Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection

Authors: Anglin, Noelle; CHAVEZ, OSWALDO - International Potato Center; SOTO-TORRES, JULIAN - International Potato Center; GOMEZ, RENE - International Potato Center; PANTA, ANA - International Potato Center; VOLLMER, RAINER - International Potato Center; DURAND,, MARISOL - International Potato Center; MEZA, CHARO - International Potato Center; AZEVEDO, VANIA - International Potato Center; MANRIQUE-CARPINTERO, NORMA - International Potato Center; KAUTH, PHILIP - Seed Savers Exchange; COOMBS, JOSEPH - Michigan State University; DOUCHES, DAVID - Michigan State University; ELLIS, DAVE - International Potato Center

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2024
Publication Date: 7/1/2024
Citation: Anglin, N.L., Chavez, O., Soto-Torres, J., Gomez, R., Panta, A., Vollmer, R., Durand,, M., Meza, C., Azevedo, V., Manrique-Carpintero, N.C., Kauth, P., Coombs, J.J., Douches, D.S., Ellis, D. 2024. Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection. Frontiers in Plant Science. 15:1341788. https://doi.org/10.3389/fpls.2024.1341788.
DOI: https://doi.org/10.3389/fpls.2024.1341788

Interpretive Summary: Errors are known to occur in plant collections especially over time when routine handling and manipulation of the material are part of their care and maintenance. In this work, almost four thousand different potatoes that are part of a germplasm collection were DNA fingerprinted. This was done in order to assess their genetic identity and flush out errors and correct them. The genetic fingerprinting data also allowed an extensive analysis of relatedness among and between individuals of various potato species. Further, analysis was carried out that provided data on which individuals were purely from one genetic group or were hybrids of two species or multiple species along with providing information important for breeding such as how many sets of chromosomes does an individual contain (ploidy). A collection wide assessment of genetic diversity was revealed for the first time in the history of this genebank collection.

Technical Abstract: A total of 3,860 accessions from the global in trust clonal potato germplasm collection maintained at the International Potato Center (CIP) in Lima, Peru were genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling of accessions. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy depending on the species in question. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster based on geographic origin. STRUCTURE analysis identified putative hybrids and suggested six populations in the cultivated potato collection at CIP with extensive gene flow occurring among the potato populations implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum [CUR] displayed significant admixture in these accessions relative to some of the other potato species. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA) / Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession / population perspective relative to the other species. A core and mini core subsets from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection (Ohio, USA) which confirmed no genetic duplication between the CIP and the Seed Savers potato collections suggesting that these organizations hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.