The hypersensitive response (HR) is one of the most-efficient forms of plant defense against biotrophic pathogens, and results in localized cell death and the formation of necrotic lesions; however, the molecular components of pathways leading to HR remain largely unknown. Barley ( Hordeum vulgare ssp. vulgare L.) cDNAs for putative hypersensitive-induced reaction ( HIR) genes were isolated based on DNA and amino-acid homologies to maize HIR genes. Analyses of the cDNA and genomic sequences and genetic mapping found four distinct barley HIR genes, Hv-hir1, Hv-hir2, Hv-hir3 and Hv-hir4, on chromosomes 4(4H) bin10, 7(5H) bin04, 7(5H) bin07 and 1(7H) bin03, respectively. Hv-hir1, Hv-hir2 and Hv-hir3 genes were highly homologous at both DNA and the deduced amino-acid level, but the Hv-hir4 gene was similar to the other genes only at the amino-acid sequence level. Amino-acid sequence analyses of the barley HIR proteins indicated the presence of the SPFH protein-domain characteristic for the prohibitins and stomatins which are involved in control of the cell cycle and ion channels, as well as in other membrane-associated proteins from bacteria, plants and animals. HIR genes were expressed in all organs and developement stages analyzed, indicating a vital and non-redundant function. Barley fast-neutron mutants exhibiting spontaneous HR (disease lesion mimic mutants) showed up to a 35-fold increase in Hv-hir3 expression, implicating HIR genes in the induction of HR.

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe [teleomorph Gibberella zea (Schwein)], reduces quality of harvested barley (Hordeum vulgare L.) because of blighted kernels and the presence of deoxynivalenol (DON), a mycotoxin produced by the pathogen. CIho 4196, a two-rowed type, is one of the most resistant accessions known in barley; however, it possesses many undesirable agronomic traits. To better understand the genetics of reduced FHB severity and DON accumulation conferred by CIho 4196, a genetic map was generated using a population of recombinant inbred lines derived from a cross between Foster (a six-rowed malting cultivar) and CIho 4196. Quantitative trait loci (QTL) analyses were performed using data obtained from 10 field environments. The possible associations of resistance QTLs and various agronomic and morphological traits in barley also were investigated. The centromeric region of chromosome 2H flanked by the markers ABG461C and MWG882A (bins 6-10) likely (P , 0.001) contains two QTLs contributing to lower FHB severity and plant height, and one QTL each for DON accumulation, days to heading, and rachis node number. The QTL for low FHB severity in the bin 8 region explained from 3 to 9% of the variation, while the QTL in the bin 10 region explained from 17 to 60% of the variation. A QTL for DON accumulation that explained 9 to 14% of the variation was found in the bin 2 region of chromosome 4H. This may represent a new QTL not present in other FHB resistant sources. Resistance QTLs in the bin 8 region and bin 10 region of chromosome 2HL were provisionally designated Qrgz-2H-8 and Qrgz-2H-10, respectively. The QTL for DON accumulation in chromosome 4H was provisionally named QDON-4H-2.

Barley homolog of the Arabidopsis necrotic (disease lesion mimic) mutant HLM1 that encodes the cyclic nucleotide-gated ion channel 4 was cloned. Barley gene was mapped genetically to the known necrotic locus nec1 and subsequent sequence analysis identified mutations in five available nec1 alleles confirming barley homolog of Arabidopsis HLM1 as the NEC1 gene. Two fast neutron (FN) induced mutants had extensive deletions in the gene, while two previously described nec1 alleles had either a STOP codon in exon 1 or a MITE insertion in intron 2 which caused alternative splicing, frame shift and production of a predicted non-functional protein. The MITE insertion was consistent with the reported spontaneous origin of the nec1 Parkland allele. The third FN mutant had a point mutation in the coding sequence which resulted in an amino acid change in the conserved predicted cyclic nucleotide-gated ion channel pore region. The expression of two pathogenesis-related genes, HvPR-1a and beta-1,3-glucanase, was elevated in two FN necrotic lines. Ten other members of the barley cyclic nucleotide-gated ion channel gene family were identified and their position on barley linkage map is reported.

Rpg1 is a stem rust resistance gene that has protected barley from severe losses for over 60 years in the US and Canada. It confers resistance to many, but not all, pathotypes of the stem rust fungus Puccinia graminis f. sp. tritici. A fast neutron induced deletion mutant, showing susceptibility to stem rust pathotype Pgt-MCC, was identified in barley cv. Morex, which carries Rpg1. Genetic and Rpg1 mRNA and protein expression level analyses showed that the mutation was a suppressor of Rpg1 and was designated Rpr1 (Required for P. graminis resistance). Genome-wide expression profiling, using the Affymetrix Barley1 GeneChip containing approximately 22,840 probe sets, was conducted with Morex and the rpr1 mutant. Of the genes represented on the Barley1 microarray, 20 were up-regulated and 33 were down-regulated by greater than twofold in the mutant, while the Rpg1 mRNA level remained constant. Among the highly down-regulated genes (greater than fourfold), genomic PCR, RT-PCR and Southern analyses identified that three genes (Contig4901_s_at, HU03D17U_s_at, and Contig7061_s_at), were deleted in the rpr1 mutant. These three genes mapped to chromosome 4(4H) bin 5 and co-segregated with the rpr1-mediated susceptible phenotype. The loss of resistance was presumed to be due to a mutation in one or more of these genes. However, the possibility exists that there are other genes within the deletions, which are not represented on the Barley1 GeneChip. The Rpr1 gene was not required for Rpg5- and rpg4-mediated stem rust resistance, indicating that it shows specificity to the Rpg1-mediated resistance pathway.

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