QTL rich genomic clusters in wheat: a catalogue for resistance to Puccinia striiformis f. sp. tritici

Abstract

Wheat stripe/yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), remains one of the most significant constraints to global wheat production. Genetic resistance breeding is the most effective, economical, and environmentally sustainable strategy for controlling stripe rust. Over the past two decades, advances in genome sequencing, molecular markers and high-throughput genotyping have led to the reporting of numerous Yr genes and an even greater number of quantitative trait loci (QTL, QYr). Alignment of QYr onto a common refence map is therefore required to consolidate dispersed reports, identify regions of co-localization, and define stable genomic regions underlying stripe rust resistance. In this review, catalogued Yr genes and published stripe rust QTL were systematically compiled from 142 studies and, where sufficient marker information was available, physically re-anchored to the IWGSC RefSeq v2.1 wheat reference genome. This integrative approach enabled consolidation of overlapping loci and delineation of 42 QTL-rich clusters (QRCs). The B-sub genome had the highest number of clusters (20), followed by the A-sub genome (16). The D-sub genome had the least number of clusters (6), with two chromosomes, 5D and 6D, lacking any clusters. Thirteen cloned Yr genes were mapped within these clusters, thereby providing functional validation of QRCs as biologically meaningful reservoirs of resistance. This cluster-based framework provides a practical roadmap for consolidating Yr/QYr loci, prioritizing novel genomic targets, and deploying resistance strategically against evolving pathogen populations.