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

Aoki JY, Kai W, Kawabata Y, Ozaki A, Yoshida K, Koyama T, Sakamoto T, Araki K - BMC Genomics (2015)

Bottom Line: The 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 synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.

View Article: PubMed Central - PubMed

Affiliation: National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan. junaoki@affrc.go.jp.

ABSTRACT

Background: Physical 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.

Results: Approximately 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.

Conclusions: The 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.

No MeSH data available.


Related in: MedlinePlus

Examples of four radiation hybrid (RH) groups. Each group has 79 markers in SQ1, 70 markers in SQ2, 60 markers in SQ3 and 69 markers in SQ4. Distances between markers are shown in centiRays (cR).
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Fig3: Examples of four radiation hybrid (RH) groups. Each group has 79 markers in SQ1, 70 markers in SQ2, 60 markers in SQ3 and 69 markers in SQ4. Distances between markers are shown in centiRays (cR).

Mentions: PCR on a dynamic array produces high-throughput gene expression data that are essentially identical in quality to conventional microliter qRT-PCR and are superior to publicly available array data from the same tissue type [36]. In our previous study, 580 markers were mapped in the first RH map [32]. 1,563 markers, containing the previous 580 markers, were used to construct the RH map. The two-point analysis, performed at a LOD score of 4.0 and a distance threshold of 50, resulted in 75 groups using CarthaGene software [37,38]. Furthermore, with reference to the locations of several markers on the constructed genetic linkage map, 1,532 markers (1433 EST markers containing SNPs and 99SSR markers) were distributed to 24 linkage groups (Tables 3 and 4, Figure 3, Additional file 2). Thirty-one markers in eight groups were not distributed among the genetic linkage groups because of their LOD score or a distance threshold error. The RH map was constructed with a final set of 1,532 markers. In each group, the RH map ranged from 640.7 to 1,343.3 centiRays (cR), with an average of approximately 1,096 cR. The combined size of all RH groups was 26,293.5 cR. The estimated size of the yellowtail genome is 800 Mbp [24], which inferred a value of 1 cR = 30 kbp (800 Mbp/26,293.5 cR). We have obtained a large quantity of data in a short time using the BioMark™ HD system since the construction of the first RH map.Table 3


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

Aoki JY, Kai W, Kawabata Y, Ozaki A, Yoshida K, Koyama T, Sakamoto T, Araki K - BMC Genomics (2015)

Examples of four radiation hybrid (RH) groups. Each group has 79 markers in SQ1, 70 markers in SQ2, 60 markers in SQ3 and 69 markers in SQ4. Distances between markers are shown in centiRays (cR).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493941&req=5

Fig3: Examples of four radiation hybrid (RH) groups. Each group has 79 markers in SQ1, 70 markers in SQ2, 60 markers in SQ3 and 69 markers in SQ4. Distances between markers are shown in centiRays (cR).
Mentions: PCR on a dynamic array produces high-throughput gene expression data that are essentially identical in quality to conventional microliter qRT-PCR and are superior to publicly available array data from the same tissue type [36]. In our previous study, 580 markers were mapped in the first RH map [32]. 1,563 markers, containing the previous 580 markers, were used to construct the RH map. The two-point analysis, performed at a LOD score of 4.0 and a distance threshold of 50, resulted in 75 groups using CarthaGene software [37,38]. Furthermore, with reference to the locations of several markers on the constructed genetic linkage map, 1,532 markers (1433 EST markers containing SNPs and 99SSR markers) were distributed to 24 linkage groups (Tables 3 and 4, Figure 3, Additional file 2). Thirty-one markers in eight groups were not distributed among the genetic linkage groups because of their LOD score or a distance threshold error. The RH map was constructed with a final set of 1,532 markers. In each group, the RH map ranged from 640.7 to 1,343.3 centiRays (cR), with an average of approximately 1,096 cR. The combined size of all RH groups was 26,293.5 cR. The estimated size of the yellowtail genome is 800 Mbp [24], which inferred a value of 1 cR = 30 kbp (800 Mbp/26,293.5 cR). We have obtained a large quantity of data in a short time using the BioMark™ HD system since the construction of the first RH map.Table 3

Bottom Line: The 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 synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.

View Article: PubMed Central - PubMed

Affiliation: National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan. junaoki@affrc.go.jp.

ABSTRACT

Background: Physical 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.

Results: Approximately 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.

Conclusions: The 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.

No MeSH data available.


Related in: MedlinePlus