Understanding the Common bean (Phaseolus vulgaris L.) Transcriptome in Response to Salinity Stress
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Abstract
Salinity is a grave threat to agriculture as it affects crop growth globally; it is known as one of the major stressors that hinders common bean production. Common bean (Phaseolus vulgaris L.) is the main source of human dietary vegetarian protein that constitutes approximately half of the consumed grain legumes globally. Additionally, common bean is of great economic weight as it provides income for millions of small farmers; however, the crop is known to be sensitive to salinity. In this study, common bean plants were salt stressed in a hydroponic system at 0 mM, 50 mM and 150 mM of NaCl for ten days (early stress) and five weeks (prolonged-flowering stage) in an effort to identify salt responsive genes. Exposure of plants to salt for several hours to a few days induces osmotic stress genes; lengthier salt stress treatments from a few days up to several weeks will ultimately induce salt specific genes that are involved in the plant’s adaptation to, and development under stress. Therefore, we isolated root RNA from ten days and five weeks salt stressed bean tissues and sequenced their transcriptomes. RNA-Seq analysis identified more differentially expressed genes (DEGs) in roots at five weeks compared to ten days salt treatment of 0 mM, 50 mM and 150 mM of NaCl. Some early and delayed salt responsive genes were identified which includes: Salt Tolerance Homolog 2 (STH2), Sodium Hydrogen Exchanger (NHX1), Chloride Chanel A (CLC-A), Late Embryogenesis Abundant (LEA) & Proline Transporter 1 (PROT1).The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the Mitogen-Activated Protein Kinase (MAPK) signaling pathway which contained ten DEGs including protein kinase (CTR1), calmodulin 1 and WRKY33. Transcription factors (TFs) that are known to be involved in flower development and flowering time such as WRKY, MADS-box and bZIP were observed to be up-regulated both at ten days and five weeks of salt stress when compared to the control (no salt treatment). The up-regulated genes identified were functionally classified using the Protein ANalysis THrough Evolutionary Relationships (PANTHER) classification system for Gene Ontology (GO) Slim (general) categories. Additionally, PANTHER overrepresentation test was done to identify granular (specific) terms that were enriched for both upregulated and down regulated genes. This first report on common bean under prolonged salt stress of five weeks has identified potential candidate genes that are perhaps needed for acclimation to salt stress and hence will serve as a genetic resource for plant salt tolerance.