Abstract
The barley disease resistance (R) gene locus mildew locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis hordei and has been introgressed into modern cultivars from diverse germplasms, including the wild relative Hordeum spontaneum. Known Mla disease resistance specificities to B. graminis hordei appear to encode allelic variants of the R gene homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Here, we sequenced and assembled the transcriptomes of 50 H. spontaneum accessions representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, linked neither to geographic origin nor population structure, and could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil (CC) signaling domains that are both capable of eliciting cell death. The presence of positively selected sites located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both CC signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the population. Unexpectedly, known MLA receptor variants that confer B. graminis hordei resistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially as adaptation to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Highlights
The RNA-Seq data generated for this study have been deposited in the National Center for Biotechnology Information Sequence Read Archive (SRA) database (BioProject accession number PRJNA432492, SRA accession number SRP132475)
We revealed a rich sequence diversity of the Rgh1/mildew locus A (Mla) gene family in wild barley accessions representing nine populations distributed throughout the Fertile Crescent in the Middle East
In wild barley Rgh1/Mla sequences can be duplicated or triplicated (Table 1), necessitating a revision of the current view that Mla recognition specificities to B. graminis hordei represent alleles of a single gene (Shen et al 2003)
Summary
Identification of Mla sequences in wild barley accessions. To gain deeper insights into Mla diversity in wild barley populations, we used transcriptome sequencing and assembly to identify Mla sequences in a set of 50 wild barley accessions that represent nine populations distributed throughout the Fertile Crescent (Pankin et al 2018). Presumptive Mla transcripts were extracted from these assemblies by BLAST searches against a database of known Mla sequences (details below) Using this workflow, we were able to efficiently recover the known Mla alleles from all six previously characterized accessions, including those from a complex case in which two Mla copies encoding polymorphic MLA variants are present in a single accession (Supplementary Fig. S1). We were able to efficiently recover the known Mla alleles from all six previously characterized accessions, including those from a complex case in which two Mla copies encoding polymorphic MLA variants are present in a single accession (Supplementary Fig. S1) As this initial test verified the suitability of our experimental and bioinformatics pipeline, we applied this analysis to all wild barley accessions and were able to retrieve Mla candidates for all but five of the 50 analyzed accessions (Table 1). For five accessions, a full-length transcript was identified but, due to a premature stop codon, the predicted proteins were truncated,
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