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Molecular marker development and primary physical map construction for the tuber shape Ro gene locus in diploid potato (Solanum tuberosum L.)

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Abstract

Potato (Solanum tuberosum L.) is an important crop worldwide that is consumed fresh and processed in many different ways. The tuber shape is a critical trait in potato breeding, because it directly affects processing quality. Previous studies have demonstrated that the Ro locus on chromosome X is the major locus controlling tuber shape, and the round shape allele, Ro, is dominant over the long shape allele, ro. However, no reports on the cloning or physical mapping of this locus have been published. In this study, whole genome sequencing and bacterial artificial chromosome (BAC) library construction were applied to develop molecular markers and construct a physical map of Ro. Eight round-tuber genotypes were used to construct the BAC library, which contains about 40,000 clones with an average insert size of 85 kb and represents approximately four haploid potato genomes. A total of 66 individuals with extreme round or long tubers were selected to construct a round-tuber shape DNA bulk and a long-tuber shape DNA bulk for WGS. Single-nucleotide polymorphisms (SNPs) identified from WGS data were used to develop nine polymorphic markers linked to Ro. These markers were used to screen the BAC library, and eight positive BAC clones were ultimately identified and then analyzed by restriction enzyme digestion and BAC end sequencing and used to develop markers and identify new positive BAC clones. Finally, a primary physical map of Ro was constructed using a chromosome walking strategy. This map provides an important reference for cloning the potato tuber shape gene and studying tuber shape variation.

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Acknowledgements

This research was supported by the National Natural Science Fund of China (31561143006, 31801421), National Key R&D Program of China (2017YFD0101905), and the China Agriculture Research System (CARS-9). We thank Prof. De Jong (Department of Plant Genetics and Breeding, Cornell University, USA) for kindly providing the potato parent materials.

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Authors and Affiliations

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences / Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture, Beijing, 100081, China

    Na Chen, Wenwen Zhu, Jianfei Xu, Shaoguang Duan, Chunsong Bian, Jun Hu, Wanxing Wang, Guangcun Li & Liping Jin

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  1. Na Chen
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  2. Wenwen Zhu
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  3. Jianfei Xu
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  6. Jun Hu
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  7. Wanxing Wang
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  8. Guangcun Li
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Correspondence to Guangcun Li or Liping Jin.

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Chen, N., Zhu, W., Xu, J. et al. Molecular marker development and primary physical map construction for the tuber shape Ro gene locus in diploid potato (Solanum tuberosum L.). Mol Breeding 39, 6 (2019). https://doi.org/10.1007/s11032-018-0913-z

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