De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure

C.B. Hill; A. Cassin; G. Keeble-Gagnère; M.S. Doblin; A. Bacic; U. Roessner

doi:10.1038/srep31558

Back

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure

Journal article

Open access

Peer reviewed

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure

C.B. Hill, A. Cassin, G. Keeble-Gagnère, M.S. Doblin, A. Bacic and U. Roessner

Scientific Reports, Vol.6, Article 31558

2016

DOI: https://doi.org/10.1038/srep31558

Files and links (2)

pdf

de novo.pdfDownload View

Published (Version of Record) Open Access

url

Free to Read *No subscription requiredView

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.

Details

Title: De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
Authors/Creators: C.B. Hill (Author/Creator) - The University of Melbourne
A. Cassin (Author/Creator) - The University of Melbourne
G. Keeble-Gagnère (Author/Creator) - The University of Melbourne
M.S. Doblin (Author/Creator) - The University of Melbourne
A. Bacic (Author/Creator) - The University of Melbourne
U. Roessner (Author/Creator) - The University of Melbourne
Publication Details: Scientific Reports, Vol.6, Article 31558
Publisher: Springer Nature
Identifiers: 991005544110507891
Copyright: © 2016 Macmillan Publishers Limited
Murdoch Affiliation: School of Veterinary and Life Sciences
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Metrics

108 File views/ downloads

60 Record Views

35 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.49 Plant Stress Responses
Web Of Science research areas: Plant Sciences
ESI research areas: Plant & Animal Science