Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata

Abstract

BackgroundJapanese amberjack/yellowtail (Seriola quinqueradiata) is a commonly cultured marine fish in Japan. For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions. In selective breeding, information of genetic markers is useful and sufficient to identify individuals carrying advantageous traits but if the aim is to determine the genetic basis of the trait, large insert genomic DNA libraries are essential. In this study, toward prospective understanding of genetic basis of several economically important traits, we constructed a high-coverage bacterial artificial chromosome (BAC) library, obtained sequences from the BAC-end, and constructed comprehensive female and male linkage maps of yellowtail using Simple Sequence Repeat (SSR) markers developed from the BAC-end sequences and a yellowtail genomic library.ResultsThe total insert length of the BAC library we constructed here was estimated to be approximately 11 Gb and hence 16-times larger than the yellowtail genome. Sequencing of the BAC-ends showed a low fraction of repetitive sequences comparable to that in Tetraodon and fugu. A total of 837 SSR markers developed here were distributed among 24 linkage groups spanning 1,026.70 and 1,057.83 cM with an average interval of 4.96 and 4.32 cM in female and male map respectively without any segregation distortion. Oxford grids suggested conserved synteny between yellowtail and stickleback.ConclusionsIn addition to characteristics of yellowtail genome such as low repetitive sequences and conserved synteny with stickleback, our genomic and genetic resources constructed and revealed here will be powerful tools for the yellowtail breeding program and also for studies regarding the genetic basis of traits.

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

“…However, mean lengths of the linkage groups were somewhat shorter (male: 41.4 cM, female: 55.5 cM) compared with linkage maps of other closely related teleosts [11] [37]- [40], suggesting the absence of a marker at the end of a chromosome and that the mapped scaffolds lack telomeric and centromeric repeats. Restriction site-associated DNA (RAD) tag sequencing [41] using a next- generation sequencer is useful to develop several thousand single nucleotide polymorphism markers close to restriction endonuclease sites.…”

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

“…To construct the second generation linkage map, a mapping population was obtained by artificial crossing, as described previously [ 25 ]. Direct sequencing of the PCR products and the SNPtype assay of BioMark™ HD system in Fluidigm (USA) were used to perform SNP genotyping.…”

“…Thermo-cycling and fluorescence detection were conducted on the BioMark™ HD system (Fluidigm). Finally, linkage analysis was performed as described previously [ 25 ]. Linkage analysis was performed using genotype data converted to a backcross format.…”

“…In genetic studies of Seriola , the first linkage map between S. quinqueradiata and S. lalandi was produced by Ohara et al [ 24 ]. Recently, the linkage map has been improved by the addition of more simple sequence repeat (SSR) markers, derived from bacterial artificial chromosome (BAC) end sequences [ 25 ]. In this study, a second generation linkage map was produced, represented by 24 linkage groups and having 601 SNP markers.…”

The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract

“…The R/qtl package 25 was employed for linkage analysis and linkage map construction with the same parameters as previously described in. 20 Linkage group (LG) numbering and orientation followed that of Fuji et al 10 To detect the possibility of misassembled chimeric scaffolds, the linkage marker sequences were mapped to the scaffold sequences with BLASTN using the same criteria as previously described in 20 ; the scaffolds attributed to two or more LGs were split into consistent scaffolds based on the locations of markers. Scaffolds >2 kb in length were used for subsequent analysis.…”