The tomato (Solanum lycopersicum) is a widely consumed fruit and holds a significant position in the global market. The domesticated tomato is a diploid species with 24 chromosomes and a genome size of approximately 950 Mb. However, tomato has undergone a whole-genome triplication event that distinguishes it from potato and pepper. The tomato genome possesses unique characteristics, including a high number of genes related to cell wall modification, flavor compounds, aroma compounds, and carotenoid biosynthesis. These traits make the tomato an excellent model for studying fruit development, ripening, and nutritional attributes.

Our Tomato SNP Panel consists of hundreds of trait-associated markers, offering valuable insights into various aspects of tomato biology and traits of interest. Among these markers, many are associated with genes that play crucial roles in major biochemical functions such as gene regulation, DNA replication, cell division, cellular structure, photosynthesis, and disease resistance.

Product Information

Our Tomato panel, developed by a consortium of academic and industry researchers and breeders from the tomato community, is a comprehensive genotyping solution consisting of 1039 SNPs. These SNPs were carefully selected based on specific criteria to ensure their relevance and utility in tomato research and breeding.

Key Features

• Chromosomal Coverage: Our panel ensures comprehensive coverage of all 12 tomato chromosomes, allowing for a representative sampling of genetic variations across the entire genome. We also offer a custom Panel service to cater to specific needs and requirements beyond our existing Tomato panel.
• Trait-Focused Design: The SNPs included in the panel have been specifically chosen for their relevance to various traits of interest in tomato breeding, such as disease resistance, fruit quality, yield, and abiotic stress tolerance.
• Optimal Spacing: We have maintained a distance of 0.2 cm or 0.2 Mbp between adjacent SNPs. This spacing corresponds to the expected recombination rate and facilitates accurate genetic mapping and analysis.
• Primer Design Compatibility: The DNA sequences flanking each SNP have been carefully chosen to facilitate primer design. This ensures ease of use and efficiency in genotyping experiments.
• Population Variability: Our panel includes both common SNPs shared across populations and population-specific SNPs. This variability allows researchers and breeders to investigate both general tomato genetic variations and specific population characteristics.
• High Accuracy: Our NGS genotyping platform, coupled with our Tomato SNP Panel, delivers accurate genotyping results, enabling precise identification and characterization of genetic variations in tomato populations.
• Scalability: Our platform allows for flexible sample multiplexing, enabling cost-effective and scalable genotyping of large populations. This scalability is crucial for breeding programs aiming to analyze a significant number of samples.
• Data Analysis Support: We provide comprehensive bioinformatics support, including data analysis pipelines and software tools, to assist you in extracting meaningful insights from your genotyping data.

Specifications

Workflow of Our Sequencing Panels

Increase Confidence in Your Tomato Research & Breeding

• Genomic Selection: The panel provides a high density of polymorphic markers suitable for genomic selection. Genomic selection utilizes genomic data to predict the breeding value of individuals, enabling breeders to select superior plants at an early stage. The panel's marker density enhances the accuracy of genomic selection models and improves the efficiency of breeding programs.
• Marker-Assisted Backcrossing: The SNP panel can be utilized in marker-assisted backcrossing programs. By combining informative background markers with trait markers, breeders can accurately estimate background recovery during the backcrossing process. This ensures the retention of valuable genes from the recipient line while confirming the presence of target genes in selected progeny. Background selection using the panel can significantly reduce the number of backcross generations required for successful recovery of the recipient parent's genetic background.
• QTL Mapping: Although not the primary focus, the SNP panel can be used for bi-parental QTL mapping. The panel provides a sufficient number of polymorphic markers to genotype a substantial portion of the genome. While there may be some gaps in the linkage map, additional marker systems or panel customization can be used to fill those gaps and improve the density of markers for QTL mapping studies.
• Trait Profiling: The SNP panel includes high-value trait markers that cover a range of important traits such as disease resistance, enzymatic profiles, abiotic stress tolerance, and taste. These markers facilitate the characterization of targeted genes and QTLs across different Solanum species and accessions, including wild relatives. They offer valuable information for trait analysis and enable the investigation of specific traits in lines of interest.
• Seed Purity and Hybridity: The panel's genome coverage allows for the identification of diagnostic marker subsets that can be used for seed-quality applications. These markers aid in genetic purity testing, ensuring uniformity and varietal identification in commercial production operations. Breeders and seed producers can utilize the panel to assess seed quality and verify the authenticity of tomato varieties.

We are proud to offer this collaborative effort from the tomato community, which reflects the expertise and knowledge of researchers and breeders who are dedicated to advancing tomato genetics and breeding programs. CD Genomics not only has the ability to provide agricultural sequencing panels, but also relies on our in-house laboratory to provide you with a range of genotyping services and analysis.

• Bovine Parentage Sequencing Panel
• Maize SNP Panel
• Rice QA/QC Sequencing Panel
• Rice SNP Panel
• Soybean SNP Panel
• Tomato SNP Panel