Using Seed Chipping to Genotype Maize Kernels

Background

Maize is an agriculturally important crop that is grown throughout the world. It has many uses including human consumption, animal feed, and ethanol production (Ranum et al., 2014). Maize is also a useful model for investigating a wide range of biological questions including plant domestication, monocot growth and development, pest resistance, and genome evolution (Strable and Scanlon, 2009). Although maize has many scientific and industrial uses, it is a large plant that requires significant space in either a greenhouse or field to grow. In addition to the cost of maintaining a greenhouse or field, considerable effort is required to perform directed crosses and collect plant material for genotyping and other analyses. Due to these factors, the ability to genotype maize kernels prior to planting is valuable. This protocol describes the process of seed chipping, where a small piece of endosperm is removed with a razor blade to be used for DNA extraction and genotyping. This protocol is a modification of a method where kernels are soaked in water prior to chipping (Gao et al., 2008). We use fully dried maize kernels for chipping to prevent problems we encountered using pre-soaked kernels such as fungal contamination and unanticipated germination. This method is also useful when genotyping a large number of kernels, because the dry kernel chips do not have to be processed immediately for DNA extraction.

Chipping seeds eliminates costs associated with leaf genotyping. Growing maize plants in a field to collect leaf material takes time, labor, and money. These factors make seed chipping cost an estimated 24.6% lower than leaf genotyping in the field (Gao et al., 2008). Seed chips can also be stored at room temperature, unlike leaf tissue which needs to be kept cool and wet in a refrigerator or dried prior to storage at room temperature.

A major advantage of seed chipping the ability to select specific genotypes before planting. Determining the genotype of seeds prior to planting allows for more efficient field planning. This technique is particularly valuable for marker-assisted selection, which relies on molecular markers associated with important crop traits (Xu et al., 2008). Seed chipping has the potential to reduce the cost and increase the efficiency of such breeding programs. We demonstrate here that germination rates are nearly identical between chipped and unchipped seeds.