QTL mapping of oat crown rust resistance in Australian fields and identification of a seedling resistance locus in oat line GS7

Authors: NGUYEN, DUONG - Commonwealth Scientific And Industrial Research Organisation (CSIRO); LEWIS, DAVID - Commonwealth Scientific And Industrial Research Organisation (CSIRO); HENNINGSEN, EVE - Commonwealth Scientific And Industrial Research Organisation (CSIRO); SU, ZHOUYANY - Commonwealth Scientific And Industrial Research Organisation (CSIRO); RATTERY, ALLAN - Intergrain Pty Ltd; MARGO, ROHIT - Commonwealth Scientific And Industrial Research Organisation (CSIRO); SPERCHNEIDER, JANA - Commonwealth Scientific And Industrial Research Organisation (CSIRO); Esvelt Klos, Kathy; Yimer, Belayneh; DODDS, PETER - Commonwealth Scientific And Industrial Research Organisation (CSIRO); FIGUEROA, MELANIA - Commonwealth Scientific And Industrial Research Organisation (CSIRO)

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/27/2025
Publication Date: 1/19/2026
Citation: Nguyen, D.T., Lewis, D., Henningsen, E.C., Su, Z., Rattery, A., Margo, R., Sperchneider, J., Esvelt Klos, K.L., Yimer, B.A., Dodds, P.N., Figueroa, M. 2026. QTL mapping of oat crown rust resistance in Australian fields and identification of a seedling resistance locus in oat line GS7. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-025-05145-x.
DOI: https://doi.org/10.1007/s00122-025-05145-x

Interpretive Summary: Crown rust caused by a fungal pathogen is the main production constraint of oats worldwide. The development of oat cultivars with resistance to crown rust is key for sustainable disease control. In this study two groups of oats were looked at to identify parts of their DNA that helps them fight off the disease in real field conditions. The study found seven key regions in the oat DNA (called QTL) that are associated with resistance to crown rust. The study also developed DNA markers (tools to find specific genes responsible for resistance) to help oat breeders easily include this resistance in new oat varieties. Overall, the resistance identified in this study may support the effort to develop oat varieties with durable crown rust resistance , thereby increasing the productivity of oats and the income of oat growers.

Technical Abstract: The development of oat cultivars with resistance to crown rust is key for sustainable disease control. This study examined two recombinant inbred line populations, Provena x GS7 and Boyer x GS7, to identify adult plant resistance QTL in Australian fields. Seven distinct QTL associated with oat crown rust resistance were identified, with KASP markers developed for SNPs tightly linked to the four most significant QTL on chromosomes 4A and 7A. A major QTL named QPc_GS7_4A.2 with resistance allele derived from oat line GS7 was mapped to chromosome 4A, overlapping with genomic regions previously associated with both the all-stage resistance gene Pc61 and adult plant resistance. Genetic mapping for rust resistance at seedling stage using a subset of Provena x GS7 lines with contrasting alleles at QPc_GS7_4A.2 confirmed the role of this locus on seedling resistance likely by Pc61. Furthermore, we found similar resistance profiles between GS7 and the Pc61 differential line against 20 Puccinia coronata f. sp. avenae isolates at the seedling stage. Haplotype analysis of QPc_GS7_4A.2 in the oat crown rust differential set and an oat collection revealed the resistance haplotype in lines previously postulated to carry resistance gene Pc61, including Coker234, Quoll, Warrego, Wizard, and Barcoo. These results suggest that the QTL QPc_GS7_4A.2 is closely linked to the Pc61 locus on chromosome 4A. The KASP markers associated with Pc61 and QTL identified in this study will be valuable tools, allowing breeders to efficiently integrate the resistance allele for gene combinations in new cultivars, particularly in regions where Pc61 remains effective.