Genome-wide association mapping of crown rust resistance in oat elite germplasm
Citation
Esvelt Klos, K., Yimer, B.A., Babiker, E.M., Beattie, A.D., Bonman, J.M., Carson, M.L., Chong, J., Harrison, S.A., Ibrahim, A.M.H., Kolb, F.L., McCartney, C.A., McMullen, M., Mitchell Fetch, J., Mohammadi, M., Murphy, J.P., Tinker, N.A. (2017). Genome-wide association mapping of crown rust resistance in oat elite germplasm. Plant Genome, [online] 10(2), http://dx.doi.org/10.3835/plantgenome2016.10.0107
Plain language summary
Crown rust is a fungal disease of oat that is a major constraint to production in many parts of the world. This work represents the first comprehensive study of genetic factors affecting resistance to crown rust using whole-genome-analysis in a diverse set of germplasm tested in many different production environments. We used 2,972 genetic markers in 631 diverse varieties of oat, and looked for associations between markers and crown rust reaction in field conditions as well as under greenhouse conditions where plants were inoculated with specific fungal strains. Overall, we found 29 markers on 12 chromosomes that were predictive of crown rust reaction. Some of these predictions confirmed previous work, while others were indicative of newly-discovered genetic sources of resistance. This work is significant because it integrates known resistance mechanisms that can be found in current germplasm on a single genetic map. The results will facilitate choice of appropriate parents in oat breeding programs, and will provide access to selectable markers to enhance the efficiency of selecting resistant oat varieties.
Abstract
Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat (Avena sativa L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location–years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale. Overall, 29 SNPs on 12 linkage groups were predictive of crown rust reaction in at least one experiment at a genome-wide level of statistical significance. The QTL identified here include those in regions previously shown to be linked with seedling resistance genes Pc48, Pc58a, Pc68, Pc71, Pc91, and PcKM and also with adult-plant resistance and adaptation-related QTL. In addition, QTL on linkage groups Mrg03, Mrg08, and Mrg23 were identified in regions not previously associated with crown rust resistance. Evaluation of marker genotypes in a set of crown rust differential lines supported Pc91 as the identity of QPc.CORE.18.3. The SNPs with rare alleles associated with lower disease scores may be suitable for use in marker-assisted selection of oat lines for crown rust resistance.