Molecular Analysis of Salt Stress Signaling Gene(s) in Potato (Solanum tuberosum L.)

Abstract

Potato (Solanum tuberosum L.) is an important crop plant around the world which produces the nutritionally valuable crop in the form of tubers. In lexes of production, the potato is the fourth utmost important crop of Pakistan. The objective of this research was to identify and analyze salt stress signaling gene(s) in different potato varieties to establish the phylogenetic relationship of sequenced genes with the already existing data and to predict the best 3-D protein model of analyzed varieties under study. In this study, In silico and molecular analysis were performed including DNA isolation, PCR amplification, and sequencing. After DNA isolation, Polymerase Chain Reaction results showed the approx. 1000bp bands with respect to SAP1 gene. The In silico studies included statistical distance analysis between sequences and phylogenetic analysis using available resources like the MEGA6 program, Clustal W, Gene Studio and Bio-edit. The phylogenetic tree was constructed using the Neighbor-joining method. Phylogenetic analysis shows that the SAP1 gene within the targeted varieties is showing 0.01-0.05% difference and three major clades were formed in which two major clades consists of Solanaceae family while the third clade belongs to family Cleome, in which it was clearly observed that specie of same family are showing some divergence with respect to SAP1 gene. Furthermore, protein modeling was performed using I-TASSER. The protein models were generated for the SAP1 gene sequence from reference gene sequence whose sequence belongs to Solanum lycopersicum and representative sequence of this present study i.e. Solanum tuberosum var. Santé (MF590183) and these were compared with each other on the basis of C-Score, TM-Score and cluster identity, which clearly shows that both the sequences having same number of residues shows slight difference. In conclusion, this work will help to study the functional pathways associated with salt stress signaling in different potato varieties, and its regulatory effects during stressed conditions through experiments performed by applying salinity stress through expression analysis. SAP1 gene can be used to confer tolerance through a transformation in other commercially important crop plants and best 3-Dimensional protein model to be selected for future references, achieved from this experiment.