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Association of Genome-Wide SNP Markers with Resistance to Common Scab of Potato

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Abstract

Common scab is a soilborne disease that occurs in potato worldwide. Scab is usually present superficially on potato tubers but nonetheless reduces marketability. A genome-wide association study for common scab resistance was performed using 13,002 genome-wide SNPs, with 165 genotypes mostly for chip-processing. We identified a novel QTL for common scab resistance that explained at most 14.7% of the total variance; this QTL was within the 640 kb interval between 0.43 Mb and 1.07 Mb on potato chromosome 1. Recessive homozygosity at this QTL increased levels of resistance. There is no agreement in terms of the locations of QTLs and their genetic modes between the results of previous studies and the present study or among any study. As such, common scab resistance is a highly complex trait, as the QTLs discovered to date are all minor-effect QTLs.

Resumen

La roña común es una enfermedad del suelo que se presenta en la papa en todo el mundo. La roña esta presente generalmente en la superficie de los tubérculos, pero de todas maneras reduce la comercialización. Se condujo un estudio de asociación amplia de genomio para la resistencia a la roña común, usando una amplitud de genomio de 13,002 SNPs con 165 genotipos, mayormente para procesamiento de fritura. Identificamos un novedoso QTL para resistencia a la roña común que explicó cuando más el 14.7% de la varianza total. Este QTL estaba dentro del intervalo de 640 kb entre 0.43 Mb y 1.07 Mb en el cromosoma 1 de la papa. La homocigocidad recesiva en este QTL aumentó los niveles de resistencia. No hay un acuerdo en términos de las ubicaciones de los QTLs y sus modos genéticos entre los resultados de estudios previos y el presente estudio o entre cualquier estudio. Como tal, la resistencia a la roña común es un rasgo altamente complejo, de manera que los QTLs descubiertos a la fecha son todos de efecto menor.

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Acknowledgments

We thank Dr. S. Naito, Hokkaido University, for supplying the S. turgidiscabies isolate. This research was supported partly by Calbee Inc.; the Hokkaido Potato Growers Association; Kewpie Corp.; KENKO Mayonnaise Co., Ltd.; and the Japan Snack Cereal Foods Association.

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EK, TI, MT, KO, KA, AK, and RS conducted scab resistance assay. EK, TI, RS, and KH extracted DNA and conducted SNP analysis. EK and KH wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Kazuyoshi Hosaka.

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Koizumi, E., Igarashi, T., Tsuyama, M. et al. Association of Genome-Wide SNP Markers with Resistance to Common Scab of Potato. Am. J. Potato Res. 98, 149–156 (2021). https://doi.org/10.1007/s12230-021-09827-2

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