Quantitative trait loci from two genotypes of oat (Avena sativa L.) conditioning resistance to Puccinia coronata

Authors: Babiker, Ebrahiem; Gordon, Tyler; OBERT, DON - Limagrain Cereal Seeds; JACKSON, ERIC - General Mills, Inc; HARRISON, STEPHEN - Louisiana State University Agcenter; Chao, Shiaoman; Carson, Martin; Bonman, John

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/6/2014
Publication Date: 1/22/2015
Publication URL: http://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-04-14-0114-R
Citation: Babiker, E.M., Gordon, T.C., Obert, D.E., Jackson, E.W., Harrison, S.A., Chao, S., Carson, M.L., Bonman, J.M. 2015. Quantitative trait loci from two genotypes of oat (Avena sativa L.) conditioning resistance to Puccinia coronata. Phytopathology. 105(2):239-245.

Interpretive Summary: Crown rust is the most important disease of oat worldwide. A key problem in rust disease management is that new resistant cultivars often become susceptible over time due to the evolution of new pathogen races. One means to overcome this problem is to develop new oat cultivars with ‘partial’ resistance, which could prove to be more durable than other types of disease resistance. To further this goal, we studied the inheritance of partial resistance in two oat lines, the cultivar ‘CDC Boyer’ from Canada and the breeding line 94197A1-9-2-2-2-5 from Indiana. Newly developed oat molecular markers, called single nucleotide polymorphisms (SNPs), were used to ‘genotype’ the population of plants developed by crossing the resistant lines with a susceptible line. With this method we found that there is a locus for partial resistance on chromosome 19A of CDC Boyer and on chromosome 13A in the Indiana oat line. We further used DNA sequence information associated with the oat SNP markers and the complete rice genome sequence available online to identify ‘candidate genes’ that might be similar to the oat genes responsible for the partial resistance from the two oat chromosomes. Our results are a first step towards breeding new oat cultivars with longer lasting resistance to crown rust disease.

Technical Abstract: Developing oat cultivars with partial resistance to crown rust would be beneficial for disease management. Two recombinant inbred line (RIL) populations were derived by crossing the susceptible cultivar ‘Provena’ with two partially resistant sources, ‘CDC Boyer’ and breeding line 94197A1-9-2-2-2-5. The populations were evaluated for crown rust severity in the field at Louisiana State University (LSU) in 2009 and 2010 and at the Cereal Disease Laboratory (CDL) in St. Paul, Minnesota in 2009, 2010, and 2011. An iSelect platform containing assays for 5744 oat single nucleotide polymorphisms (SNPs) was used to genotype the populations. From the 2009 CDL test, linkage analyses revealed two QTL for partial resistance in the Provena/CDC Boyer population on chromosome 19A. One of the 19A QTL was also detected in the 2009 LSU test. These QTL explained 10-15% and 11-20% of the phenotypic variation. Another QTL for partial resistance, explaining 10-11% of the phenotypic variation was detected in on chromosome 12D in the CDL 2009 test. In the Provena/94197A1-9-2-2-2-5 population, only one QTL for partial resistance was detected on chromosome 13A in the CDL 2011 test. This QTL explained 19-35% of the phenotypic variation. Only the 13A QTL from the Provena/94197A1-9-2-2-2-5 population was validated in CDC Boyer /94197A1-9-2-2-2-5 population in the CDL 2010 and 2011 tests. This QTL explained 18-19% and 28-53% of the phenotypic variations respectively. To find candidate genes for resistance within each of the detected QTL, the significant SNP markers sequences were used as queries for BLASTN searches against the rice genome database. Fifteen candidate genes were identified on chromosomes 4 and 6 of rice. These genes could be potential targets for further marker develop and gene identification from the two resistant parents.