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.
Genotyping / sequencing tools and services
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 NARS breeding institutions, aggregating demand across institutions to offer genotyping at a cost of US $10-11 per sample, and a turnaround time of 10-15 days.
A DNA-based molecular marker is a genomic DNA (gDNA) fragment located within a genome at a specific position that may or may not be linked to a specific trait of agricultural interest. Trait linked DNA based markers allow us to easily screen breeding materials for favorable alleles associated with traits of interest.
The EiB low-density genotyping service is based on KASP markers. Kompetitive Allele Specific PCR (KASP) is a simplified fluorescence-based methodology to genotype specific polymorphisms or INDELS. This approach is cost effective and offers rapid turnaround for low-density marker applications (between 1 and 200 markers), with applications including specific trait screening, quality control and marker assisted selection (MAS).
The markers available for use in low-density genotyping can be consulted below. This list is continuously updated and improved: kindly remember to revise the list of markers and consult with EiB genotyping services when planning for genotyping, especially new users.
Genotyping/ Sequencing Tools and Services
Michael (Mike) Olsen has 14 years of private sector experience in conventional and molecular maize breeding as part of Syngenta and Monsanto North America breeding teams. Presently, as trait pipeline and upstream research coordinator at the International Maize and Wheat Improvement Centre (CIMMYT), he leads the molecular breeding team of the Global Maize Program and provides strategic direction to upstream research efforts. He is currently serving as project lead for Improved Maize for African Soils (IMAS), a multi-institutional public-private partnership to develop maize varieties with improved performance under low fertility conditions common in Sub-Saharan Africa. He is also principal investigator for the Genomic Open-source Breeding and Informatics Initiative (GOBII), at Cornell University – U.S., to enable routine use of genomic data in applied CGIAR breeding programs through integration of appropriate infrastructure, databases, analysis pipelines, and user interfaces.
Faster and cheaper genotyping and sequencing services have opened up the wealth of diversity in crop and animal varieties for study, and when applied effectively have the potential to accelerate the rate at which new varieties can be developed.
The genotyping/sequencing module supports Platform members to access user-validated, application-appropriate genotyping services and technologies by:
- Aggregating demand and brokering access lower-cost, user validated genotyping services.
- Documenting use cases and incorporating expert knowledge for users to be accessed through the Platform Toolbox.
The Bioinformatics, biometrics and data management module supports users to manage and apply genotypic data in breeding programs.