Limits...
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 two linkage groups (female and male). Squ1 has 53 and 48 markers, including 20 and 14 SNPs, in the female and male, respectively. Squ2 has 82 and 77 markers, including 11 and 11 SNPs, in the female and male, respectively. Distances between markers are shown in centiMorgans (cM).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Examples of two linkage groups (female and male). Squ1 has 53 and 48 markers, including 20 and 14 SNPs, in the female and male, respectively. Squ2 has 82 and 77 markers, including 11 and 11 SNPs, in the female and male, respectively. Distances between markers are shown in centiMorgans (cM).

Mentions: Direct sequencing identified 143 informative SNPs that were heterozygous in either one of the parents, and these heterozygous SNPs were used for linkage analysis using the F1 mapping progeny. In the SNPtype assay, 458 SNPs were mapped to the linkage map (Tables 1 and 2, Figure 2, Additional file 1). 2081 markers containing 601 SNPs, which were polymorphic in the F1 mapping progeny, were mapped in the linkage map, and 606 markers were common for both sexes. In this study, SNPs were mapped for the first time in a yellowtail linkage map.Table 1


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 two linkage groups (female and male). Squ1 has 53 and 48 markers, including 20 and 14 SNPs, in the female and male, respectively. Squ2 has 82 and 77 markers, including 11 and 11 SNPs, in the female and male, respectively. Distances between markers are shown in centiMorgans (cM).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Examples of two linkage groups (female and male). Squ1 has 53 and 48 markers, including 20 and 14 SNPs, in the female and male, respectively. Squ2 has 82 and 77 markers, including 11 and 11 SNPs, in the female and male, respectively. Distances between markers are shown in centiMorgans (cM).
Mentions: Direct sequencing identified 143 informative SNPs that were heterozygous in either one of the parents, and these heterozygous SNPs were used for linkage analysis using the F1 mapping progeny. In the SNPtype assay, 458 SNPs were mapped to the linkage map (Tables 1 and 2, Figure 2, Additional file 1). 2081 markers containing 601 SNPs, which were polymorphic in the F1 mapping progeny, were mapped in the linkage map, and 606 markers were common for both sexes. In this study, SNPs were mapped for the first time in a yellowtail linkage map.Table 1

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