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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #402386
Research Project: Potato Genetic Improvement for Enhanced Tuber Quality and Greater Productivity and Sustainability in Western U.S. Production

Location: Small Grains and Potato Germplasm Research

Title: The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids

Author
item ACHAKKAGARI, SAI - McGill University - Canada
item BOZAN, ILLYADA - McGill University - Canada
item CAMARGO-TAVARES, J - McGill University - Canada
item MCCOY, H - University Of New Brunswick
item PORTAL, L - International Potato Center
item SOTO, J - International Potato Center
item BIZIMUNGU, BENOIT - Agriculture Canada
item Anglin, Noelle
item MANRIQUE-CARPINTERO, NORMA - International Potato Center
item LINDQVIST-KREUZE, HANNELE - International Potato Center
item TAI, HELEN - Agriculture Canada
item STROMVIK, MARTINA - McGill University - Canada

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2024
Publication Date: 5/4/2024
Citation: Achakkagari, S., Bozan, I., Camargo-Tavares, J.C., McCoy, H.J., Portal, L., Soto, J., Bizimungu, B., Anglin, N.L., Manrique-Carpintero, N., Lindqvist-Kreuze, H., Tai, H., Stromvik, M. 2024. The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids. Scientific Data. 11. Article 454. https://doi.org/10.1038/s41597-024-03300-5.
DOI: https://doi.org/10.1038/s41597-024-03300-5

Interpretive Summary: Wild potato species, while mostly not suitable for human consumption or agronomic production, are of value to improve cultivated potato. The wilds are highly diverse and contain traits that are often not found in cultivated potato especially traits such as disease and virus resistance. These traits can be utilized in cultivated potato and provide value by decreasing crop loss for growers which are inflicted by pathogens in the environment, and thus, increasing the overall yield of cultivated potato grown in the field. However, in order to harness these traits from the wilds, their DNA needs to be sequenced, characterized, and the genes containing these valuable traits need to be identified. In this study, the authors identified wild species that had known resistant traits and had been frequently used by potato breeders to improve cultivated potato by traditional breeding methods. These species were targeted for whole genome sequencing revealing their DNA content. This work describes the wild species targeted, release of their whole genome sequence data, the evaluation of gene content and the diversity among the species targeted.

Technical Abstract: Potato is an important crop in the genus Solanum section Petota. Potato is susceptible to abiotic and biotic stress and improvement through breeding which is carried out worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance potato germplasm. The current data set is a contribution of Illumina short read sequences and de novo assemblies for genomes of 22 wild species in section Petota that were noted for stress resistance and were of interest to potato breeders. An additional genome from S. etuberosum, which is outside of section Petota was also included. The genomes are from tetraploids and diploids as well as hybrids with cultivated potato. Both nuclear and organellar genome sequences are provided. Annotation used transcriptome sequence data. High quality assemblies were achieved with genome sizes ranging from 575 to 795 Mbp. Genomes were compared for presence/absence of genes and phylogenetic analysis was done using plastome and nuclear genomes.