SGS IF TraitGenetics announces the development of new cost-efficient and optimized SNP genotyping array panels for major vegetables

Date:12-17-2024

Genotyping of vegetable species using Single Nucleotide Polymorphisms (SNP) is an important tool for breeding improved varieties through marker-trait-association studies, genomic selection, genetic relationship analyses, and marker-assisted backcrossing. For these purposes, the TraitGenetics Section of SGS Institut Fresenius GmbH has developed novel genotyping panels for a variety of important vegetable species. Specifically, SNP genotyping arrays have been developed for:

5K Array for Tomato

A new 5K SNP genotyping array has been established that contains the best 5,089 markers from the previously available Illumina Infinium 10K SOLCAP array.

10K Array for pepper (Capsicum)

This array contains 9,339 markers which are mostly a selection of the best markers from the previous 19K Illumina Infinium array. It is optimized for large- and small-fruited pepper.

Onion 5K array

This array consists of 4,254 markers that have been selected for a high level of polymorphism and functionality in this highly polymorphic species based on a 40K Axiom marker screening array.

Lettuce 5K array

The array includes a representative set of more than 5,000 SNP markers from two previously developed Axiom and Illumina arrays selected for functionality, genome distribution and polymorphism

Pea 10K array

For pea, a new genotyping array with 9,744 markers has been developed based on selected high-quality SNP markers from the INRAE 13K Illumina array and other marker sources.

Faba Bean 8K array

A new genotyping array with 7,776 markers has been established based on data derived from previously developed Axiom arrays and genome sequencing

These new arrays provide either an alternative to the discontinued Illumina HD arrays and large Axiom arrays or new genotyping possibilities for lettuce and onion for which until now no optimized genotyping arrays were available. These arrays can be offered to customers at significantly lower sample analysis prices compared to the previously available SNP genotyping arrays.