Development of Efficient Genotyping Workflow for Accelerating Maize Improvement in Developing Countries

Abstract BackgroundMolecular breeding has been recognized as one of the pillars to accelerate the rate of genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost and flexible genotyping platforms in small and public laboratories and regionally can stimulate the application of molecular breeding in developing countries where many plant breeding projects require low to medium density markers for genomics-assisted selection and quality control (QC) activities. ResultsHere we present an optimization of the entire genotyping workflow (from sample collection to genotyping and data analysis) to accelerate the QC and genomic-assisted selection process, which can readily be adopted by National agricultural research system (NARS) partners in developing countries to fast-track molecular marker-based genotyping for crop improvement. An in-house KASP genotyping system combined with optimized sample collection and DNA preparation processes expedited the genotyping workflow from over five weeks (when outsourcing) to approximately three weeks (5 days per week) for a total of 637 samples. The QC experiment using a subset of 28 KASP SNPs validated for maize revealed the genetic identity of 4 maize varieties taken from 5 seed sources. Another subset of 10 KASP SNPs was sufficient in verifying the parentage of 388 F1 lines. The marker-based selection of high PVA maize lines identified nine lines harboring the favorable allele of the crtRB1 gene, which could serve as donor lines for the maize PVA breeding program. The ongoing marker-assisted backcrossing experiment to introgress resistance to aflatoxin accumulation in elite tropical maize lines has so far identified twenty-four maize lines harboring the favorable alleles associated with resistance to aflatoxin accumulation, and are currently undergoing field evaluation. The optimized genotyping workflow has so far generated over 1700 datapoints.ConclusionThe result of this work could serve as a prototype to fast-track maize improvement activities of IITA’s MIP group, and facilitate DNA fingerprinting for adoption tracking of improved crop varieties. It will also provide public and small laboratories in developing countries with the knowledge of efficient genotyping workflow to accelerate crop improvement activities.