4.7 Article

The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family

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SCIENTIFIC REPORTS
卷 6, 期 -, 页码 -

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NATURE PORTFOLIO
DOI: 10.1038/srep34849

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  1. Special Scientific Research Funds for Central Non-profit Institutes Special Funds, Chinese Academy of Fishery Sciences [2015B03XK01]
  2. National Natural Science Foundation of China [31402353]
  3. China Ministry of Science and Technology 863 Hi-Tech Research and Development Program [2011AA100402]
  4. King Saud University [RG-1435-012]

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A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.

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