Fine Mapping of the All-Stage Stripe Rust Resistance Gene Yr4EL and Its Utilization in Wheat Resistance Breeding

Tetraploid Thinopyrum elongatum represents a valuable tertiary genetic pool for wheat improvement, harbouring numerous valuable agronomic traits. Our previous study identified Yr4EL, which confers all-stage resistance to stripe rust, was initially characterized from the tetraploid Th. elongatum chromosome (chr) 4E. To further fine-map Yr4EL, we generated 140 chr 4E structural variants using ⁶⁰Co-γ irradiation, ph1b-induced, and double monosomy centromere breakage-fusion methods. All variants were cytogenetically characterized using genomic in situ hybridization and fluorescence in situ hybridization. These variants comprised 90 distinct chr 4E structural variants, including 20 fragment deletions, 14 large segment translocations, 19 whole-arm translocations, 10 chr 4E insertion translocations, and 27 terminal small fragment translocations. A high-resolution chr 4E physical map was constructed using molecular markers, delineated into 15 distinct bins. Subsequently, the diploid Th. elongatum reference genome (ASM1179987v1) enabled the fine-mapping of Yr4EL to a 1.8 Mb interval within the distal chr 4EL. Transcriptomic profiling, evolutionary analysis, and qRT-PCR validation identified five genes that might be the Yr4EL candidate. In addition, we deployed Yr4EL into susceptible common wheat varieties, conferring effective stripe rust resistance without a yield penalty, demonstrating its high potential value for wheat breeding programmes.