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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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Related in: MedlinePlus

Yellowtail female (left) and male (right) maps for linkage groups Squ1- Squ24. Total lengths of linkage groups are expressed in Kosambi cM. BES-derived SSR markers are coded “BAC” after a number, and microsatellite markers developed from genomic library are coded “TUF”.
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Figure 1: Yellowtail female (left) and male (right) maps for linkage groups Squ1- Squ24. Total lengths of linkage groups are expressed in Kosambi cM. BES-derived SSR markers are coded “BAC” after a number, and microsatellite markers developed from genomic library are coded “TUF”.

Mentions: Resultant yellowtail female and male genetic map consists of 715 and 702 markers including 232 and 271 framework markers, spanning 1,026.65 and 1,057.83 cM Kosambi with an average interval 4.96 and 4.32 cM on 24 linkage groups respectively (Table 4, Figure 1). The number of chromosomes in yellowtail has been reported to be 2n = 48 and hence the SSR markers we developed are distributed throughout the yellowtail genome [28]. The “gaps” observed in Squ21 and 24 in male and both map respectively might be caused by “recombination hot-spots” where recombination occurs frequently (Figure 1). The genome length was estimated to be 1,274.64 (L1) and 1,284.34 (L2) cM in the female and 1,282.35 (L1) and 1,285.45 (L2) cM in the male map by the two different methods respectively (see Materials and Methods). Using formula c = 1 – e-2dn/L and estimated genome length L, coverage of the female and male map is estimated to be 83.3 to 83.9% respectively (Table 4). Considering the average interval less than 10 cM and the genome coverage, we concluded that the yellowtail genetic map was sufficient for further QTL studies [29].


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)

Yellowtail female (left) and male (right) maps for linkage groups Squ1- Squ24. Total lengths of linkage groups are expressed in Kosambi cM. BES-derived SSR markers are coded “BAC” after a number, and microsatellite markers developed from genomic library are coded “TUF”.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Yellowtail female (left) and male (right) maps for linkage groups Squ1- Squ24. Total lengths of linkage groups are expressed in Kosambi cM. BES-derived SSR markers are coded “BAC” after a number, and microsatellite markers developed from genomic library are coded “TUF”.
Mentions: Resultant yellowtail female and male genetic map consists of 715 and 702 markers including 232 and 271 framework markers, spanning 1,026.65 and 1,057.83 cM Kosambi with an average interval 4.96 and 4.32 cM on 24 linkage groups respectively (Table 4, Figure 1). The number of chromosomes in yellowtail has been reported to be 2n = 48 and hence the SSR markers we developed are distributed throughout the yellowtail genome [28]. The “gaps” observed in Squ21 and 24 in male and both map respectively might be caused by “recombination hot-spots” where recombination occurs frequently (Figure 1). The genome length was estimated to be 1,274.64 (L1) and 1,284.34 (L2) cM in the female and 1,282.35 (L1) and 1,285.45 (L2) cM in the male map by the two different methods respectively (see Materials and Methods). Using formula c = 1 – e-2dn/L and estimated genome length L, coverage of the female and male map is estimated to be 83.3 to 83.9% respectively (Table 4). Considering the average interval less than 10 cM and the genome coverage, we concluded that the yellowtail genetic map was sufficient for further QTL studies [29].

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