Neogen® Genomics offers extensive options for plant genotyping. Neogen Genomics can utilise fixed arrays, genotyping by sequencing (GBS), as well as SNP discovery for genotpying projects of all sizes and species of plant. With this sequencing information, GeneSeek® can aid in developing custom genotyping tools tailored to your precise needs of genomic content from different plants. We offer services for every step of genomic improvement for a plant of interest.

Our services include:

  • Sequencing for SNP discovery
  • Bioinformatics to select the best SNPs for genome-wide association studies
  • Build high or medium density SNP arrays to create genomic models
  • Build low density arrays and panels for marker assisted selection
  • Use diagnostic tools to identify resistant of susceptible lines

GeneSeek can offer fixed array testing in the following plant species.

Apple

The apple genotyping array was developed by RosBREED and includes 80,000 genetic markers.

Brassica

The Brassica genotyping array includes more than 13,000 SNPs collected from more than 80 Brassica lines.

Cherry

The cherry genotyping array was developed by RosBREED and includes 80,000 genetic markers. The SNPs were developed for use on worldwide breeding germplasm.

Cotton

The International Cotton SNP Consortium genotyping panel is a 70,000 marker array developed with SNPs from Gossypium hirsutum, G. barbadense, G. tomentosum and G. mustelinum. Small numbers of attempted bead types will be devoted to G. longicalyx and G. armourianum.

Cowpea

The cowpea genotyping array was developed by The International Cowpea Consortium and includes 60,000 genetic markers.

Eucalyptus

The Eucalyptus tree array includes more than 60,000 SNPs and was developed to be informative in multiple eucalyptus species. Between 29,000 and 33,000 SNPs are polymorphic (MAF>0.01) in each one of the four species that make up >90% of eucalypt planted forests worldwide (E. grandis, E. urophylla, E. camaldulensis, E. globulus), with 15,033 SNPs simultaneously polymorphic in all four.

Grape

The grape genotyping panel was designed by the GrapeReSeq Consortium and includes approximately 20,000 SNPs.

Maize

MaizeLD BeadChip includes high discrimination coverage with 3047 evenly spaced markers.

Maize SNP50 BeadChip contains more than 50,000 validated markers derived from the B73 reference sequence and was subjected to rigorous functional testing across over 30 diverse maize lines to ensure strong performance.

Oat

This array contains nearly 6000 SNPs and was validated in 1,100 samples from six RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3,500 discernible Mendelian polymorphisms.

Peach

The peach genotyping array was developed by RosBREED and includes approximately 9,000 genetic markers.

Pepper

The Pepper Consortium Array is designed to enable cost-effective genotyping of multiple pepper species and includes more than 16,000 SNPs.

Potato

The GeneSeek Genomic Profiler Potato Array utilises more than 12,000 SNPs. Array content includes:

  • 7157 SNPs from the original GGP Potato LD Array with increased density in candidate and resistance regions
  • ~3100 SNPs in candidate genes
  • ~5000 SNPs for tetraploid genotyping

Rice

The Rice array includes more than 42,000 markers and offers comprehensive genomic coverage, which allows researchers to easily assay the natural variation of rice varieties worldwide to identify genes underlying important phenotypic traits

Soy

The array includes 180,961 markers spaced across the genome as follows:

  • 114,735 SNPs or 63.4% of total markers are located in 40,631 genes.
  • 22,952 SNPs are in 13,259 regions within 5 kilobase pairs upstream or downstream of genes.
  • 43,274 SNPs located in intergenic regions.
  • SNP discovery and validation were completed by using a diverse set of soybean accessions.

Tomato

The SolCAP Tomato genotyping panel was designed by the Solanaceae Coordinated Agricultural Project (SolCAP) and includes more than 7000 genetic markers.

Wheat

The Axiom Wheat HD Genotyping Array, a high-density research tool with 817,000 SNPs in a two-array set in the 96-array plate format.

The Axiom Wheat Breeder's Genotyping Array, which includes 35,000 SNPs for worldwide elite wheat lines in the 384-array plate format.

Custom Panels & Arrays

Create assays tailored directly to your specific needs for targeted region genotyping, validation studies, association studies, or marker-assisted breeding programs. GeneSeek offers custom Illumina Infinium BeadChips and Affymetrix Axiom Arrays.

  • As few as 1000 samples
  • Sample capacity to hundreds of thousands
  • Choose from 1,000–600,000 SNP assays
  • Multiple species on the same chip
  • Average genotyping success rates > 99%