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RNAseq analysis of differentially expressed genes between two barley cultivars with contrasting yield under drought.

AutorGarcía-Pereira, M. J. ; Pérez Cantalapiedra, Carlos ; Casas Cendoya, Ana María ; Igartua Arregui, Ernesto ; Contreras-Moreira, Bruno
Fecha de publicación29-jun-2014
CitaciónEucarpia Cereals Section - I.T.M.I Joint Conference (June 29- July 4, 2014. Wernigerode, Germany)
ResumenThe traditional cultivars and landraces of the Spanish Barley Core Collection [1] harbour genetic variability of potential interest for breeding e lite varieties adapted to Mediterranean environments. Here we compare in vivo gene expression profiles of two contrasting cultivars when grown under drought-stress: SBCCO73, a local landrace with high yield under drought conditions, and elite cultivar Scarlett, an European variety that performs poorly with low water supply. Plants of both varicties werc cultivated under different watering treatments and RNA extracted from severa! tissucs for subsequent library preparation ami high throughput sequencing of biological replicates with Illumina HiScq 2000 instruments. A total of 1.2 billion 2x100 reads were obtained, which werc subject to removal of adapters and low-quality sequences. As the only available refcrences are thc genomic sequences of European and American cultivars Morex, Barke and Bowman, reference transcriptomes of SBCCO73 and Scarlett were also sequenced and assembled using Trinity [3]. Afier removing chimeras and other unlikely constructs, nearly 298941 transcripts wcre validated by stringent alignments (coverage 95% and identity 80%) to barley and other Triticeae sequenees. Gene and isoform quantification was performed with RSEM [4] and differential expression analyses with edgeR [5]. We compared expression profiles between watering treatments for each assayed tissue. Differentially expressed genes and isoforms of each comparison were mapped to high and low confidence barley genes and used in posterior GO enrichment analysis (custom scripts). Preliminary results suggest a higher expression of proteins related to stress in SBCCO73. We also identify the protein kinases and transeription factors present in each set of differentially expressed genes and isoforms using software iTAK [6]. This study reveals molecular dctails of the adaptation of Mediterranean barley cultivars to drought.
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