Building Genomic Resources to Facilitate the Study and Use of Solanum microdontum, a Wild Relative of Cultivated Potato

Sep 29, 2026

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Solanum microdontum, a diploid wild Andean potato relative, offers untapped genetic diversity that can address key challenges in potato breeding. The work presents a high-quality 772 Mb reference genome anchored to 12 chromosomes, with strong assembly completeness and robust scaffold metrics. Annotation identifies 37,324 protein-coding genes, 65% repetitive sequence, and 1,187 predicted NLR genes, with most aligning to high-confidence models. A k-mer-based kinship matrix from a 107-member diversity panel reveals population structure by geography, supporting enhanced public potato resources for diploid breeding.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages10

Reading Time25 min

AccessFree to download

Introduction

Solanum tuberosum and potato diversity

Solanum microdontum: native range and traits

Resistance to pathogens and key introgressions

G3, 2026, 16(1), jkaf253 [https://doi.org/10.1093/g3journal/jkaf253](https://doi.org/10.1093/g3journal/jkaf253) Advance Access Publication Date: 23 October 2025 Genome Report Building genomic resources to facilitate the study and use of Solanum microdontum, a wild relative of cultivated potato Anne Frances Jarrell , 1 John P. Hamilton,2 ,3 Joshua C. Wood ,2 Brieanne Vaillancourt,2 Jessica Norling,4 David Douches,4 Carol Robin Buell 1 ,2 ,3 ,5 ,* 1Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens GA 30602, United States 2Center for Applied Genetic Technologies, University of Georgia, Athens GA 30602, United States 3Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, United States 4Department of Plant, Microbial and Soil Sciences, Michigan State University, East Lansing, MI 48824, United States 5The Plant Center, University of Georgia, Athens, GA 30602, United States *Corresponding author: Department of Crop and Soil Sciences, University of Georgia, 111 Riverbend Rd, Athens, GA 30602, United States. Email: [robin.buell@uga.edu](robin.buell@uga.edu) Solanum microdontum Bitter is a diploid wild Andean relative of potato that has shaped the domestication and adaptation of modern cultivated potato to diverse environments. S. microdontum has the potential to provide a wealth of untapped genetic material for use in addressing current challenges in potato breeding. Here, we report a high-quality 772 Mb reference genome sequence for S. microdontum that is anchored to 12 chromosomes. The resulting genome assembly has 99.0% complete benchmarking universal single copy orthologs and an N50 scaffold length of over 57 Mb, indicating a high level of completeness. Annotation of the assembly resulted in the identification of 37,324 protein-coding genes and 65% repetitive sequence. A total of 1,187 nucleotide-binding leucine-rich repeat genes were predicted from the assembly, of which, 93.1% overlapped an annotated high-confidence gene model. A k-mer-based kinship matrix derived from a 107-member S. microdontum diversity panel revealed an underlying population structure that corresponds to geographic proximity. The S. microdontum dataset enhances publicly available potato genome resources by providing breeders with genetic, molecular, and germplasm resources for newly developed diploid potato breeding programs. Keywords: Solanum microdontum; potato; diversity; disease resistance Introduction Solanum tuberosum L. , commonly known as the potato, is a tuberous crop that is a staple food crop across the globe. Currently, it is the world’s third most important food crop in terms of consumption, behind only wheat and rice (Devaux et al. 2014) . Potato also delivers more edible biomass and caloric energy per acre than any other food crop (Narváez-Cuenca et al. 2018) . Potato was domesticated 8,000–10,000 years ago in the Andes in South America and brought to Europe during the Columbian exchange. Today, potatoes are cultivated on every continent except Antarctica, due in part to their adaptability. The remarkable diversity of potatoes is reflected in their germplasm resources, which include over 100 recognized wild and cultivated species (Spooner et al. 2014) . While many landraces and wild relatives are diploids, cultivated potato is an autotetraploid; however, the majority of these diploid relatives can hybridize with cultivated potato either directly or through techniques that overcome ploidy barriers (Hanneman 1989; Camadro 2010) . Historically, potato landraces and wild relatives have played an important role in contributing adaptive traits to cultivated potato varieties (Riemanet al. 1954; Plaisted and Hoopes 1989; Jansky et al. 2013) . Solanum microdontum Bitter is a diploid wild species of potato native to the Andes mountains, specifically from Northern Bolivia to Northwestern Argentina (van den Berg and Spooner 1992) . S. microdontumis found across a wide

FAQs

What genome resources are reported for Solanum microdontum?

A high-quality 772 Mb reference genome sequence anchored to 12 chromosomes is reported, including assembly completeness benchmarks and extensive gene and repeat annotations.

Which genetic features were identified from the genome assembly?

The annotation identified 37,324 protein-coding genes and 65% repetitive sequence, and predicted 1,187 NLR genes, with most overlapping high-confidence gene models.

How does the study link Solanum microdontum diversity to population structure?

A k-mer-based kinship matrix derived from a 107-member diversity panel reveals population structure that corresponds to geographic proximity.

Sep 29, 2026

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