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Genome-Wide Association Analysis of Common Scab Resistance and Expression Profiling of Tubers in Response to Thaxtomin A Treatment Underscore the Complexity of Common Scab Resistance in Tetraploid Potato

Abstract

Common scab of potato caused by pathogenic Streptomyces species poses an economic burden to commercial potato cultivation. Despite decades of research, no molecular markers linked to this trait are currently available, making the development of scab resistant potato varieties inefficient. We evaluated common scab lesion type and tuber coverage in 198 individuals segregating for common scab resistance in replicated field trials with high natural disease pressure over two growing seasons. To identify genetic features associated with resistance, we genotyped the tetraploid (4x) population and parental lines (Kalkaska and Tundra) using the Illumina Infinium 8303 Potato Array and conducted genome-wide association analysis. Here, we report two significant single nucleotide polymorphism (SNP) markers on chromosome 1 associated with both scab traits in both years as well as a SNP marker on chromosome 2 associated with scab tuber coverage. Gene expression profiling of the parents of this population in response to Thaxtomin A treatment revealed differential expression of genes in tubers putatively involved in cell wall biosynthesis and hormone signaling.

Resumen

La roña común de la papa, causada por especies patogénicas de Streptomyces, representa una carga económica al cultivo comercial de papa. A pesar de décadas de investigación, actualmente no se encuentran disponibles marcadores moleculares ligados a este carácter, haciendo ineficiente el desarrollo de variedades de papa resistentes a la roña. Evaluamos el tipo de lesión de la roña común y cubrimiento de tubérculo en 198 individuos segregantes para resistencia a la roña común en ensayos de campo repetidos con alta presión natural de la enfermedad en dos ciclos de cultivo. Para identificar características genéticas asociadas con la resistencia, genotipamos a la población tetraploide (4x) y a las líneas parentales (Kalkaska y Tundra) usando la matriz de papa Illumina infinitum 8303 y se condujo el análisis de la asociación amplia del genoma. Aquí reportamos dos marcadores significativos de polimorfismo de nucleótido individual (SNP) en el cromosoma 1 asociados tanto a caracteres de la roña en ambos años como al marcador SNP en el cromosoma 2 asociado con el cubrimiento de la roña en el tubérculo. El perfil de la expresión génica de los progenitores de esta población en respuesta a tratamiento con Thaxtomin A reveló expresión diferencial de genes en tubérculos putativamente involucrados en la biosíntesis de pared celular y en señalamiento hormonal.

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Funding

This work was supported by funds from the U.S. Department of Agriculture, National Institute of Food and Agriculture, Agriculture and Food Research Initiative Plant Breeding, Genetics, and Genome grant 2009-85606-05673 to David Douches. This project was also supported by Project GREEEN (Generating Research and Extension to meet Economic and Environmental Needs) funding awarded to Project Director David Douches and funds from the Solanaceae Coordinated Agriculture Project (SOLCAP).

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Kaiser, N., Coombs, J., Felcher, K. et al. Genome-Wide Association Analysis of Common Scab Resistance and Expression Profiling of Tubers in Response to Thaxtomin A Treatment Underscore the Complexity of Common Scab Resistance in Tetraploid Potato. Am. J. Potato Res. 97, 513–522 (2020). https://doi.org/10.1007/s12230-020-09800-5

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Keywords

  • Streptomyces
  • Common scab
  • GWAS
  • RNAseq