Construction of a High-Density Microsatellite Genetic Linkage Map and Mapping of Sexual and Growth-Related Traits in Half-Smooth Tongue Sole (Cynoglossus semilaevis)

Abstract

High-density genetic linkage maps of half-smooth tongue sole were developed with 1007 microsatellite markers, two SCAR markers and an F1 family containing 94. The female map was composed of 828 markers in 21 linkage groups, covering a total of 1447.3 cM, with an average interval 1.83 cM between markers. The male map consisted of 794 markers in 21 linkage groups, spanning 1497.5 cM, with an average interval of 1.96 cM. The female and male maps had 812 and 785 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1527.7 cM for the females and 1582.1 cM for the males. Based on estimations of the map lengths, the female and male maps covered 94.74 and 94.65% of the genome, respectively. The consensus map was composed of 1007 microsatellite markers and two SCAR markers in 21 linkage groups, covering a total of 1624 cM with an average interval of 1.67 cM. Furthermore, 159 sex-linked SSR markers were identified. Five sex-linked microsatellite markers were confirmed in their association with sex in a large number of individuals selected from different families. These sex-linked markers were mapped on the female map LG1f with zero recombination. Two QTLs that were identified for body weight, designated as We-1 and We-2, accounted for 26.39% and 10.60% of the phenotypic variation. Two QTLs for body width, designated Wi-1 and Wi-2, were mapped in LG4f and accounted for 14.33% and 12.83% of the phenotypic variation, respectively. Seven sex-related loci were mapped in LG1f, LG14f and LG1m by CIM, accounting for 12.5–25.2% of the trait variation. The results should prove to be very useful for improving growth traits using molecular MAS.

Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish

“…Of the 10,584 SSR identified in the 5'-UTR, the most abundant is also dinucleotide accounting for 74.3% (7868), followed by tri-, tetra-, penta-and hexa-nucleotide with 14.5% (1532), 10% (1061), 1.1% (118) and 0.04% (5), respectively. Of the 11,654 SSR in the 3'-UTR, the percentage (and number) of di-, tri-, tetra-, penta-and hexa-nucleotide is 77.4% (9015), 13.4% (1559), 8.2% (961), 0.9% (107) and 0.1% (12), respectively ( Figure 1B). Different locations of SSR markers in ESTs may suggest their possible for gene expression and functions [17].…”

“…Based on their locations, SSRs can be classified into genomic SSRs (gSSRs) and Expressed Sequence Tag-SSRs (EST-SSRs) [9]. Because of high level of polymorphism, SSRs have wide applications in population genetics, such as parentage analysis [10], Quantitative Trait Locus (QTL) mapping [11], marker assisted selection (MAS) [12], and phylogenetic studies [13]. Traditional methods of developing gSSR markers require fragmented genomic DNA and are usually time-consuming and labor-intensive.…”

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

“…We selected a flatfish for our study on the basis that these fish would have young sex chromosomes and offer the advantage of a relatively small genome, one that is not much larger than that of pufferfishes. We selected the Chinese half-smooth tongue sole, C. semilaevis, because of good genomic resources, as well as an available molecular marker genetic map [16][17][18][19][20] . This species is also an example of a group of fish with specific adaptations to a benthic lifestyle, most strikingly an asymmetric body shape with lateralization of the eyes to the same side during metamorphosis 21,22 .…”

Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids

“…(http://www.ensembl.org/index.html). Welldefined or high-density genetic linkage maps have been constructed for several food fishes, e.g., rainbow trout Oncorhynchus mykiss (Guyomard et al 2012;Rexroad et al 2008), Atlantic salmon Salmo salar (Lien et al 2011;Brenna-Hansen et al 2012), gilthead seabream Sparus aurata (Sarropoulou et al 2007), half-smooth tongue sole Cynoglossus semilaevis (Song et al 2012a) and Japanese flounder Paralichthys olivaceus (Song et al 2012b). Physical maps have also been reported in a few commercial fishes, such as channel catfish Ictalurus punctatus (Quiniou et al 2007), Nile tilapia Oreochromis niloticus (Katagiri et al 2005) and European seabass Dicentrarchus labrax (Kuhl et al 2010).…”