Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D

Authors: Rivera-Burgos, Luis; VANGESSEL, CARL - North Carolina State University; GUEDIRA, MOHAMMED - North Carolina State University; Smith, Jared; MARSHALL, DAVID - Retired ARS Employee; Jin, Yue; Rouse, Matthew; Brown-Guedira, Gina

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2024
Publication Date: 8/19/2024
Citation: Rivera-Burgos, L.A., Vangessel, C., Guedira, M., Smith, J.H., Marshall, D., Jin, Y., Rouse, M.N., Brown Guedira, G.L. 2024. Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D. Journal of Theoretical and Applied Genetics. 137: Article 206. https://doi.org/10.1007/s00122-024-04702-0.
DOI: https://doi.org/10.1007/s00122-024-04702-0

Interpretive Summary: Highly virulent races of the pathogen causing wheat stem rust present a major challenge to global wheat production. Growing resistant varieties is the most economically feasible method of disease control and wheat breeders strive to develop lines having more than one resistance gene to increase durability. Reliable DNA markers that allow tracking of resistance genes are needed for deployment strategies to combat highly virulent pathogen races. In this study, we used populations derived from breeding line MD01W28-08-11 and the cultivar AGS200 to locate a resistance gene to the short arm of wheat chromosome 6D where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. We exploited new DNA sequencing data to enrich the region around the gene and identify a predictive DNA marker. Evaluation of our new assays demonstrate that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in complex regions of the genome.

Technical Abstract: The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.