DNA extraction from sweetpotato (Ipomoea batatas) root tissues supports routine genotyping

Sweetpotato (Ipomoea batatas) breeders increasingly rely on genomic tools to enhance selection decisions. However, regrowing plants with sufficient leaf material for sampling requires several months, delaying genotyping and downstream decisions. Sampling storage root tissue would provide an earlier genotyping option, but root versus leaf tissue DNA extractions have not been compared for genotyping applications. Here, we compared genomic DNA from two storage root tissues, the cambium ("flesh") and periderm ("skin"), and evaluated their performance against fresh leaf tissue. Root samples were taken at two storage times postharvest: 4 and 16 months. The approach produced adequate DNA, as assessed by sequencing depth and missing data rates, across all tissue types and storage times. Genotyping with a targeted 3,120 DArTag SNP panel revealed highly similar allele frequencies between root and leaf tissues (R² > 0.96). Within-line dosage calls showed mean concordance of 81.3-85.5% for exact matches, increasing to 97.3-98.5% when allowing a ± 1 dose difference. While leaf tissue had higher read depth and lower missing rates, all root tissue types exceeded the minimum 90 mean read depth recommended for hexaploid dosage calling and fell within 5% of leaf tissue missing rates. Within-root tissue comparisons did not differ significantly across tissue type or storage time. Genetic relationships in principal component analysis were consistent across tissue types, supporting repeatability. Root tissues are therefore a suitable replacement for leaf tissue in routine genotyping workflows. This methodology enables faster selection decisions, resource savings, and genotyping outside the busy growing season.

The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01718-w.