Tomato
Genetics
and Breeding Program
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Translational Genomics
Translation. n. The rendering from one language to another.
SNP Discovery in Tomato
In plant science, “translational genomics” implies the adaptation of information derived from genome technologies for crop improvement. Molecular marker-assisted selection (MAS) offers an opportunity to circumvent some of the problems associated with classical plant breeding while increasing the efficiency of selection. A limitation to the use of molecular markers in breeding for many crop plants is low levels of genetic differences. The lack of genetic markers that detect differences between elite breeding lines has prevented detailed study of traits of agricultural importance. Most academic studies in tomato have used wide crosses between weedy relatives and cultivated varieties. This approach maximizes genetic variation and has lead to the discovery of new genes, but it has also left a void in our knowledge of and ability to manipulate many traits of agricultural importance. For this reason, the application of MAS to tomato improvement is primarily for the introduction of traits from poorly adapted plant materials, and has not been utilized to more fully compliment conventional plant breeding.
Our efforts in translational genomics include the development of molecular markers for use within cultivated tomato germplasm. We are taking three approaches to discover genetic differences between cultivated varieties including:
Tomato SNP database
Bioinformatic approaches to SNP discovery in public databases.
Identification of SNPs in introns.
Use of oligonucleotide Gene chips to detect SNPs
Project description
We have also screened published SSR markers for the ability to detect different alleles between cultivated varieties. A summary of primers, detection conditions, and allele numbers are available as an EXCEL file from the link: SSR data (below). Primers and detection conditions for SNPs are also available as an EXCEL file.
Data links:
SSR data EXCEL spread sheet of SSR primers found to be polymorphic
SNP data EXCEL spread sheet of SNP markers found to be polymorphic
Relevant Links
Tomato mapping resource (SNP database)
Solanaceae Genomics Network (SGN)
