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.

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

“…The association between single nucleotide change and gene function has been reported for a number of traits 44,59,[64][65][66][67] . Therefore, the identification of non-synonymous SNPs would be biologically meaningful, and useful for functional genomics, molecular genetics, and marker-assisted selection in breeding.…”

“…The discovery and identification of genomic variants such as SNPs, together with the determination of their location in the genome, can provide valuable information for breeding programs. In plants, many traits of interest have been linked with SNPs 23,42,43 and these linkages have been exploited to understand individual variation, community diversity, and the evolution of species 44 . In this study, we conducted deep Genotyping-by-Sequencing and genome-wide SNP discovery on a diverse collection of accessions representing three different subgenera of the genus Prunus (Amygdalus, Prunus and Cerasus).…”

Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize

“…The impacts of SNPs on the function of genes they are in can be considered high, low, or moderate (also termed modifiers) [ 48 ]. High impact SNPs usually cause a gain or loss of a stop codon, thereby resulting in a major change in the function of a gene.…”

Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

“…Downstream interacting partners of 7 selected genes identified through the variant interaction network and their functional annotation, further specified their role in several seed specific processes, particularly permeability. A similar approach has been used to associate 28 deleterious SNPs identified at a genomic scale with genes involved in plant-pathogen interaction and plant hormone pathways for trait targeting in tomato [ 53 ].…”

“…Non-synonymous variation can make an impact on the gene expression due to the functional consequences of differential motif binding at variation sites [ 53 ]. Gene expression studies of selected genes further supported the hypothesis of their direct or indirect involvement in controlling soybean seed permeability.…”