Non-destructive seed genotyping via microneedle-based DNA extraction

Abstract

Crop breeding plays an essential role in addressing food security by enhancing crop yield, disease resistance and nutritional value. However, the current crop breeding process faces multiple challenges and limitations, especially in genotypic evaluations. Traditional methods for seed genotyping remain labour-intensive, time-consuming and cost-prohibitive outside of large-scale breeding programs. Here, we present a handheld microneedle (MN)-based seed DNA extraction platform for rapid, non-destructive and in-field DNA isolation from crop seeds for instant marker analysis. Using soybean seeds as a case study, we demonstrated the use of polyvinyl alcohol (PVA) MN patches for the successful extraction of DNA from softened soybean seeds. This extraction technology maintained high seed viability, showing germination rates of 82% and 79%, respectively, before and after MN sampling. The quality of MN-extracted DNA was sufficient for various genomic analyses, including PCR, LAMP and whole-genome sequencing. Importantly, this MN patch method also allowed for the identification of specific genetic differences between soybean varieties. Additionally, we designed a 3D-printed extraction device, which enabled multiplexed seed DNA extraction in a microplate format. In the future, this method could be applied at scale and in-field for crop seed DNA extraction and genotyping analysis.