Project description:Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.

| S-EPMC3842579 | biostudies-literature

Solanum lycopersicum

Project description:Genome resequencing of the bifuricate (bif) mutant and LAM183

| PRJNA378916 | ENA

Solanum lycopersicum

Project description:Generation and characterization of a tomato DCL3 silencing mutant

| PRJNA227312 | ENA

Solanum lycopersicum

Project description:Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

| PRJNA97773 | ENA

Solanum lycopersicum

Project description:Tomato colonization by wt R. solanacearum and a hrp mutant

| PRJNA101129 | ENA

Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme.

Project description:Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato.

| S-EPMC3411241 | biostudies-literature

Solanum lycopersicum

Project description:Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant

| PRJNA339564 | ENA