Genotyping / sequencing tools and services
CGIAR Excellence in Breeding has launched new low-cost, high throughput genotyping services, positioning CGIAR and national breeding programs to take a leap forward in delivering vital crop varieties.
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.
The new LDSG service is the latest evolution from the “High Throughput Genotyping - HTPG” project, made possible through the strong partnerships and support of many CGIAR, public and private research organizations.
As CGIAR centers continue their journey toward becoming One CGIAR, the LDSG service is a trailblazing service designed to cater to the needs of new CGIAR and NARs breeding networks. The ultimate goal is to provide quality and affordable genotyping solutions to all.
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.
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.
On January 15, the CGIAR Excellence in Breeding Platform (EiB) held a one-day workshop with users of its genotyping and data analytics services at the 2020 International Plant and Animal Genome (PAG) conference, held in San Diego, USA.
CGIAR and public sector experts met at the International Potato Center (CIP, Peru) to evaluate genomics resource needs and demonstrate new tools and methods for polyploid crop breeding.