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.
Highlights
Japanese amberjack/yellowtail (Seriola quinqueradiata) is a commonly cultured marine fish in Japan
It is known that a minimum of 5-10 × coverage across the entire genome is required for a bacterial artificial chromosome (BAC) library to be useful for positional cloning, physical mapping, and genome sequencing [19]
The yellowtail BAC library is sufficient for further genomic/ genetic analysis except for studies regarding W-linked genes because of our ZZ male derived DNA source [20]
Summary
Japanese 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. 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. To isolate simple sequence repeats (SSRs) such as microsatellites and to further investigate the genetic basis of the traits, genomic information is essential. BAC libraries have been developed in several domestic animals, e.g. cattle [9], pig [10] and sheep [11], and in fishes, salmon [12], catfish [13], rainbow trout, carp, tilapia [14,15], European sea bass [16,17] and barramundi [18] but in yellowtails a BAC library has not yet been constructed
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