title: De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure.
abstract: Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes.
authors.affiliation: School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia.
authors.forename: Camilla Beate
authors.initials: CB
authors.lastname: Hill
authors.affiliation: ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Cassin
authors.affiliation: School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia.|School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Keeble-Gagnère
authors.affiliation: ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia.
authors.forename: Monika S
authors.initials: MS
authors.lastname: Doblin
authors.affiliation: ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia.
authors.forename: Antony
authors.initials: A
authors.lastname: Bacic
authors.affiliation: School of BioSciences, The University of Melbourne, Parkville, Vic 3010, Australia.
authors.forename: Ute
authors.initials: U
authors.lastname: Roessner
mesh_terms: D020869:Gene Expression Profiling; D017343:Genes, Plant; D005838:Genotype; D001467:Hordeum / Q000235:genetics*; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics / Q000502:physiology*; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics*; D059467:Transcriptome