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A System for Identification of Potato Varieties Using SNP Dosage

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Abstract

As in autoteraploids, five genotypes are possible in a biallelic locus, allele dosage could be useful for variety identification in potato. DNA sequences of 13 genes associated with tuber yield, tuber starch content or late blight resistance were surveyed for single nucleotide polymorphism (SNP) in eight tetraploid varieties. A total of 193 potential SNPs was found by Sanger-sequencing, of which 58 were measured for nucleotide frequencies using a pyrosequencer. Of the 58 SNPs, 35 yielded distinct clusters, corresponding to allele dosages. Among these, six were highly correlated with another, leaving 29 independent SNP loci for use in variety discrimination. By using dosage scores at the 29 SNP loci, it was possible to differentiate 115 varieties, except for a sport with red tuber skin color, with at least three different SNP dosages. Therefore, using SNP dosages is a simple, fast and reliable tool for variety identification.

Resumen

Como en los autotetraploides, cinco genotipos son posibles en un locus bialelico, la dosis de alelo podría ser útil para la identificación de variedades en papa. Se estudiaron las secuencias de ADN de 13 genes asociados con el rendimiento de tubérculo, su contenido de almidón, o resistencia al tizón tardío, para un polimorfismo de nucleótido simple (SNP en inglés) en ocho variedades tetraploides. Se encontró un total de 193 SNPs mediante secuenciación Sanger, de los cuales se midieron 58 para frecuencias de nucleótidos utilizando un polisecuenciador. De los 58 SNPs, 35 arrojaron diferentes agrupamientos, correspondientes a dosis de alelo. Entre estos, seis estuvieron altamente correlacionados con otro, dejando 29 loci SNP independientes para utilizarse en la discriminación varietal. Mediante el uso de mediciones de dosis en los 29 loci SNP fue posible diferenciar 115 variedades, excepto una con tubérculo de piel roja, con por lo menos tres diferentes dosis de SNP. De aquí que, el uso de dosis de SNP es una herramienta simple, rápida y confiable, para la identificación varietal.

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Acknowledgments

We would like to thank Senior Editor Richard Veilleux for his help in correcting the manuscript and Eri Kakuta for technical assistance. This research was supported by Calbee Inc., Hokkaido Potato Growers Association, Kewpie Corp., KENKO Mayonnaise Co., Ltd., and Japan Snack Cereal Foods Association.

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  1. Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan

    Harumitsu Sasaki, Rena Sanetomo & Kazuyoshi Hosaka

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  1. Harumitsu Sasaki
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  2. Rena Sanetomo
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  3. Kazuyoshi Hosaka
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Correspondence to Kazuyoshi Hosaka.

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Sasaki, H., Sanetomo, R. & Hosaka, K. A System for Identification of Potato Varieties Using SNP Dosage. Am. J. Potato Res. 94, 513–523 (2017). https://doi.org/10.1007/s12230-017-9588-y

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