A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus)

Abstract

BackgroundJapanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations.ResultsSex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots.ConclusionsThe improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms.

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…Genetic linkage maps were constructed also for some other species important for aquaculture, as gilthead sea bream, Sparus aurata (Tsigenopoulos et al, 2014); Asian seabass, Lates calcarifer Sun et al, 2017); mandarin fish, Siniperca chuatsi ; turbot, Scophthalmus maximus (Wang et al, 2015b); Japanese flounder, Paralichthys olivaceus (Castaño-Sánchez et al, 2010;Shao et al, 2015); large yellow croaker, Larimichthys crocea (Ao et al, 2015); black tiger shrimp, Penaeus monodon (Baranski et al, 2014); Pacific white shrimp, L. annamei (Du et al, 2010); Pacific abalone, Haliotis discus hannai (Qi et al, 2010); South African abalone, Haliotis midae (Vervalle et al, 2013) and silver-lipped pearl oyster, Pinctada maxima (Jones et al, 2013). Linkage maps of commercial fish and shellfish have been listed in other review papers (Wenne et al, 2007;Yue, 2014;Abdelrahman et al, 2017).…”

A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs

“…SNPs are the most frequent type of variation in the genome and provide powerful tools for linkage mapping, and for identifying complex traits in humans (Wang et al 1998) and other model organisms (Zimdahl et al 2004;Guryev et al 2006). However, the application of SNPs in linkage mapping of aquaculture fish is somewhat rare (Moen et al 2008;Kucuktas et al 2009;Castaño-Sánchez et al 2010).…”

Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder

“…Compared to the former ones, this genetic linkage map was constructed with 574 markers including 446 type II SSRs and 128 EST-SSRs, which makes it denser than the maps published before the year of 2008 (Coimbra et al 2003;Castaño-Sánchez et al 2008;Kang et al 2008), but not presently the densest flatfish linkage map. The second generation genetic linkage map of the Japanese flounder were constructed by 1375 markers (Castaño-Sánchez et al 2010). However, the female maps have only 184 unique positions.…”

“…Genetic linkage maps based on molecular markers at a large number of sites in the genome constitute an essential prerequisite to identify individual loci controlling targeted traits. In previous studies, the published Japanese flounder maps (Combria et al 2003;Kang et al 2008;Castaño-Sánchez et al 2010) have provided the framework for identifying a single major controlling the resistance to lymphocystis disease in hybrid family (Fuji et al 2006). A new linkage map of Japanese flounder constructed by Song et al (2012) and QTL associated with four growth traits were mapped.…”