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.
A faster and easier way to order and track key services
A Service Request Portal is now available to make it easier for users to request and track a large range of CGIAR breeding support services. This portal speeds up submissions and reduces human error. It is accessible to both CGIAR staff and partners, including NARES.
In Africa, people mostly eat what they grow, and the potential for trade and processed foods largely depends on how much they can produce. But the population is growing rapidly – by 2050, it will double.
Due to the recent inflationary pressures affecting various industries, including ours, a price adjustment of our Breeding Resources Initiative's genotyping shared services is scheduled to come into effect by the 15th of August.
The success of breeding will depend on our ability to deliver reliable data, information and insights into market segments. CGIAR is preparing to officially launch a genotyping sample submission portal as a step towards these goals.
The shared genotyping services will be the sole entry point for all shared services submissions. This is expected to streamline sample forecasting, logistic management and reduce administrative burden for all users.
CGIAR Breeding Resource Initiative (led and managed by Genetic Innovation’s Breeding Research Services unit) sends out periodic updates to inform partners about plans, progress, events and resources. These updates are collated on this page. For more information, please contact: a.hunt@cgiar.org
CGIAR collaborative efforts are helping Mozambican partners meet food security and environmental challenges. Crop breeding is key to unlocking agricultural potential, and ensuring breeders can access advanced genotyping practices will facilitate Mozambique in reaching its goals.
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.
Genomics interventions in pigeonpea during the last decade, in particular the availability of a reference genome (Varshney et al. 2012) and whole genome sequence data on multiple lines, have enhanced the level of crop improvement(Varshney et al. 2017; Saxena et al. 2021). Cost-effective genotyping platforms are required to deploy genomics assisted breeding in routine crop improvement programs. Therefore, a mid-density genotyping platform has been developed targeting pigeonpea.
The CIMMYT Global Wheat Program currently optimizes, and pilots accelerated breeding schemes to increase overall genetic gains through the ‘Accelerating Genetic Gains in Maize and Wheat’ and ‘Zinc mainstreaming in Wheat’ projects funded by the BMGF, FCDO, USAID, and FFAR. A robust, cost-effective mid-density SNP platform is ideal for this type of genomic-assisted breeding approach.
Over the last year, global supply chains and service providers have been affected by rising inflation, costs and challenges. Genotyping services and inputs in particular are affected by rising demand due to the global COVID-19 pandemic.
The CGIAR Excellence in Breeding Platform (EiB) has been proactive in maintaining the availability and quality of our brokered genotyping services throughout ongoing challenges. For 2022, there will be a small cost increase to our partners as a result of the higher prices charged by our trusted service partners.
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.
Banana breeding programs in East Africa are starting to use genetic analysis to speed up varietal improvement, thanks to open data and access to low-cost services.
Abhishek Rathore (ICRISAT) presents the current state of tools for data management and genomic prediction available at ICRISAT and national programs in India. Abhishek presents a path to the proper implementation of data management tools that ensures the successful deployment of GS in breeding programs. Case examples of crops adopting these systems and their current state are also presented.
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.
Groundnut (Arachis hypogaea L.), also known as peanut, is cultivated over 34.1 million hectares with an annual production of 66.3 million tonnes (FAOSTAT, 2020). The availability of reference genomes for both the subspecies (A. hypogaea ssp fastigiata and A. hypogaea ssp hypogaea) of cultivated groundnut in 2019 have boosted more precise genomic studies and higher integration of genomic tools in the modern breeding programs across the world (Pandey et al. 2020).
With newly accessible genotyping technologies, African crop breeding programs have partnered with EiB to start using genotyping resources to improve accuracy and efficiency.
As breeders strive for higher-yielding, climate-resilient and nutritious crops, genotyping is intensifying the speed and accuracy of achieving breeding goals. But new technologies have often been out-of-reach for national breeding programs in developing countries.
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.
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.
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.
