Mid-density genotyping services

S. Dreisigacker, S. Esposito, Fillipo Bassi, Paolo Vitale, K. Ammar, and Pasquale de Vita

The biological complexity of cassava—including its heterozygous nature, lengthy cropping cycles, asynchronous flowering, and poor seed sets—drives a lengthy product development process (Ceballos et al., 2004; Ceballos et al., 2012). Incorporating genomic information into breeding programs and using efficient, cost‑effective genotyping improves breeding decisions, shortens the breeding cycle, increases selection intensity, maximizes genetic gain, and accelerates the development of breakthrough products that can replace widely grown varieties.

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 sorghum SNP mid-density panel (MDP) comprises 3,491 genome wide markers, including 42 QC and 50 trait markers used currently in a great number of sorghum breeding programs.

Distribution of the 3,491 DArTag SNP markers along the 10 sorghum chromosomes.

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.

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.

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).

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.