Cannabis and Hops Share Ancient Sex Genes

Cannabis plants do not all develop in identical ways. Some form exclusively female flowers, some produce male flowers, and others bear both types.

This distinction is hugely important to growers, as flower sex influences crop quality, breeding choices and harvest schedules.

Scientists have now found a small set of genes that seems to influence these outcomes.

As well as offering insight into cannabis development, the finding shows that cannabis and hops retain ancient sex-related genes connected with flowering, millions of years after the species separated.

The DNA behind plant sex

A narrow section of the cannabis X chromosome contains a concentrated signal governing plant sex, within one sharply defined DNA region.

Matteo Toscani of University College Dublin (UCD) mapped the inheritance of male, female and mixed traits, finding that three adjacent genes repeatedly corresponded with these outcomes.

The same area separates plants bearing only female flowers from those producing both flower types, helping explain how one genome can create several reproductive forms.

Since the effect comes from a compact genetic region rather than one gene alone, the results suggest a coordinated system. Further work is needed to establish how each part shapes the final result.

How sex affects cannabis crops

While most flowering plants contain both male and female structures within a single flower, cannabis generally divides those functions between different plants.

Female Cannabis sativa plants have two X chromosomes, whereas males usually possess one X and one Y chromosome, including genes commonly associated with maleness.

Certain hemp lines depart from this arrangement by developing both types of flower on the same plant, a useful yet complex characteristic for breeders.

“Which of those genes determines whether a plant becomes male or female is unknown,” said the study’s senior author Rainer Melzer, an assistant professor at UCD.

A surprising genetic discovery

Although many people are taught that Y chromosomes determine maleness, the cannabis signal was located on the X chromosome.

The evidence identified a small region of the X chromosome, rather than the Y chromosome, challenging expectations based on humans and many animals.

“We were quite surprised,” said Toscani. The finding was consistent with earlier hemp research involving fibre-type cannabis and directed the team towards genes active before flowers visibly developed as male or female.

Three genes work together

Across 60,000 DNA letters, researchers identified CsREM16, lncREM16 and CsKAN4 – three genes displaying distinct activity patterns.

CsREM16 was active in female and mixed plants, whereas lncREM16 was found mainly in male samples and may suppress female signals.

Mixed-flower plants showed reduced CsKAN4 activity, a change that may relax the hormone control that normally promotes female development.

Rather than a lone gene serving as the switch, the system appears to involve three genes whose activity steers plants towards different sexual forms.

Shared genes in hops and cannabis

Hops, the brewing plant Humulus lupulus, contains related REM16 and KAN4 genes in a corresponding neighbourhood of its X chromosome.

Previous studies placed cannabis and hops on the same ancient sex-chromosome pair, with shared sex-linked genes estimated to be roughly 12 to 28 million years old.

As the newly identified genes occupy this old region, the shared regulatory system probably existed before the two plants diverged.

However, hop plants seldom display the mixed-flower trait, suggesting that the details changed after the lineages split.

Why growers want females

Brewers favour female hop plants because only females produce cones, the papery flower clusters responsible for beer’s aroma and flavour.

Cannabis growers frequently favour female plants because their flower clusters make resin containing high levels of plant compounds called cannabinoids, including cannabidiol.

For fibre hemp, mixed-flower plants may grow more consistently, as fields avoid mismatched timing between male and female plants.

Accurate sex prediction could allow growers to remove unwanted plants early, cutting wasted space, labour and yield losses.

Plant sex is not fixed

The DNA region associated with mixed flowering, called Monoecy1, accounted for around 15% of the trait, indicating that other influences remain involved.

In the team’s second generation, flowering plants comprised 43 percent females, 29 percent mixed plants, and 20.1 percent males.

The maternal background was also significant: male offspring varied from 6.8 percent to 35.9 percent according to the female parent that produced the seeds.

These figures caution breeders that a single DNA marker can inform choices but cannot guarantee the eventual form of every plant.

Evolution left genetic scars

Gene losses were concentrated near the same chromosome end, indicating that the Y chromosome has gradually lost corresponding copies.

The researchers calculated that 40 percent of proteins encoded in this area had no obvious equivalent on the Y chromosome.

This type of loss accumulates when X and Y chromosomes cease exchanging DNA, allowing differences to build up through generations.

In cannabis, the oldest signal of divergence lies close to the newly mapped sex-control region.

Predicting plant sex earlier

Breeders may be able to use this map to create early tests that identify probable plant sex before fields become filled with unwanted flowers.

A leaf sample could indicate whether seedlings carry versions of the region associated with female or mixed-flower development.

Even so, the research identifies candidate genes rather than a completed tool, because scientists must first demonstrate that these genes directly regulate flower development.

Future studies could activate or deactivate the genes and assess whether flower patterns alter.

This new map connects flower sex, crop planning and chromosome evolution through one compact DNA region containing genes shared by cannabis and hops.

For farmers and brewers, the near-term benefit may be improved prediction; direct genetic control will require further testing.