Title : Transcriptome Profiling of Coffee (C. arabica L) Seedlings Irrigated with Diluted Sea water.
Abstract:
Salinity is one of the important abiotic stress factors that limit plant growth and crop production. This research aimed to generate information about the gene expression of coffee seedlings under salt stress conditions and thereby to identify salt responsive genes. The treatments were normal irrigation water (0.2 dS/m) as a control treatment, and 5% diluted deep sea water (2.3 dS/m) as a salt treatment. The processed reads were mapped to the reference genes sequences (C. canephora) available on the coffee genome hub (http://coffee-genome.org) database and a total of 19,581 genes obtained. Gene ontology (GO) analysis was performed and among the 19581genes; 7369 (37.64%) associated with the biological process, 5909 (30.18%) with cellular components, 5325 (27.19%) with molecular function and 978 (4.99%) genes categorized under no hit (unclassified) group. Differential gene expression analysis was performed with the DESeq2 package to identify differentially expressed genes based on the fold change and p-value. The result revealed that a total of 611 differentially expressed genes were identified (treatment/control). Among the differential expressed genes, 336 genes classified into up-regulated, and 275 genes were down-regulated. Among the total of 611 DEGs, 60 genes were significantly (p<0.05) expressed and 44 genes classified into up-regulated and 16 genes were down-regulated. A total of four differentially expressed transcription factor genes identified, and two of them up-regulated, and the other two were down-regulated. The data generated in this study will help in understanding the response of coffee seedlings at the genomic level associated with abiotic stresses in general, salinity stress in particular. This study will also provide resources for functional genomic studies.
Keywords: Coffee, Coffee genome hub (CGH), Differential expressed gene (DEGs), Diluted deep sea water (DDSW), Gene Ontology (GO)
