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SSR and e-PCR Provide a Bridge Between Genetic Map and Genome Sequence of Potato for Marker Development in Target QTL Region

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Abstract

The aim of this study was to increase marker density in a previously identified late blight resistance QTL in a diploid potato population. SSR markers from the reference potato genome sequence were located by e-PCR in the QTL region in the chromosome 9 genetic map of the diploid potato population B3C1HP, and utilized to identify more candidate genes locating between the SSR markers. After verified by PCR and genetic mapping, two SSR markers and two DM candidate genes were mapped in the QTL peak in the maternal genetic map of B3C1HP. The new markers narrowed down the average 2-LOD support interval from 2.6 to 1.4 cM. The new markers on the LOD peak are valuable for fine mapping and positional cloning of the alleles in late blight resistance QTL. This study proves that combination of SSR and e-PCR is an effective way to develop markers in target QTL region.

Resumen

El objetivo de este estudio era aumentar la densidad de marcadores en un QTL de resistencia a tizón tardío previamente identificado en una población diploide de papa cultivada. Marcadores de SSR de la secuencia del genoma de la papa fueron localizados por e-PCR en la región QTL en el mapa genético del cromosoma 9 del diploide población B3C1HP, y utilizadas para identificar más genes candidatos con la localización entre los marcadores de SSR. Después de verificación por PCR y mapeo genético dos marcadores de SSR y dos genes candidatos DM fueron asignadas en el pico de QTL en el mapa genético de B3C1HP. Los nuevos marcadores redujeron el intervalo medio de soporte 2-LOD de 2.6 a 1.4 cM. Los nuevos marcadores en el pico LOD son valiosos para el mapeo fino y la clonación posicional de los alelos de QTL de resistencia al tizón tardío. Este estudio demuestra que la combinación de SSR y e-PCR es una manera eficaz para desarrollar marcadores en la región QTL.

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Acknowledgments

This work was funded by the National Natural Science Foundation of China (NSFC No. 31261140362) and the China Postdoctoral Science Foundation (2013 M542032).

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Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Biology (Huazhong Agricultural University), Ministry of Education; National Center for Vegetable Improvement (Central China); Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China

    Jingcai Li, Conghua Xie, Zhendong Tian & Jun Liu

  2. International Potato Center, Lima 12, P.O. Box 1558, Lima, Peru

    Hannele Lindqvist-Kreuze & Merideth Bonierbale

Authors
  1. Jingcai Li
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  2. Conghua Xie
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  3. Zhendong Tian
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  4. Hannele Lindqvist-Kreuze
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  5. Merideth Bonierbale
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  6. Jun Liu
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Correspondence to Conghua Xie.

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Li, J., Xie, C., Tian, Z. et al. SSR and e-PCR Provide a Bridge Between Genetic Map and Genome Sequence of Potato for Marker Development in Target QTL Region. Am. J. Potato Res. 92, 312–317 (2015). https://doi.org/10.1007/s12230-015-9432-1

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