Tiny DNA Fragments Unlock Hidden Crop Diversity in Seed Banks and Wild Wheat Relatives

Start with a problem breeders have long faced: the genes that could help crops withstand drought, heat, and disease probably already exist somewhere. They sit inside ancient plant varieties and half-forgotten seed collections, buried among millions of small DNA differences that are hard to pick out. At King Abdullah University of Science and Technology, KAUST, researchers are working with a different way of reading crop genomes to find them, and their recent work appears in the journal Nature Genetics.

The usual method compares a plant's DNA against a single reference genome. The newer approach treats each genome as a collection of k-mers, short strings of genetic code typically a few dozen bases long. Each acts like a molecular barcode, so scientists can quickly tell which fragments appear in which plants. Because of that, variation can be compared across thousands of samples at once. The source describes the method as opening a window onto the diversity within corn, rice, and other major food crops that feed billions of people and face mounting pressure from climate change.

Simon Krattinger, an associate professor of plant science at KAUST, describes the logic plainly. Representing genomes as k-mer collections, he says, gives a scalable way to capture and compare diversity across large datasets. The goal is to rapidly identify, test, and bring genetic diversity for specific genes into crop improvement pipelines. He calls it a significant change in how breeders and researchers will use gene banks in the future, turning seed banks from static archives into dynamic research resources.

Several KAUST faculty in the Plant Science program, including Ikram Blilou, Jesse Poland, Rod Wing, and Brande Wulff, are applying k-mer methods to crops and desert-adapted plants. Those include date palm, pomegranate, thorn jujube, and other species native to Saudi Arabia. Wheat, though, shows the value of the approach most clearly.

In 2024, Krattinger and Wulff led the creation of a genomic resource for Tausch's goatgrass, Aegilops tauschii, a wild grass that contributed part of bread wheat's complicated genome. The team sequenced dozens of goatgrass plants collected across the species' natural range, from Turkey in the west to China in the east. They broke each genome into millions of k-mers and merged the overlapping fragments into a large searchable database. Comparing goatgrass with modern wheat varieties let them measure how much genetic diversity was lost over thousands of years of domestication.

Krattinger says those missing genes are the raw material for selection and breeding, and that reintroducing them is a key priority. As a proof of concept, the team focused on one goatgrass gene that protects against a destructive fungal pathogen. He says it offers a promising starting point for breeders trying to develop wheat that better resists fungal infection, a major cause of yield loss worldwide.

More recently, Krattinger and his former Ph.D. student Emile Cavalet-Giorsa used k-mer analysis to trace the origin of grain retention, the change that let wheat be harvested. Wild cereals normally shatter their seed heads, scattering grain, which helps reproduction but complicates harvest. Early farmers selected plants whose seeds stayed on the stalk. The analysis showed this was not the product of a single mutation, as previously believed. Several mutations that keep grains attached appeared in wild wheat populations tens of thousands of years before agriculture began. Scattered across different wild populations, they were likely combined and selected later by early farmers.

The broader lesson the KAUST team draws is that many traits needed for future crops may already be waiting in seed banks and wild plants. What to watch is whether these collections become searchable maps of crop diversity for breeders, and whether the finding about pre-existing grain-retention variants changes how wheat's domestication is told.