The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of fungal haustoria. It is not known which of these candidate genes have allelic variation that contributes to the natural variation in powdery mildew resistance, because many of them may be highly conserved within the barley species and may act downstream of the basal resistance reaction. Twenty-two expressed sequence tag or cDNA clone sequences that are likely to play a role in the barley-Blumeria interaction based on transcriptional profiling, gene silencing, or overexpression data, as well as mlo, Ror1, and Ror2, were mapped and considered candidate genes for contribution to basal resistance. We mapped the quantitative trait loci (QTL) for powdery mildew resistance in six mapping populations of barley at seedling and adult plant stages and developed an improved high-density integrated genetic map containing 6,990 markers for comparing QTL and candidate gene positions over mapping populations. We mapped 12 QTL at seedling stage and 13 QTL at adult plant stage, of which four were in common between the two developmental stages. Six of the candidate genes showed coincidence in their map positions with the QTL identified for basal resistance to powdery mildew. This co-localization justifies giving priority to those six candidate genes to validate them as being responsible for the phenotypic effects of the QTL for basal resistance.

Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 x 'Vada' mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei.

Summary The genetic basis of nonhost resistance of barley to nonadapted formae speciales of Blumeria graminis is not known, as there is no barley line that is susceptible to these nonadapted formae speciales, such as the wheat powdery mildew pathogen, Blumeria graminis f.sp. tritici (Bgt). Barley accessions with rudimentary susceptibility to an isolate of the nonadapted Bgt were identified. Those accessions were intercrossed in two cycles and two lines, called SusBgtSC and SusBgtDC, with substantial susceptibility to Bgt at the seedling stage were selected. The quantitative variation among barley accessions and in the progenies after convergent crossing suggests a polygenic basis for this nonhost resistance. Both lines allowed an unusually high level of haustorium formation and colony development by Bgt. The SusBgt lines and their ancestor lines also allowed haustorium formation and conidiation by four out of seven isolates of other nonadapted B. graminis forms. Analysis of the infection process suggested that nonhost resistance factors are specific to the form and developmental stage of B. graminis. Resistances to establishment (first haustorium), colonization (subsequent haustoria) and conidiation are not associated. The lines developed will be of use in elucidating the genetic basis of nonhost resistance to Bgt in barley, and in gene expression and complementation studies on nonhost resistance.

Association analysis based on linkage disequilibrium has become a common and powerful approach for detection of QTLs underlying complex agronomic traits including drought tolerance. To determine marker/trait association, 148 modern European spring barley cultivars were evaluated under drought stress. Associations of morphological traits with AFLP/SSR markers were investigated based on the mixed linear model using the TASSEL3.0. Population structure was estimated using various methods including Bayesian clustering model by STRUCTURE software, PCoA analysis, NJ dendrogram and Hierarchical Clustering. Linkage disequilibrium patterns were explored among the whole genome and each chromosome separately. All the analysis for population structure divided the population into two sub-groups. Linkage disequilibrium analysis showed that by increasing genetic distance, LD decreases. Totally, 167 significant marker trait associations were found which delineated into 65 QTLs in both treatments. Two stable QTLs on 5H at 86.880 cM were detected for Internode Length and on 3H at 126.421 cM for flag leaf length in drought stress treatment. Fourteen QTLs were co-localized with previously reported QTLs and others were novel. The results indicate that these putative genomic regions contain genes that have pleiotropic effects on morphological traits in drought condition.