IITA improving maize genotyping workflow in developing countries
30 September 2022
With growing concerns around food and nutrition security globally due to the Ukraine−Russia war, there is also an increased need for improving food systems through research. With a mandate to transform agriculture and increase food production sustainably, IITA–CGIAR researchers are consistently delivering technologies that impact the livelihood of smallholder farmers.
Using selective breeding, IITA-CGIAR is developing a wide range of staple varieties and biofortified crops that address hunger and micronutrient deficiencies. Maize, one of the most important cereal and staple crops in sub-Saharan Africa (SSA), accounts for about 50% of low-income household expenditure and is a good source of protein, carbohydrates, minerals, vitamins, and dietary fiber. Maize provides over 30% of caloric intake for more than 300 million Africans.
At IITA, the Maize Improvement Program has recorded remarkable success developing Striga-resistant, provitamin-A-enhanced, and early maturing varieties, enabling maize production to expand into new areas in SSA. However, with biotic and abiotic constraints causing losses both on the field and post-harvest, there is a need for genetic improvement of maize, which would address nutrition quality, yield potential, and disease and pest resistance, among other issues.
As part of efforts to accelerate maize improvement in developing countries, scientists from IITA’s Bioscience Center and the Maize Improvement Program researched DNA fingerprinting for tracking improved crop varieties and assessing the effective application of genetic diversity in maize to understand the population structure and genetic variability among 439 early and extra-early maize inbred lines.
The study highlighted various bottlenecks that have hindered the substantial impact of molecular breeding for crop improvement, particularly in developing countries. Despite this, the improved workflow from the study can help National Agricultural Research Systems (NARS) in developing countries to fast-track molecular marker-based genotyping for crop improvement.
Some of these bottlenecks, such as logistics, shipping costs, and inefficient courier services, which often result in reduced or damaged perishable specimens, can be avoided if a reasonably affordable system is available locally.
According to the study, two quality control (QC) and marker-assisted selection (MAS) experiments consisting of 637 maize lines were performed using an optimized genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimized sample collection, preparation, and DNA extraction and quantitation process.
Also, a smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified Cetyltrimethylammonium Bromide (CTAB)-based Diversity Array Technology (DArT) DNA extraction protocol. The DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis were performed in a laboratory at IITA.
With the study, an improved genotyping workflow promises to accelerate the marker-assisted selection process and push crop improvement activities to attain better yield potential over a shorter period.
Molecular breeding is an essential tool for accelerating genetic gain in crop improvement toward feeding an ever-growing population in Africa and across the world. With the high cost of carrying out breeding research, establishing low-cost, flexible genotyping platforms in small, public, and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for MAS and QC activities.
Contributed by Timilehin Osunde and Iyaniwura Savage
