Fig 3 -

a. Genetic linkage map of Pc (TTTG) resistance constructed with Illumina 6K SNPs and oat F5:6 RILs derived from a cross between PI 258731 and PI 573582. The flanking SNP markers are highlighted in red color. b. Genetic linkage map of Pc (QTRG) resistance constructed with Illumina 6K SNPs and oat F5:6 RILs derived from a cross between PI 258731 and PI 573582. The flanking SNP markers are highlighted in red color.</p

S1 File -

Oat crown rust, caused by Puccinia coronata Corda f. sp. avenae Eriks. (Pca), is a major biotic impediment to global oat production. Crown rust resistance has been described in oat diploid species A. strigosa accession PI 258731 and resistance from this accession has been successfully introgressed into hexaploid A. sativa germplasm. The current study focuses on 1) mapping the location of QTL containing resistance and evaluating the number of quantitative trait loci (QTL) conditioning resistance in PI 258731; 2) understanding the relationship between the original genomic location in A. strigosa and the location of the introgression in the A. sativa genome; 3) identifying molecular markers tightly linked with PI 258731 resistance loci that could be used for marker assisted selection and detection of this resistance in diverse A. strigosa accessions. To achieve this, A. strigosa accessions, PI 258731 and PI 573582 were crossed to produce 168 F5:6 recombinant inbred lines (RILs) through single seed descent. Parents and RILs were genotyped with the 6K Illumina SNP array which generated 168 segregating SNPs. Seedling reactions to two isolates of Pca (races TTTG, QTRG) were conditioned by two genes (0.6 cM apart) in this population. Linkage mapping placed these two resistant loci to 7.7 (QTRG) to 8 (TTTG) cM region on LG7. Field reaction data was used for QTL analysis and the results of interval mapping (MIM) revealed a major QTL (QPc.FD-AS-AA4) for field resistance. SNP marker assays were developed and tested in 125 diverse A. strigosa accessions that were rated for crown rust resistance in Baton Rouge, LA and Gainesville, FL and as seedlings against races TTTG and QTRG. Our data proposed SNP marker GMI_ES17_c6425_188 as a candidate for use in marker-assisted selection, in addition to the marker GMI_ES02_c37788_255 suggested by Rine’s group, which provides an additional tool in facilitating the utilization of this gene in oat breeding programs.</div

Fig 1 -

Avena strigosa primary leaf infection type (IT) phenotypes inoculated with two Pca races TTTG and QTGB and shown 14 dpi; A. Susceptible parent, PI573582, with IT 4 B and C. PI 258731 carrying resistance with two different IT: “; N” (TTTG) and “0N” (QTRG).</p

Segregation of F_5:6 573582/<i>258731</i> recombinant inbred lines (RILs) to two <i>Pca</i> races in greenhouse experiments and χ2 test analysis of F_5:6 progeny.

Segregation of F5:6 573582/258731 recombinant inbred lines (RILs) to two Pca races in greenhouse experiments and χ2 test analysis of F5:6 progeny.</p

Phenotypic grouping of <i>A</i>. <i>strigosa</i> accessions by reaction to <i>Pca</i> races (TTTG and QTRG); mean phenotypic values of field resistance (IR, DS, CI) in each phenotypic group.

Phenotypic grouping of A. strigosa accessions by reaction to Pca races (TTTG and QTRG); mean phenotypic values of field resistance (IR, DS, CI) in each phenotypic group.</p

Frequency of the resistant parent allele for three putative PACE markers in each phenotypic group.

Frequency of the resistant parent allele for three putative PACE markers in each phenotypic group.</p

Logarithm of odds (LOD) score profiles of quantitative trait loci (QTL) for field phenotype adjusted for PI 258731 seedling resistance allele, colored dotted lines on linkage group 07 based on multiple interval mapping.

A threshold of LOD = 3.2 was determined by a permutation test with 1000 iterations (P<0.05).</p

Fig 5 -

Disease severity effect plots for major QTL (QPc.FD-AS-AA4), based on the allelic distributions determined at the peak SNP marker of the QTL (GMI_DS_LB_3547) at A. LSU location B. UFL location. The two possible alleles are indicated in each group (AA = alleles associated with resistant parent, BB = alleles associated with susceptible parent).</p

Logarithm of odds (LOD) score profiles of quantitative trait loci (QTL) for field resistance, colored dotted lines on linkage group 07 based on multiple interval mapping.

Linkage group 07 corresponds to 573582/258731 population in Fig 2. The X-axis indicates cM position of the SNPs. The position of the phenotypic markers is indicated with blue star. A threshold of LOD = 3.2 was determined by a permutation test with 1000 iterations (p<0.05).</p

Phenotypic scores for disease severity (DS) at LSU, UFL and MN locations and phenotypic scores for infection reaction (IR) and coefficient of infection (CI) at LSU and UFL locations in the RIL population.

The y-axis in each plot represents the number of lines from the population that display scores shown in the x-axis, while locations are shown on the right y-axis; LSU = Louisiana State University Central Research Station in Baton Rouge, LA, UFL = University of Florida crown rust field nursery in Gainesville, FL, MN = University of Minnesota Matt Moore buckthorn nursery in Saint Paul, MN. Mean score of the parents is indicated in the legend.</p