Genome-wide association mapping of major QTLs for resistance to bacterial leaf-streak disease (Xanthomonas translucens pv. undulosa) in elite hard winter wheat germplasm

Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa ( Xtu ), is an increasing threat to wheat ( Triticum aestivum L .) production in the Northern Great Plains of the United States, where severe epidemics can cause up to 60% yield losses in susceptible genotypes [1]. Despite its growing economic impact, genetic resistance in wheat remains poorly characterized, and only limited resistant germplasm has been identified. For that purpose, this study aimed to evaluate a diverse Regional Germplasm Observation Nursery (RGON) panel composed of elite contemporary winter wheat lines for BLS resistance and to identify genomic regions associated with resistance using genome-wide association studies (GWAS). A total of 412 elite hard winter wheat lines were phenotyped for BLS response under controlled greenhouse conditions using a 1–9 disease severity scale. A broad range of phenotypic responses was observed, although most accessions exhibited moderate susceptibility, with disease severity scores ranging from 3 to 7 (mean = 5.5). Overall, 32 lines were identified as resistant, exhibiting disease severity scores below 3. Multiplex Restriction Amplicon Sequencing (MRASeq) produced 15,368 high-quality SNPs after quality filtering. Population structure analyses revealed five genetically distinct subpopulations. GWAS using BLINK and FarmCPU models identified seven significant marker trait associations (MTAs) on chromosomes 1B, 2B, 3B, 3D, 4 A, 4B, and 6B, respectively, explaining a range of 0.04% to 16.6% of the phenotypic variance. Out of the seven, four are major QTL explaining > 10% phenotypic variance. Chromosome 3B showed strong co-occurrence with previously reported resistance loci, while several loci on 2B, 4 A, 4B, 1B, 6B, and 3D represent putative novel regions for BLS resistance. Seventeen highly resistant lines consistently carried favorable alleles across major loci on chromosomes 3B, 4 A, 4B, and 6B. This study elucidates the genetic architecture of BLS resistance in hard winter wheat adapted to the Northern Great Plains of the US and identifies both known and novel resistance loci. The resistant germplasm and SNP markers reported herein will provide valuable resources for marker-assisted breeding to accelerate the development of BLS-resistant winter wheat cultivars.