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

Fuji K, Koyama T, Kai W, Kubota S, Yoshida K, Ozaki A, Aoki JY, Kawabata Y, Araki K, Tsuzaki T, Okamoto N, Sakamoto T - BMC Res Notes (2014)

Bottom Line: For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions.Oxford grids suggested conserved synteny between yellowtail and stickleback.In 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo 108-8477, Japan. takashis@kaiyodai.ac.jp.

ABSTRACT

Background: 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. 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.

Results: The 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.

Conclusions: In 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.

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Oxford grids between yellowtail and five model fish genomes. Numbers in boxes indicate the number of orthologous gene pairs. Boxes containing more than ten, seven and five orthologous gene pairs are highlighted in red, yellow and blue respectively.
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Figure 2: Oxford grids between yellowtail and five model fish genomes. Numbers in boxes indicate the number of orthologous gene pairs. Boxes containing more than ten, seven and five orthologous gene pairs are highlighted in red, yellow and blue respectively.

Mentions: In addition to the BAC or whole genome sequence, comparative genome analysis especially conserved synteny would be helpful for fine-scale QTL analyses and/or understanding the genetic basis of the traits [30,31]. BLAST searches of the 818 mapped yellowtail loci against medaka, Tetraodon, stickleback, fugu and zebrafish proved that 25.7, 23.0, 42.2, 24.4 and 9.4% of the loci were mapped to each genome sequence. Oxford grids showed that eighteen linkage group pairs between yellowtail and stickleback retained a one-to-one relationship, and another three stickleback and six yellowtail linkage groups had a one-to-two relationship, implying that chromosomal fusions or breakages occurred after divergence from ancestor of both species (Figure 2). Nevertheless, the result suggests conserved synteny between yellowtail and stickleback and hence the stickleback genome data would be useful as a reference of yellowtail genome.


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

Fuji K, Koyama T, Kai W, Kubota S, Yoshida K, Ozaki A, Aoki JY, Kawabata Y, Araki K, Tsuzaki T, Okamoto N, Sakamoto T - BMC Res Notes (2014)

Oxford grids between yellowtail and five model fish genomes. Numbers in boxes indicate the number of orthologous gene pairs. Boxes containing more than ten, seven and five orthologous gene pairs are highlighted in red, yellow and blue respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230249&req=5

Figure 2: Oxford grids between yellowtail and five model fish genomes. Numbers in boxes indicate the number of orthologous gene pairs. Boxes containing more than ten, seven and five orthologous gene pairs are highlighted in red, yellow and blue respectively.
Mentions: In addition to the BAC or whole genome sequence, comparative genome analysis especially conserved synteny would be helpful for fine-scale QTL analyses and/or understanding the genetic basis of the traits [30,31]. BLAST searches of the 818 mapped yellowtail loci against medaka, Tetraodon, stickleback, fugu and zebrafish proved that 25.7, 23.0, 42.2, 24.4 and 9.4% of the loci were mapped to each genome sequence. Oxford grids showed that eighteen linkage group pairs between yellowtail and stickleback retained a one-to-one relationship, and another three stickleback and six yellowtail linkage groups had a one-to-two relationship, implying that chromosomal fusions or breakages occurred after divergence from ancestor of both species (Figure 2). Nevertheless, the result suggests conserved synteny between yellowtail and stickleback and hence the stickleback genome data would be useful as a reference of yellowtail genome.

Bottom Line: For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions.Oxford grids suggested conserved synteny between yellowtail and stickleback.In 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo 108-8477, Japan. takashis@kaiyodai.ac.jp.

ABSTRACT

Background: 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. 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.

Results: The 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.

Conclusions: In 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.

Show MeSH
Related in: MedlinePlus