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Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus

Jonathan Richards, Shiaoman Chao, Timothy Friesen, Robert Brueggeman
G3 2016 v.6 no.7 pp. 1809-1818
Brachypodium distachyon, Hordeum vulgare, Pyrenophora teres, alleles, bacterial artificial chromosomes, barley, centromeres, chromosome mapping, cultivars, fungi, genetic markers, germ cells, loci, molecular cloning, net blotch, pathogens, phenotype, progeny, quantitative trait loci, virulence
Net form net blotch (NFNB) caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt) is a destructive foliar disease of barley with the potential to cause significant yield loss in major production regions throughout the world. Characterization of diverse genetic resistances to this pathogen show a high level of complexity, with both dominant and recessive resistances identified. The complexity of the host-parasite genetic interactions in this pathosystem has hindered the deployment of effective resistance in barley cultivars, warranting a deeper understanding of the interactions. Here we report on the high-resolution mapping of the dominant susceptibility locus near the centromere of barley chromosome 6H in the barley cultivars Rika and Kombar that are putatively targeted by necrotrophic effectors from Ptt isolates 6A and 15A, respectively. The previous genetic mapping of pathogen virulence QTL in this specific pathosystem identified four major virulence QTL, two from each of the Ptt isolates 6A and 15A, which all appear to target a major susceptibility QTL at the centromeric region of barley chromosome 6H in the cultivars Rika and Kombar. Isolation of these specific virulence QTL by identifying progeny isolates derived from a cross of Ptt isolates 6A × 15A harboring single major virulence loci (VK1, VK2 and VR2) allowed for the Mendelization of single inverse gene-for-gene interactions in a high-resolution population consisting of 2976 Rika × Kombar recombinant gametes. This genetic characterization further resolved the location of the gene(s) at the dominant susceptibility locus, designated SPtt1 (susceptibility to P. teres f. teres 1), that was previously characterized as the recessive rpt.r/rpt.k resistance locus in barley. Brachypodium distachyon synteny was exploited to develop and saturate the Sptt1 region with markers delimiting it to ~0.24 cM. Additionally, the high-resolution genetic markers were physically anchored to BAC MTP contigs to create a partial physical map through the use of several barley sequencing and BAC library resources. The high-resolution map and single virulence QTL progeny phenotyping enabled the refined mapping of specific necrotrophic effector sensitivities to a region of the barley genome containing the susceptibility gene/s Sptt1.R and Sptt1.K that possibly represent tightly linked genes in repulsion or alleles targeted by different necrotrophic effectors. These newly developed barley genomic resources greatly enhance the efficiency of positional cloning efforts in barley as demonstrated by the Sptt1 fine mapping and physical contig identification reported here.