a key advance, in 2007, a team including Li reported they'd discovered the genetic cause of the spread-out architecture trait. The scientists named the responsible gene TAC1, short for "tiller angle control." A functional TAC1 gene increases rice's tiller angle, leading to open, widely branching plants. Mutations in TAC1 lead to the opposite: plants with erect shoots that reach up, instead of out.

That same year, Li's team and a group in Japan both reported another major achievement: finding a long-sought gene behind a curious trait in some rice varieties that gives plant branches a scruffy, lounging look. The trait, known as "lazy," had intrigued plant breeders and geneticists since the 1930s, when researchers described its extreme manifestation in corn: "The lazy plants grow along the ground, following the unevenness of the surface."

In ordinary rice (left), the hormone auxin helps to tell the plant which direction is up. Auxin transport within the plant goes awry when a gene called LAZY malfunctions, leading to confused plants with sprawling branches (right). | (B. WANG ET AL / AR PLANT BIOLOGY 2018/Courtesy Knowable Magazine)

The cause, it turns out, was errors in a gene that normally makes branches shoot straight up. Li and his colleagues surveyed some 30,000 mutant rice plants to pin down that gene, now called LAZY (names of genes, confusingly, often refer to what happens when a gene is mutated and doesn't work, rather than when it is functioning properly). And they provided convincing evidence for an idea batted around for decades — that lazy plants have muddled perceptions of gravity and that the plant hormone auxin is centrally involved.

Scientists now know that LAZY genes come in multiple versions. Some appear to operate in plant roots, telling them which way is down, probably using similar, hormone-related signals. If those genes are absent or inactive, confused roots grow upward. And researchers now know that LAZY genes exist in numerous plants, including the plums growing in the fruit research station in West Virginia.

A lazy mutant of corn (left) compared with normal corn (right). Such corn mutants were described nearly 100 years ago, but it took 21st century molecular biology to nail down the growth habit’s cause: genetic malfunctions that meddle with responses to gravity. | (T.P. HOWARD III ET AL / PLOS ONE 2014)

Reaching upward and outwards

As our boots crunch along the uneven ground, Dardick points at an errant orchard cat watching our tree tour from a distance. One row of trees stands so upright that a fencepost at the end of it is enough to block the row from view. These regimented trees are "pillar" peaches, and they are favorites of landscapers (one reason: it's easy to get around them with a lawnmower). They also were key to uncovering genes like LAZY and TAC1 at the Shenandoah Valley station.

By comparing ordinary peaches to pillar peaches, a team of station scientists and others in the U.S. and Germany discovered the cause of the pillar trait: mutations in the peach version of TAC1.

(C. DARDICK/Courtesy Knowable Magazine)

The team also found that LAZY was at work in many of their misfits. Just as with the corn plants described nearly 100 years ago, mutations in LAZY made plums grow topsy-turvy, their branches seeking the soil. Apple trees with LAZY mutations have similarly disoriented roots. And when multiple copies of LAZY genes malfunction in the weed Arabidopsis, its roots grow up, its shoots down.

In the last decade, researchers have found that TAC1 influences branch angle in plums, poplar trees, the grass Miscanthus and Arabidopsis, and it appears to affect leaf angle in corn. But LAZY genes have even deeper roots. They're found in all manner of plants, including the evolutionarily older Loblolly pine and even more ancient mosses.

This finding suggests a very old role for LAZY: It may have allowed plants to grow up, literally, when they first colonized land. Plants got their start in water. There, rootless and leafless, they were buoyed, unconcerned with gravity. The transition to land spurred the development of proper roots and stems, and plants then had to figure out up from down. LAZY seems to have allowed plants to orient their above-ground growth away from gravity and up toward the sun.

Scientists think that TAC1 evolved somewhat later, providing a counterpoint to LAZY — ensuring that branches don't only grow straight up, but also reach out. Together, these genes laid critical groundwork for the diversity of plant forms we see today, all seeking sustenance in their own ways.

This kind of research has broad economic implications. Fruit and nut trees bring $25 billion annually in the U.S. alone and there are hefty costs associated with pruning, bending and tying branches; spraying hormones; and the manual labor of picking fruit from an unruly cacophony of limbs. Understanding the genetic controls behind tree architecture could help scientists breed trees that make the whole fruit-farming enterprise more efficient and environmentally friendly.

"Orchard systems are not the most sustainable in the world," Dardick says. "The idea is, if we can modify tree architecture, if we could reduce their size and limit the amount of area they take up, then we could plant them at higher density and potentially increase their sustainability."

Those ambitions aside, Dardick has his hands full trying to answer numerous basic-science questions about how trees do what they do. Researchers still don't know how different tree species set the angles of their branches — going wide like an oak, or arching like an elm. They don't know how trees alter those angles during the course of mature growth, as branches sprout from branches sprouted from branches, until some of them finally point down. Trees are both kindred and foreign to us, their various forms so familiar, but their architectural rules still in so many ways opaque.

"I find myself looking at trees all the time now in a new way; they fill space so beautifully and efficiently," Dardick says. "They are the biggest organism we have that's visible, that's in our face all the time. But there's so much we don't know."

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This article originally appeared in Knowable Magazine, an independent journalistic endeavor from Annual Reviews. Sign up for the newsletter.