Multiple wheat genomes reveal global variation in modern breeding

TLDR

Advances in genomics have accelerated crop improvement, yet wheat breeding lags because of its large, complex genome and limited multi‑line assembly data. The study generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore genomic diversity among breeding lines and to provide a foundation for functional gene discovery and breeding of next‑generation cultivars. The authors illustrate the genomes’ utility by detailing a multi‑genome‑derived NLR protein repertoire for disease resistance and characterizing the insect‑resistance gene Sm1. Comparative analysis uncovered extensive structural rearrangements, wild‑relative introgressions, and gene‑content differences reflecting breeding for adaptation, yield, quality, and stress resistance.

Abstract

Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4,5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.