title: Transcriptome and allele specificity associated with a 3BL locus for Fusarium crown rot resistance in bread wheat.
abstract: Fusarium pathogens cause two major diseases in cereals, Fusarium crown rot (FCR) and head blight (FHB). A large-effect locus conferring resistance to FCR disease was previously located to chromosome arm 3BL (designated as Qcrs-3B) and several independent sets of near isogenic lines (NILs) have been developed for this locus. In this study, five sets of the NILs were used to examine transcriptional changes associated with the Qcrs-3B locus and to identify genes linked to the resistance locus as a step towards the isolation of the causative gene(s). Of the differentially expressed genes (DEGs) detected between the NILs, 12.7% was located on the single chromosome 3B. Of the expressed genes containing SNP (SNP-EGs) detected, 23.5% was mapped to this chromosome. Several of the DEGs and SNP-EGs are known to be involved in host-pathogen interactions, and a large number of the DEGs were among those detected for FHB in previous studies. Of the DEGs detected, 22 were mapped in the Qcrs-3B interval and they included eight which were detected in the resistant isolines only. The enrichment of DEG, and not necessarily those containing SNPs between the resistant and susceptible isolines, around the Qcrs-3B locus is suggestive of local regulation of this region by the resistance allele. Functions for 13 of these DEGs are known. Of the SNP-EGs, 28 were mapped in the Qcrs-3B interval and biological functions for 16 of them are known. These results provide insights into responses regulated by the 3BL locus and identify a tractable number of target genes for fine mapping and functional testing to identify the causative gene(s) at this QTL.
authors.affiliation: CSIRO Agriculture Flagship, St Lucia, QLD, Australia; Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.affiliation: CSIRO Agriculture Flagship, St Lucia, QLD, Australia.
authors.forename: Jiri
authors.initials: J
authors.lastname: Stiller
authors.affiliation: National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain, ACT, Australia.
authors.forename: Colin
authors.initials: C
authors.lastname: Cavanagh
authors.affiliation: CSIRO Agriculture Flagship, Black Mountain, ACT, Australia.
authors.forename: Penghao
authors.initials: P
authors.lastname: Wang
authors.affiliation: CSIRO Agriculture Flagship, St Lucia, QLD, Australia.
authors.forename: Donald
authors.initials: D
authors.lastname: Gardiner
authors.affiliation: INRA-UBP Joint Research Unit 1095, Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Choulet
authors.affiliation: INRA-UBP Joint Research Unit 1095, Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China.
authors.forename: You-Liang
authors.initials: YL
authors.lastname: Zheng
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China.
authors.forename: Yuming
authors.initials: Y
authors.lastname: Wei
authors.affiliation: School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
authors.forename: Guijun
authors.initials: G
authors.lastname: Yan
authors.affiliation: National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.affiliation: CSIRO Agriculture Flagship, St Lucia, QLD, Australia.
authors.forename: John M
authors.initials: JM
authors.lastname: Manners
authors.affiliation: CSIRO Agriculture Flagship, St Lucia, QLD, Australia; School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
authors.forename: Chunji
authors.initials: C
authors.lastname: Liu
mesh_terms: D000483:Alleles; D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D060467:Disease Resistance / Q000235:genetics; D005670:Fusarium / Q000502:physiology*; D018506:Gene Expression Regulation, Plant; D005838:Genotype; D054884:Host-Pathogen Interactions; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D059467:Transcriptome; D014908:Triticum / Q000235:genetics* / Q000382:microbiology*