ArticleScientific reports2016
In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).BMC plant biology · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Review of protein structure-based analyses that illuminate plant stress mechanisms.Computational and structural biotechnology journal · 2025Review
- Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation.International journal of molecular sciences · 2023Article
- Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach.PLoS computational biology · 2022Article
- Review
- Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA.Scientific reports · 2021Article
- Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits.Genome biology · 2021Article
- Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris).Scientific reports · 2020Article
- Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize.International journal of molecular sciences · 2020Article
- 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.Scientific reports · 2020Article
- Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering inHorticulture research · 2019Article
- Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits.BMC plant biology · 2018Article
- A profound computational study to prioritize the disease-causing mutations in PRPS1 gene.Metabolic brain disease · 2018Article
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4 authors.
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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.
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