Skip to main content
ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Improvement Research » Research » Publications at this Location » Publication #430066
Research Project: Improvement of Disease and Pest Resistance in Barley, Durum, Oat, and Wheat Using Genetics and Genomics

Location: Cereal Crops Improvement Research

Title: Development of diagnostic markers for Lr53, Lr56, and Lr59 to facilitate deployment of leaf rust resistance in wheat

Author
item JUNG, WOO-JOO - North Dakota State University
item GUDI, SANTOSH - North Dakota State University
item MARAIS, FRANCOIS - North Dakota State University
item Gupta, Rajeev
item GILL, UPINDER - North Dakota State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/12/2025
Publication Date: 1/9/2026
Citation: Jung, W., Gudi, S., Marais, F., Gupta, R., Gill, U. 2026. Development of diagnostic markers for Lr53, Lr56, and Lr59 to facilitate deployment of leaf rust resistance in wheat. Meeting Abstract. Poster No. P763.

Interpretive Summary:

Technical Abstract: Leaf rust, caused by Puccinia triticina (Pt), continues to erode wheat yields and durability of resistance, prompting ongoing efforts to discover and deploy effective Lr genes from wild relatives. We investigated three introgressed resistance genes, Lr53 (from Triticum dicoccoides), Lr56 (from Aegilops sharonensis), and Lr59 (from Ae. peregrina), that map to telomeric regions of chromosome 6 but have lacked robust diagnostic markers. We combined RNA-seq with comparative genomics to (i) delineate the chromosomal boundaries of the introgressions and (ii) develop Kompetitive Allele-Specific PCR (KASP) markers suitable for marker-assisted selection. RNA-seq reads from translocation lines and their recurrent parents were aligned to the wheat reference genome and summarized as chromosome-wide coverage profiles. Regions with pronounced coverage depletion in the translocation lines indicated alien chromatin, 6B:0-696.8 Mb for Lr53, 6A:0–2.4 Mb for Lr56, and 6B:0–6.9 Mb for Lr59, along with near-background alignment on chromosome 1A. Using genes within the minimal shared interval, we interrogated homologs in T. dicoccoides and Ae. sharonensis, filtered reciprocal BLAST hits, and mined single-nucleotide polymorphisms (SNPs) conserved in the donors but absent across wheat genomes. Six candidate SNPs were converted to KASP and two of them (markers ‘contig_8085_1(1)’ and ‘contig_8085_1(2)’) effectively distinguished the Lr53, Lr56, and Lr59 translocation lines from their respective non-translocation parents. In two doubled-haploid populations segregating for Lr53 or Lr56, these markers co-segregated with resistance to race MNPSD, validating their utility for line classification. When applied to diverse developing germplasm, the markers also flagged most Lr53/Lr56/Lr59-positive lines but occasionally grouped a subset of Lr-negative entries with positives, indicating background-dependent specificity and underscoring the importance of parental controls and, where possible, phenotypic confirmation. To nominate candidates for Lr56, we exploited synteny between wheat 6A (0–2.4 Mb) and Ae. sharonensis 6S, identifying an ~8.9-Mb orthologous window that contains multiple NLRs and a wall-associated kinase gene, WAK5. qRT-PCR following MNPSD inoculation showed increased expression of NLR7 and WAK5 at 1 day post inoculation (dpi) and at 2 dpi, respectively, making them plausible candidates underlying the Lr56 locus. Collectively, this study (i) demonstrates a cost-effective RNA-seq coverage approach to localize alien segments at chromosome scale, (ii) delivered two operational KASP assays to track three high-value Lr introgressions, and (iii) prioritized a small set of defense-related genes for functional validation and eventual cloning. These tools will facilitate pyramiding and stewardship of leaf-rust resistance in wheat improvement programs.