GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE83237 Query DataSets for GSE83237
Status Public on Oct 05, 2016
Title Identification of avirulence genes in the barley powdery mildew fungus (Bgh) by RNA-sequencing and transcriptome-wide association analysis on a set of Bgh isolates
Organism Blumeria graminis f. sp. hordei
Experiment type Expression profiling by high throughput sequencing
Summary Disease resistance (R) genes encoding intracellular nucleotide-binding domain and Leucine-rich repeat proteins (NLRs) are key components of the plant innate immune system and typically detect the presence of isolate-specific avirulence (AVR) effectors from pathogens. NLRs define the fastest evolving gene family of flowering plants and are often arranged in gene clusters containing multiple paralogs, contributing to extensive copy number and allele-specific NLR variation within a host species. Barley mildew resistance gene locus A (MLA) represents one of only few R genes that have been subject to extreme functional diversification, resulting in allelic resistance specificities each recognizing a cognate but largely unidentified AVRA gene of the powdery mildew fungus, Blumeria graminis f sp hordei (Bgh). We performed RNA-sequencing of Bgh-infected barley leaves at two different time-points to obtain transcriptome data for 16 Bgh isolates, containing different AVRA genes. Subsequently, we analyzed the expression levels in the different isolates with a specific focus on previously described candidate secreted effectors (CSEPs) and additionally performed a transcriptome-wide association analysis including these 16 isolates and the previously published reference isolate DH14. These analyses identified AVRA1 and AVRA13, encoding two CSEPs that are recognized by MLA1 and MLA13 alleles, respectively. The avirulence function of both candidates could be verified by transient expression of the effector genes in barley leaves or protoplasts that was sufficient to trigger an MLA1 or MLA13 allele-specific cell death response. AVRA1 recognition by MLA1 is also retained in transgenic Arabidopsis lines.
Overall design Detached leaves of the barley cultivar Pallas or Manchuria were infected with 16 different Bgh isolates, each containing different AVRA effectors. For each isolate, samples were collected at 18 and 48 hours post inoculation (hpi), resulting in a total of 32 RNA-seq samples that were analyzed.
Contributor(s) Lu X, Kracher B, Maekawa T, Schulze-Lefert P
Citation(s) 27702901, 30777147
Submission date Jun 10, 2016
Last update date May 15, 2019
Contact name Barbara Kracher
Organization name Max Planck Institute for Plant Breeding Research
Department Plant-Microbe Interactions
Street address Carl-von-Linné-Weg 10
City Cologne
ZIP/Postal code 50829
Country Germany
Platforms (1)
GPL22002 Illumina HiSeq 2500 (Blumeria graminis f. sp. hordei)
Samples (32)
GSM2197460 K1_16h
GSM2197461 K1_48h
GSM2197462 NCI_16h
BioProject PRJNA325323
SRA SRP076402

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83237_CountTable_BghIsolates_perTP_raw.txt.gz 284.9 Kb (ftp)(http) TXT
GSE83237_TranscriptomeVariants_BghIsolates.vcf.gz 37.1 Mb (ftp)(http) VCF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap