Scientists Unlock Hidden Regions of Plant Chromosomes, Opening New Doors for Crop Breeding

Scientists in the group of Raphael Mercier at the Max Planck Institute for Plant Breeding Research in Cologne have discovered how to access large regions of the plant genome that have been effectively locked away from breeders for generations. The findings, published this week in Nature Plants, could have significant implications for developing improved crop varieties with better disease resistance, yield, and climate resilience.
 

When plants reproduce sexually, their chromosomes shuffle genetic material through a process called crossover recombination — essentially swapping sections of DNA between chromosome pairs. This reshuffling is what allows breeders to combine desirable traits from different plant varieties. However, large regions of chromosomes surrounding structures called centromeres are effectively off-limits to this process. In many crops, these "cold zones" can be enormous — in wheat and barley, they cover more than half of each chromosome. Genes trapped in these regions are essentially invisible to breeders, who cannot combine or separate them from neighboring traits. In barley, for example, 18% of all genes sit in these inaccessible regions. In tomato, an important gene conferring resistance to a damaging virus is locked in such a region alongside millions of base pairs of unwanted genetic material that breeders have been unable to remove for decades.

The new study identifies three genes — CTF18, SGO2, and SPF2 — that act as gatekeepers, actively preventing genetic recombination near centromeres. When the researchers disabled any one of these genes in the model plant Arabidopsis thaliana, crossovers occurred in regions where they had never been seen before. Further, disabling SPF2 alone increased recombination by more than three times in the previously cold regions. When multiple genes were disabled simultaneously, the effects were even greater, revealing that several independent molecular mechanisms work together to keep these chromosomal regions locked.

Importantly, the plants with disabled genes were largely healthy and fertile, producing normal numbers of seeds. Only the most extreme combinations of mutations caused any reduction in fertility, and no growth defects were observed in any of the mutant plants. This suggests that unlocking these chromosomal regions is biologically safe, at least to a considerable extent.

A particularly promising finding is that plants carrying just one disrupted copy of SPF2 or SGO2 — rather than two — already showed increased recombination in the previously suppressed regions. This so-called co-dominant effect means that the mutations could be more easily deployed in breeding programs without requiring both copies of a gene to be altered.

The three identified genes are conserved across the plant kingdom, and also in more distant species, including in animals.  The researchers believe their findings could be translated to major crops such as wheat, barley, maize, and tomato, where the locked chromosomal regions are even larger. The authors envision that these mutations could be temporarily introduced into breeding lines to unlock desired genetic combinations, and then removed once the job is done — meaning the final crop varieties would not carry the mutations themselves.