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The genome sequence of ‘Kurodagosun’, a major carrot variety in Japan and China, reveals insights into biological research and carrot breeding

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Abstract

Carrot (Daucus carota L.) is one of the most economically important root vegetables in the world, providing numerous nutrients for human health. China is the largest country of carrot production in the world, and ‘Kurodagosun’ has been a major carrot variety in China. Carrot material used in this study was the inbred line ‘DC-27’, which was derived by forced selfing from ‘Kurodagosun’. To understand the genetic system and plant-specific genes of ‘Kurodagosun’, we report the draft genome sequence of carrot ‘DC-27’ assembled using a combination of Roche454 and HiSeq 2000 sequencing technologies to achieve 32-fold genome coverage. A total of 31,891 predicted genes were identified. These assembled sequences provide candidate genes involved in biological processes including stress response and carotenoid biosynthesis. Genomic sequences corresponding to 371.6 Mb was less than 473 Mb, which is the estimated genome size. The availability of a draft sequence of the ‘DC-27’ genome advances knowledge on the biological research and breeding of carrot, as well as other Apiaceae plants. The ‘DC-27’ genome sequence data also provide a new resource to explore the evolution of other higher plants.

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Acknowledgements

The research was supported by the New Century Excellent Talents in University (NCET-11-0670); Jiangsu Natural Science Foundation (BK20130027); Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). We are grateful to Shanghai Personal Biotechnology Limited Company Co., Ltd. for providing technical help.

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Author notes

  1. Feng Wang and Guang-Long Wang contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China

    Feng Wang, Guang-Long Wang, Xi-Lin Hou, Meng-Yao Li, Zhi-Sheng Xu & Ai-Sheng Xiong

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  1. Feng Wang
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  2. Guang-Long Wang
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  3. Xi-Lin Hou
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  4. Meng-Yao Li
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  6. Ai-Sheng Xiong
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Contributions

Conceived and designed the experiments: ASX, FW. Performed the experiments: FW GLW. Analyzed the data: MYL, XLH, ZSX, FW. Contributed reagents/materials/analysis tools: ASX. Wrote the paper: FW, GLW. Revised the paper: ASX, XLH. All authors read and approved the final manuscript.

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Correspondence to Ai-Sheng Xiong.

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Communicated by S. Hohmann.

Morphological phenotypes, genome sequence, and other related data from this study are available at http://apiaceae.njau.edu.cn/carrotdb.

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Wang, F., Wang, GL., Hou, XL. et al. The genome sequence of ‘Kurodagosun’, a major carrot variety in Japan and China, reveals insights into biological research and carrot breeding. Mol Genet Genomics 293, 861–871 (2018). https://doi.org/10.1007/s00438-018-1428-3

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  • DOI: https://doi.org/10.1007/s00438-018-1428-3

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