title: In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations.
abstract: Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program.
authors.affiliation: Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India.|Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
authors.forename: Archana
authors.initials: A
authors.lastname: Bhardwaj
authors.affiliation: Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India.|Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
authors.forename: Yogeshwar Vikram
authors.initials: YV
authors.lastname: Dhar
authors.affiliation: Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
authors.forename: Mehar Hasan
authors.initials: MH
authors.lastname: Asif
authors.affiliation: Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India.|Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
authors.forename: Sumit K
authors.initials: SK
authors.lastname: Bag
mesh_terms: D003198:Computer Simulation; D017343:Genes, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D010937:Plant Growth Regulators / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins