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

• Published in: Scientific reports Vol. 6; no. 1; p. 31558
• Main Authors: Hill, Camilla Beate, Cassin, Andrew, Keeble-Gagnère, Gabriel, Doblin, Monika S., Bacic, Antony, Roessner, Ute
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.08.2016; Nature Publishing Group
• Subjects: 631/114/2785; 631/1647/514/1949; 631/208/212/2019; 631/449/2661/1797; 631/61/191/2018; Barley; Cell walls; Cultivars; Elongation; Gene expression; Gene Expression Profiling; Generalized linear models; Genes, Plant; Genetic diversity; Genomes; Genotype; Genotypes; Hordeum - genetics; Humanities and Social Sciences; multidisciplinary; Nucleotide sequence; Plant breeding; Plant Roots - drug effects; Plant Roots - genetics; Plant Roots - physiology; Salinity; Salinity effects; Salt Tolerance - genetics; Science; Statistical analysis; Sugar; Transcriptome
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep31558

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.