Structural genomics of the barley Mla powdery mildew resistance complex

Powdery mildew of barley, caused by Blumeria ( Erysiphe) graminis f. sp. hordei, is a model system for investigating the mechanism of gene-for-gene interaction between large-genome cereals and obligate-fungal pathogens. We used AFLP markers to saturate the Mla region in a high-resolution mapping population. These tightly linked genetic markers were used to develop a physical contig of YAC and BAC clones spanning the Mla cluster. A lowpass and BAC-end sequencing strategies revealed three distinct NBS-LRR resistance-gene homologue (RGH) families in the contig. Genetic and physical mapping delimited the RGH families to a 240-kb interval. Recombination suppression was found within the RGH.; The 261,265 by complete sequence of two overlap BACs spanning the Mla locus revealed thirty-two protein-encoding and two tRNA ser genes. The protein-encoding genes are organized as three gene-rich islands separated by two 40-kb complexes of nested transposable elements and a gene-poor region. Sixteen of these genes are plant-defense related; 12 of these 16 are associated with defense against powdery mildew disease, but function in different signaling pathways. The clustering of those plant defense-related genes is similar to that in the mammalian major histocompatibility complex (MHC). Evolutionary analysis indicated that the present Mla region was developed over 7 million years through several duplication and inversion events in addition to nested TE insertion.; A heterochromatic knob-like sequence, KL1HS1, is present in this barley Mla complex. KL1HS1 is hypermethylated and recombination in the region is suppressed. KL1HS1 combines the structural characteristics of the two cloned knobs from Arabidopsis. This knob-like sequence is comprised of a gene-poor core with diverse tandem repeats, a genedense island resulting from a 4Q-kb tandem duplication, and a nested transposable element complex. In contrast to other knobs, KL1HS is gene-rich and transcriptionally active. A positional shift was observed and this shifting resulted from a bidirectional expansion of KL1HS1. Extensive arrays of various tandem duplications in the knob are postulated to arise from a DNA replication slippage mechanism in combination with a hairpin structure of the knob-associated repeats.