Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

12 December 2017

Salinity-induced Alteration of Root-omics in Barley (Hordeum vulgare L.)

William Ho
School of BioScience, University of Melbourne

Due to increases in soil salinity in the temperate region optimal for cultivation, barley (Hordeum vulgare L.) has been suffered from substantial yield loss in Australia during the last decade. To understand the impact of high salinity in different cultivars of barley, de novo transcriptome assemblies of a malting cultivar (cv. Clipper) and a landrace (cv. Sahara) with known contrasting responses to salinity during their seedling stage were generated. However, stemmed from the relatively low level of functional annotations (~23%) of the assemblies in the previous study, gene-clusters enriched and differential transcripts identified upon salt stress were not conclusive. In this study, taking advantage of the newly available barley reference genome (cv. Morex) with substantial improvement in genomic coverage and sequencing depth, more than 78% of the transcripts were functionally annotated. With more than 90% transcript-mapping efficiency achieved, limma-based generalized linear models were then applied to statistically assess treatment-, root zone-, and cultivar-specific differentially expressed genes. From this analysis, we pinpoint contrasting enrichment of gene ontology categories related to secondary metabolism and lipid metabolism between the root-elongation and/or -maturation zone of Clipper and Sahara seedlings. Together with the integrated pathway analyses of the corresponding metabolomes and lipidomes obtained from the same sample-set, we propose that cv. Clipper could adopt a more effective mechanism to cope with the ambient high salt conditions. The availability of this integrated root-omics dataset will serve as a valuable resource for identifying valuable traits to assist breeding programmes of barley research community in future.


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