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.
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.
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
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Mentions: In total, 10 significant QTLs for V. anguillarum disease resistance were distributed on LG6, LG19, and LG21 of Japanese flounder (Table 2 and Fig. 2). Most of these QTLs were clustered together on their respective LGs. One major cluster containing six QTLs (qVA-1, qVA-2, qVA-3, qVA-4, qVA-5, and qVA-6) was detected between the narrow positions of 89.8–108.7 cM on LG6. Among them, qVA-2 located at 95.9–99.3 cM had the highest LOD value, 5, and correspondingly had the highest contribution to phenotypic variation, 8.38%. The other QTLs on LG6 were detected at positions 89.8–90.8, 100.7–102.5, 104.1–105.0, 105.0–105.4, and 107.8–108.7 cM, with LOD values of 3.0–3.6 and contributions to phenotypic variation of 5.1–7.59% (Supplementary Fig. S3). On LG21, another cluster situated within a short region (98.7–101.3 cM) consisted of three QTLs (qVA-8, qVA-9, and qVA-10) with a LOD value of 3.3–3.7 and was able to explain 6.06–6.56% of the phenotypic variation (Supplementary Fig. S3). Finally, qVA-7 containing a single SNP was centred around 115.6 cM on LG 19; it had a LOD value of 15.8 and explained 1.19% of the phenotypic variation. Although these 10 QTLs explained >59.25% of the total phenotypic variation, no major loci (explaining >20% of the total variation) were detected. The fact that these loci do not independently have higher contributions to such a complicated trait is not unexpected. Several genes related to V. anguillarum disease resistance were identified from the higher density map based on the Japanese flounder genome assembly. As shown in Supplementary Table S4, 218 genes were identified from the QTL regions, 12 of which were immune-related genes (tap1, rftn1, satb1, cd40, cd69, aicda, mtss1, ccr4, azi2, mrc1, nod1, and tgfbr2) functioning as key factors in different immune-gene signalling pathways or as antigen receptors. Interestingly, tap1 and satb1 act as molecular organizers for the major histocompatibility complex (MHC) class I,33 while cd40 and cd69 are accessory molecules of MHC class II34 directly involved in V. anguillarum disease resistance in Japanese flounder.Table 2.
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.