Yams are crucial for food security in Africa, with cultivation expanding in tropical regions (FAO, 2020). To keep pace with this rising demand for yam, rapid adoption of new technologies is crucial. One promising approach is genomic selection. This technique leverages genetic markers to identify superior yam plants with improved production and food quality traits (Aguilar et al., 2010; Legarra et al., 2014).
Sweet potato mid-density genotyping services
Genotyping panel containing 3,210 SNP markers distributed evenly throughout the 15 chromosomes of sweet potato (Ipomoea batatas L.). This panel is suitable for marker-assisted breeding, linkage and introgression mapping, QTL analyses, outlier removal, and germplasm management applications.
The maize mid-density panel is an SNP panel developed and optimized by the collaboration between the International Maize and Wheat Improvement Center (CIMMYT) and the International Institute of Tropical Agriculture (IITA) to implement genomic assisted breeding routinely in the maize breeding programs.
The 1k RiCA panel for rice is the mid-density genotyping panel developed at the International Rice Research Institute (IRRI) to enable affordable, efficient genomic selection. It has been implemented at several service providers and platforms, but currently is offered at Agriplex and DArT. Both platforms use custom amplicon workflows that reliably deliver almost all markers from all samples.
The common bean mid-density marker panel was developed from sequencing data of 1,700 breeding lines and landraces belonging to different breeding nurseries for biotic and abiotic resistances, commercial and agronomic traits, interspecific introgressions, and major representation from America and Africa breeding programs.
This mid-density marker platform for cowpea (Vigna unguiculata [L.] Walp.) genotyping contains 2,602 SNP markers with an average density of about 3 SNPs per cM (or 4 per Mbp) throughout the 11 cowpea chromosomes. Marker density is higher by physical distance in high recombination regions and lower in low recombination regions.
Within the “Accelerating Genetic Gains in Maize and Wheat” and “Zinc mainstreaming in Wheat” projects funded by the BMGF, the UK FCDO, the USAID, and the FFAR; CIMMYT is piloting to further shortening its breeding cycle to increase its breeding efficiency. A robust, cost-effective mid-density SNP platform is ideal for this type of genomic-assisted breeding approach.
Potato (Solanum tuberosum L.) was originated and firstly domesticated in South America (https://cipotato.org/potato/). This crop occupies an important position in human consumption, with developing countries expanding its production by nearly 200 million t. from 1961 to 2016/18 (FAOSTAT 2020).
The EiB mid-density genotyping service is a DArTAg genotyping method primarily suited to genomic selection applications, but that can also be used for diversity studies, material fingerprinting, or background recovery in marker-assisted selection (MAS) to complement low-density genotyping.
The service is targeted at CGIAR and NARES breeding institutions, aggregating demand across institutions to offer genotyping at a cost of $12-17 per sample (depending on the number of sample plex), and a turnaround time of 10-15 days.
Galaxy is an open-source application to enable researchers without informatics expertise to perform computational analyses through the web. A user interacts with Galaxy through the web by uploading and analyzing the data. Galaxy interacts with underlying computational infrastructure (servers that run the analyses and disks that store the data) without exposing it to the user.
SNPviewer is a tool that enables genotyping data to be viewed as a cluster plot, but that does not include data analysis or reporting functionality.
Opening genotyping service project results in SNPviewer will allow you to view the genotyping clusters plate by plate. Genotyping calls cannot be changed within SNPviewer; if you need to be able to edit the calls then you will require our KlusterCaller software.
Coordinate replaces our previous DNA Plate App and Seed Tray App with a unified data collection app. Coordinate is based on defining templates and then collecting data in grids created from those templates. Two templates are included by default: Seed Tray and DNA Plate.
Notice: New 2022 pricing plan for genotyping services
The EiB low-density genotyping service (formerly the High Throughput Genotyping Profect [HTPG]) is a shared KASPTM genotyping platform serving all CGIAR centers and their partner programs.