k-mer-based approaches to unlock genebank genomics for targeted crop improvement

Abstract

Genebanks have a vital role in safeguarding plant genetic resources and providing access to valuable genetic diversity that is absent from modern breeding gene pools. Yet, a major challenge for using genebank materials in crop improvement programs lies in selecting manageable subsets of accessions that maximize genetic diversity for traits of interest. The integration of genomic information is creating new opportunities to address this challenge. Recent studies have shown that k-mer-based bioinformatic approaches capture and reveal previously hidden functional diversity that is missing in elite cultivars. Here we present a perspective on how such approaches enable a precise identification of allele and haplotype diversity across large genebank collections that can guide the strategic selection of accessions for crop improvement. Incorporating this untapped genetic diversity from genebanks into crop improvement pipelines is increasingly recognized as a crucial strategy for developing climate-resilient cultivars.