Abstract
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.
Highlights
The Cyprinidae family (Telestei) includes about 3,000 species and is the largest family in vertebrate
The raw RNA-sequencing reads of all samples were deposited in the European Nucleotide Archive (ENA) under the project of PRJEB12518
The large-scale synteny in members of the Cyprinidae family and the presence of 1:1, 1:2 and 1:3 synteny correspondences between zebrafish and medaka indicated that complex genome rearrangements took place in Cyprinidae ancestor after its separation from other teleosts
Summary
The Cyprinidae family (Telestei) includes about 3,000 species and is the largest family in vertebrate. Cross-species comparisons revealed that grass carp had a chromosome fusion in relative to zebrafish and that common carp had one more round of whole genome duplication (WGD) than zebrafish. Teleosts are widely believed to have experienced a “fish-specific” third-round (3R) of WGD event This additional round of WGD was considered as the fourth-round (4R) of WGD goldfish would be a valuable model to study the consequences of genome duplication[7]. It is a useful model to study genetic variance as a result of domestication. We examined gene syntenies in goldfish, three Cyprinidae fish (zebrafish, grass carp and common carp), and medaka, to study the genome evolution events in this family. We identified candidate regions and genes related to goldfish growth traits on this map using QTL analysis and association study
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