Genotyping wild potato (Solanum) seedlots improves with high-read bulks

Authors: Bamberg, John; ALFONSO, DEL RIO - University Of Wisconsin; Fenstemaker, Sean

Submitted to: American Journal of Potato Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2025
Publication Date: 6/23/2025
Citation: Bamberg, J.B., Alfonso, D., Fenstemaker, S.M. 2025. Genotyping wild potato (Solanum) seedlots improves with high-read bulks. American Journal of Potato Research. https://doi.org/10.1007/s12230-025-10002-0.
DOI: https://doi.org/10.1007/s12230-025-10002-0

Interpretive Summary: Most of the potato varieties grown in the USA were bred with stocks from the US Potato Genebank in their pedigree. To make the most efficient use of those stocks, genebank staff need techniques that accurately and efficiently characterize the genetic components of seedlots that often have variable individuals within them. We tested DNA of many individuals within four different potato species to confirm the genetics within the population, then developed a technique to take a single bulk DNA sample that returns a fingerprint that catches 100% of the individuals’ genetics. That gives us a 25-fold reduction in time and costs for the same information. We are going to apply this to genebank populations in order to better advise researchers and breeders which populations are the best for use in improving the yield, quality and profitability of the US potato crop for farmers and consumers.

Technical Abstract: Most of the germplasm in the US Potato Genebank is in the form of seedlots with varying degrees of genetic diversity within and among them, so we want to know the most efficient way to measure it. One seedlot of each of four species with different ploidies and breeding systems (S. fendleri, jamesii, microdontum, sucrense) were sown to produce 24 individuals. Three types of bulk samples were also composed. Samples were GBS genotyped with enhanced read depth. We used the shorthand term “Cap2” for loci for which the two SNP alleles known to be present among individuals were detected in the bulk (i.e., Captured). After loci with any missing calls or with one fixed allele were eliminated, 100% of the remaining loci were potentially Cap2. Cap2 was assessed in loci categorized by different combinations of average minor allele frequencies (MAF) of individuals and read depth of the bulks. For loci with at least 5% MAF and at least 100 reads, the average individual had a Cap2 of only 81%, but all bulks, regardless of species or bulking method had a Cap2 bulk average of 100% (average 8K loci with average 144 reads). Of course, one could precisely assess a seedlot’s diversity by genotyping many of its individuals, but bulking followed by assessing just the high-read loci with MAF of at least 5% gives efficient optimal detection of the whole genetic picture of a population in a single sample.