Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish

Abstract

BackgroundPhysical and linkage maps are important aids for the assembly of genome sequences, comparative analyses of synteny, and to search for candidate genes by quantitative trait locus analysis. Yellowtail, Seriola quinqueradiata, is an economically important species in Japanese aquaculture, and genetic information will be useful for DNA-assisted breeding. We report the construction of a second generation radiation hybrid map, its synteny analysis, and a second generation linkage map containing SNPs (single nucleotide polymorphisms) in yellowtail.ResultsApproximately 1.4 million reads were obtained from transcriptome sequence analysis derived from 11 tissues of one individual. To identify SNPs, cDNA libraries were generated from a pool of 500 whole juveniles, and the gills and kidneys of 100 adults. 9,356 putative SNPs were detected in 6,025 contigs, with a minor allele frequency ≥25%. The linkage and radiation hybrid maps were constructed based on these contig sequences. 2,081 markers, including 601 SNPs markers, were mapped onto the linkage map, and 1,532 markers were mapped in the radiation hybrid map.ConclusionsThe second generation linkage and physical maps were constructed using 6,025 contigs having SNP markers. These maps will aid the de novo assembly of sequencing reads, linkage studies and the identification of candidate genes related to important traits. The comparison of marker contigs in the radiation hybrid map indicated that yellowtail is evolutionarily closer to medaka than to green-spotted pufferfish, three-spined stickleback or zebrafish. The synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1600-7) contains supplementary material, which is available to authorized users.

Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species

“…Our results suggest that the chromosome structure of the Pacific bluefin tuna could also be the conserved structure of the MTZ-ancestor because of the high similarity between the chromosome structures of the two species. Yellowtail (Perciformes) chromosome structure is highly similar with that of the MTZ ancestor [48]. Our results support these yellowtail results at the whole genome level.…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…The sex-averaged map contained a total of 4608 SNPs, which covered 1581.7 cM, with average distance between SNPs of 0.34 cM. Physical and linkage maps for yellowtail (Seriola quinqueradiata), an important species in fish aquaculture in Japan was constructed using SNP obtained from NGS results and synteny with four model fish species was analyzed (Aoki et al, 2015). A double digest RAD (ddRAD)-based genetic linkage map was generated for the Japanese eel Anguilla japonica (Kai et al, 2014).…”

Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili

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