An effective and safe maize seed chipping protocol using clipping pliers with applications in small-scale genotyping and marker-assisted breeding

In applications such as marker-assisted breeding and positional cloning, tissue sampling and plant tracking are vital steps in the genotyping pipeline. They enable the identification of desirable seedlings, saving time and reducing the cost, space, and handling required for growing adult plants, especially for greenhouses and winter nurseries. Small-scale marker-assisted selection laboratories rely heavily on leaf-based genotyping, which involves over-planting large, segregating populations followed by leaf sampling, genotyping, and backtracking to identify desired individuals, which is costly and laborious. Thus, there is a need to adopt seed-based genotyping to reduce costs and save time. Therefore, we developed a safe and cheap seed-chipping protocol using clipping pliers to chip seeds to genotype before planting. To identify a cost-effective and high throughput DNA extraction method, we tested four extraction methods and assessed the quality of the seed DNA using PCR. For three of the methods, seed-based DNA was of comparable quality to DNA extracted from leaf punches. We also compared seed- and leaf-derived DNA from the same individuals in a segregating population to test for genotyping miscalls that could arise due to the presence of maternally derived pericarp in the seed samples and found zero miscalls of 43 potential instances. Germination rates of chipped and unchipped seeds were the same for the inbreds tested, B73 and Mo17. However, chipped seeds grew slower until [~]14 days after sowing. Overall, seed sampling using clipping pliers provides a simple, reliable, and high-throughput method to identify specific genotypes before planting. Key FeaturesO_LIProvides a quick, safe, and cheap sampling technique for maize kernels that may also be suitable for other plants with relatively large seeds. C_LIO_LIIncludes procedures and materials to track and organize samples within and across batches involving hundreds to thousands of seeds. C_LIO_LISeeds can be sampled and genotyped relatively quickly for planting; in one day 384 seeds can be sampled, processed for DNA, and genotyped by PCR. C_LI