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Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing

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This manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population.

Abstract

Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of R. sativus cv. WK10039 whose genome has been sequenced onto the chromosomes, we developed a reference genetic map based on genotyping of two parents (maternal WK10039 and paternal WK10024) and 93 individuals of the F2 mapping population by whole-genome resequencing. To develop high-confidence genetic markers, ~83 Gb of parental lines and ~591 Gb of mapping population data were generated as Illumina 100 bp paired-end reads. High stringent sequence analysis of the reads mapped to the 344 Mb of genome sequence scaffolds identified a total of 16,282 SNPs and 150 PCR-based markers. Using a subset of the markers, a high-density genetic map was constructed from the analysis of 2,637 markers spanning 1,538 cM with 1,000 unique framework loci. The genetic markers integrated 295 Mb of genome sequences to the cytogenetically defined chromosome arms. Comparative analysis of the chromosome-anchored sequences with Arabidopsis thaliana and Brassica rapa revealed that the R. sativus genome has evident triplicated sub-genome blocks and the structure of gene space is highly similar to that of B. rapa. The genetic map developed in this study will serve as fundamental genomic resources for the study of R. sativus.

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Acknowledgments

This work was supported by grants from the National Academy of Agricultural Science (PJ009795), RDA to JHM and the Next-Generation Biogreen21 program (PJ008019), RDA to HJY.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The authors declare that the experiments complied with current laws of the country in which they were performed.

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Authors and Affiliations

  1. Department of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea

    Jeong-Hwan Mun

  2. Department of Life Science, The Catholic University of Korea, Bucheon, 420-743, Korea

    Hee Chung, Young-Min Jeong & Hee-Ju Yu

  3. Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea

    Won-Hyong Chung & Namshin Kim

  4. Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea

    Mijin Oh & Byung Ohg Ahn

  5. The Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Korea

    Beom-Seok Park

  6. Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon, 440-706, Korea

    Suhyoung Park

  7. Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Korea

    Ki-Byung Lim

  8. Department of Life Science, Sahmyook University, Seoul, 139-800, Korea

    Yoon-Jung Hwang

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  1. Jeong-Hwan Mun
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Correspondence to Hee-Ju Yu.

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Communicated by Isobel Parkin.

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Mun, JH., Chung, H., Chung, WH. et al. Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing. Theor Appl Genet 128, 259–272 (2015). https://doi.org/10.1007/s00122-014-2426-4

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  • DOI: https://doi.org/10.1007/s00122-014-2426-4

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