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A Consensus Linkage Map Provides Insights on Genome Character and Evolution in Common Carp (Cyprinus carpio L.)

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Abstract

Common carp (Cyprinus carpio L.) is cultured worldwide and is a major contributor to the world’s aquaculture production. The common carp has a complex tetraploidized genome, which may historically experience additional whole genome duplication than most other Cyprinids. Fine maps for female and male carp were constructed using a mapping panel containing one F1 family with 190 progeny. A total of 1,025 polymorphic markers were used to construct genetic maps. For the female map, 559 microsatellite markers in 50 linkage groups cover 3,468 cM of the genome. For the male map, 383 markers in 49 linkage groups cover 1,811 cM of the genome. The consensus map was constructed by integrating the new map with two published linkage maps, containing 732 markers and spanning 3,278 cM in 50 linkage groups. The number of consensus linkage groups corresponds to the number of common carp chromosomes. A significant difference on sex recombinant rate was observed that the ratio of female and male recombination rates was 4.2:1. Comparative analysis was performed between linkage map of common carp and genome of zebrafish (Danio rerio), which revealed clear 2:1 relationship of common carp linkage groups and zebrafish chromosomes. The results provided evidence that common carp did experienced a specific whole genome duplication event comparing with most other Cyprinids. The consensus linkage map provides an important tool for genetic and genome study of common carp and facilitates genetic selection and breeding for common carp industry.

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Acknowledgments

The authors would like to thank Yu Chang, Tingting Sun, Yulan Xu, Sen Yin, Wei Liu, Binbin Yu, Baoyong Zhang, Zhiwu Jia, Xuanpeng Wang, Wensheng Li, Tianqi Zhang, Zhu Cao, Cui Liu, Zhiyuan Chu, Zhaojun Tan, Weihua Lv, and Qian Yu. This study was supported by the Key Project of Chinese National Programs for Fundamental Research and Development (2010CB126305), the National Department Public Benefit Research Foundation of China (200903045), the National High-tech R&D Program of China (2011AA100401), and the Introduction of Advanced Agricultural Science and Technology Key Project (“948” Project: 2011-G12).

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Authors and Affiliations

  1. Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China

    Xiaofeng Zhang, Xianhu Zheng, Youyi Kuang, Chao Li, Dingchen Cao, Cuiyun Lu & Xiaowen Sun

  2. Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China

    Yan Zhang, Zixia Zhao, Lan Zhao, Li Jiang & Peng Xu

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  1. Xiaofeng Zhang
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  2. Yan Zhang
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  3. Xianhu Zheng
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  6. Lan Zhao
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  7. Chao Li
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  8. Li Jiang
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  9. Dingchen Cao
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  10. Cuiyun Lu
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  11. Peng Xu
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  12. Xiaowen Sun
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Corresponding authors

Correspondence to Peng Xu or Xiaowen Sun.

Additional information

X. Zhang and Y. Zhang contributed equally.

Appendix 1

Appendix 1

Table 1 Markers were used in linkage mapping and their distances: some markers did not have NCBI accession in the map of Zheng et al. (2011)
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Table 2 The markers and their pair-wise lengths on sex-specific linkage groups of the common carp
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Table 3 Homolog anchors between common carp genetic map and zebrafish genome
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Zhang, X., Zhang, Y., Zheng, X. et al. A Consensus Linkage Map Provides Insights on Genome Character and Evolution in Common Carp (Cyprinus carpio L.). Mar Biotechnol 15, 275–312 (2013). https://doi.org/10.1007/s10126-012-9485-9

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