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

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 perfor...

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Bibliographic Details
Published in:Scientific reports 2016-10, Vol.6 (1), p.34849-34849, Article 34849
Main Authors: Kuang, You-Yi, Zheng, Xian-Hu, Li, Chun-Yan, Li, Xiao-Min, Cao, Ding-Chen, Tong, Guang-Xiang, Lv, Wei-Hua, Xu, Wei, Zhou, Yi, Zhang, Xiao-Feng, Sun, Zhi-Peng, Mahboob, Shahid, Al-Ghanim, Khalid A., Li, Jiong-Tang, Sun, Xiao-Wen
Format: Article
Language:English
Subjects:
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45/91
631/181/2474
631/208/207
Animals
Biological Evolution
Carp
Chromosome Mapping
Chromosome rearrangements
Cyprinidae - genetics
Cyprinidae - physiology
Divergence
Evolution
Fish
Genome
Genomes
Goldfish - genetics
Goldfish - growth & development
Goldfish - physiology
Humanities and Social Sciences
multidisciplinary
Oryzias - genetics
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Ribonucleic acid
RNA
Science
Selective breeding
Single-nucleotide polymorphism
Speciation
Synteny
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/srep34849