Genotyping / sequencing tools and services

Yam mid-density genotyping services

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).

Tool demo & pre-launch: CGIAR’s online genotyping sample submission system

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.

Pigeonpea mid-density genotyping services

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.

New pricing plan for genotyping services from April 2022

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.

Rice mid-density genotyping service

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.

Basics of Genomic Selection 9. Computational Aspects and Implementation

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.

Groundnut mid-density genotyping services

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).

African breeding programs leap forward by accessing new genotyping data

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.

Low Density SNP Genotyping Services: An EiB Launch Event

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.

KASP low density genotyping Platform

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.