Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes

Abstract

Crown rust (Puccinia coronata f. sp. Avenae Erikss.) poses a significant threat to oat production worldwide. The most effective strategy for managing this disease involves identifying, mapping, and deploying resistance genes to develop cultivars with enhanced resistance. In this study, we conducted a meta-analysis of quantitative trait loci (QTLs) linked to crown rust resistance across diverse oat populations and environments. From 11 studies conducted between 2003 and 2024, we selected 167 QTLs, of which 127 were successfully mapped onto an oat consensus linkage map. These QTLs were mainly located on chromosomes of the D and C sub-genomes, showing considerable variation in genetic distances and marker associations. Based on the integration of these QTLs in a meta-QTL (MQTL) analysis, 23 MQTLs were identified for crown rust resistance in the oat genome. Gene mining within the MQTL intervals identified 1526 candidate genes, most of which were located in the D sub-genome. Functional analysis revealed that these genes play key roles in stress response, hormonal regulation, and polyamine metabolism, which are crucial for plant defense. Conserved regulatory elements (cis-acting regulatory element [CAREs]) were also identified in the promoter regions of key resistance genes, indicating their involvement in light response, stress regulation, and hormone signaling. This study represents a significant advancement in understanding the genetic architecture of crown rust resistance in oat and provides a valuable resource for breeding programs focused on improving disease resistance.