Genomic and Molecular Characterization of Wheat Streak Mosaic Virus Resistance Locus () in Common Wheat ( L.)

Wheat streak mosaic virus (WSMV) is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains of the United States. The locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in wheat and aid the development of perfect markers for breeding. In this study, linkage mapping in a doubled-haploid (DH) mapping population confirmed as a major locus conferring WSMV resistance in wheat. The flanking markers were mapped to a 4.0 Mbp region at the distal end of chromosome 3BS containing 142 candidate genes. Eight haplotypes were identified from seventeen wheat genotypes collected from different agroecological zones, indicating that lies in a dynamic region of the genome with extensive structural variation and that it is likely a rare allele in most available genome assemblies of common wheat varieties. Exome sequencing of the variety "Snowmass", which carries , revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the interval. Six of these genes are differentially expressed in "Snowmass" compared to "Antero," a variety lacking , including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A assembly of unmapped RNA-seq reads identified nine transcripts expressed only in "Snowmass," three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying and provides a list of candidate genes for subsequent validation.