Abstract
There is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.
Highlights
There is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes
Paralogous gene clusters are shown to contribute to important agronomic traits such as adaptation to abiotic and biotic s tresses[10]; plant disease resistance genes such as lectin receptor kinases (LecRK), wall-associated receptor kinases (WAK) and nucleotide-binding leucine-rich repeat (NLR) containing proteins are often organised into clusters[11,12,13]
Differential expression analysis identified 10,567 high confidence (HC) genes that were differentially expressed in response to F. graminearum treatment in at least one of the timepoint x near-isogenic lines (NILs) combinations
Summary
There is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. Based on evidence that stress-responsive genes can be clustered in plant genomes, we designed a pipeline to determine if diverse functionally related genes cluster in the genome, using FHB of wheat as a model Using this pipeline, we captured paralogous and nonhomologous clusters encoding metabolic and non-metabolic genes that were responsive to F. graminearum infection of wheat. We captured paralogous and nonhomologous clusters encoding metabolic and non-metabolic genes that were responsive to F. graminearum infection of wheat These Fusarium-responsive gene clusters (FRGCs) were assessed for their biological significance using gene co-expression analysis and are discussed with respect to their homology with other plants, their links to defence mechanisms, and their proximity to published FHB QTL
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