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Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.

Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, Wang L, Jiang Y, Tai S, Tian Y, Sakamoto T, Chen S - DNA Res. (2015)

Bottom Line: Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance.The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes).Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence.

View Article: PubMed Central - PubMed

Affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan.

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Related in: MedlinePlus

Linkage group lengths and marker distribution of the high-resolution restriction site-associated DNA sequencing-based SNP genetic map of Japanese flounder. Within each linkage group, red, blue, and yellow lines, respectively, represent maternal heterozygous SNPs, paternal heterozygous SNPs, and SNPs heterozygous in both parents. Genetic map details are given in Supplementary Table S3.
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DSV001F1: Linkage group lengths and marker distribution of the high-resolution restriction site-associated DNA sequencing-based SNP genetic map of Japanese flounder. Within each linkage group, red, blue, and yellow lines, respectively, represent maternal heterozygous SNPs, paternal heterozygous SNPs, and SNPs heterozygous in both parents. Genetic map details are given in Supplementary Table S3.

Mentions: A high-resolution RAD-based SNP genetic map of Japanese flounder based on a pseudo-testcross population was first constructed using Lep-MAP. A total of 12,712 segregating SNPs (95.14%) were successfully classified into 24 LGs (Table 1 and Fig. 1). The paternal map contained 8,784 SNPs with a total genetic distance of 2,561.17 cM; the length of each LG ranged from 19.53 cM (LG8) to 145.08 cM (LG19), with an average genetic length of 106.72 cM (Supplementary Fig. S1). The corresponding maternal map consisted of 6,343 SNPs representing a total length of 2,356.86 cM and ranging from 0.6 cM (LG8) to 187.33 cM (LG1) (Supplementary Fig. S2). More interestingly, LG8 was the smallest LG on both maternal (0.6 cM) and paternal maps (19.53 cM). LG8 on the maternal map contained only 3 SNPs heterozygous in both parents; on the paternal map, LG8 included 135 paternal heterozygous SNPs and 3 SNPs heterozygous in both parents. The resulting integrated map consisted of 24 LGs including 12,712 SNPs, which corresponded to 7,430 effective loci. The total map length was 3,497.29 cM, with an average inter-locus distance of 0.47 cM; the genetic length of each LG ranged from 21.64 cM (LG8) to 221.14 cM (LG20), with an average inter-locus distance of 0.37–0.75 cM. LG1 was the densest, having 495 effective loci with an average density of 0.42 cM, whereas LG8 had the least number of effective loci (only 59). On average, each LG contained 310 effective loci spanning 145.72 cM (Table 1 and Fig. 1). Locus names and SNP positions on the 24 LGs of the integrated genetic map are listed in Supplementary Table S3.Table 1.


Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.

Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, Wang L, Jiang Y, Tai S, Tian Y, Sakamoto T, Chen S - DNA Res. (2015)

Linkage group lengths and marker distribution of the high-resolution restriction site-associated DNA sequencing-based SNP genetic map of Japanese flounder. Within each linkage group, red, blue, and yellow lines, respectively, represent maternal heterozygous SNPs, paternal heterozygous SNPs, and SNPs heterozygous in both parents. Genetic map details are given in Supplementary Table S3.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401326&req=5

DSV001F1: Linkage group lengths and marker distribution of the high-resolution restriction site-associated DNA sequencing-based SNP genetic map of Japanese flounder. Within each linkage group, red, blue, and yellow lines, respectively, represent maternal heterozygous SNPs, paternal heterozygous SNPs, and SNPs heterozygous in both parents. Genetic map details are given in Supplementary Table S3.
Mentions: A high-resolution RAD-based SNP genetic map of Japanese flounder based on a pseudo-testcross population was first constructed using Lep-MAP. A total of 12,712 segregating SNPs (95.14%) were successfully classified into 24 LGs (Table 1 and Fig. 1). The paternal map contained 8,784 SNPs with a total genetic distance of 2,561.17 cM; the length of each LG ranged from 19.53 cM (LG8) to 145.08 cM (LG19), with an average genetic length of 106.72 cM (Supplementary Fig. S1). The corresponding maternal map consisted of 6,343 SNPs representing a total length of 2,356.86 cM and ranging from 0.6 cM (LG8) to 187.33 cM (LG1) (Supplementary Fig. S2). More interestingly, LG8 was the smallest LG on both maternal (0.6 cM) and paternal maps (19.53 cM). LG8 on the maternal map contained only 3 SNPs heterozygous in both parents; on the paternal map, LG8 included 135 paternal heterozygous SNPs and 3 SNPs heterozygous in both parents. The resulting integrated map consisted of 24 LGs including 12,712 SNPs, which corresponded to 7,430 effective loci. The total map length was 3,497.29 cM, with an average inter-locus distance of 0.47 cM; the genetic length of each LG ranged from 21.64 cM (LG8) to 221.14 cM (LG20), with an average inter-locus distance of 0.37–0.75 cM. LG1 was the densest, having 495 effective loci with an average density of 0.42 cM, whereas LG8 had the least number of effective loci (only 59). On average, each LG contained 310 effective loci spanning 145.72 cM (Table 1 and Fig. 1). Locus names and SNP positions on the 24 LGs of the integrated genetic map are listed in Supplementary Table S3.Table 1.

Bottom Line: Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance.The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes).Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence.

View Article: PubMed Central - PubMed

Affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan.

Show MeSH
Related in: MedlinePlus