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

et al. (2012) Construction of a High-Density Microsatellite Genetic Linkage Map and Mapping of Sexual and Growth- Related Traits in Half-Smooth Tongue Sole (Cynoglossus semilaevis). PLoS ONE 7(12): e52097. doi:10.1371/journal.pone.0052097 Construction of a High-Density Microsatellite Genetic Linkage Map and Mapping of Sexual and Growth-Related Traits in Half-Smooth Tongue Sole (Cynoglossus semilaevis ) Wentao Song 0 Yangzhen Li 0 Yongwei Zhao 0 Yang Liu 0 Yuze Niu 0 Renyi Pang 0 Guidong Miao 0 Xiaolin Liao 0 Changwei Shao 0 Fengtao Gao 0 Songlin Chen 0 Zhanjiang Liu, Auburn University, United States of America 0 1 Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Qingdao , China , 2 Weihai Vocational College, Department of Biological and Chemical Engineering , Weihai , China , 3 College of Fisheries and Life Science, Shanghai Ocean University , Shanghai , China 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. - . These authors contributed equally to this work. Genetic linkage maps have become important tools in many areas of genetic research. To perform a linkage study, it is necessary to genotype and map large numbers of the available genetic markers on mapping families. Microsatellites comprise an excellent choice for genomic mapping due to their abundance in most of the vertebrate genomes, including the genomic distribution, high polymorphism and ease of typing via PCR. Meanwhile, the simple sequence repeat (SSR) alleles are typically co-dominant, and their polymorphisms can be scored in either a simple polyacrylamide gel separation format or with high-throughput capillary arrays. Genetic linkage maps based on microsatellite markers have been generated for economically important marine species, such as salmon [1], tilapia [2], European sea bass [3], rainbow trout [4], sea bream [5], Barramundi [6], catfish [7], grass carp [8], Japanese flounder [9] and Asian sea bass [10]. The traditional methods of genetic improvement of quantitative traits have relied mainly on phenotype and pedigree information [11], which are easily influenced by environmental factors. It is generally accepted that marker-assisted selection (MAS) accelerates genetic improvement in a relatively short period, especially when the target characteristics are disease-related and there is a sufficient amount of observed genetic variation in a given trait. A genetic map constructed from a population segregated for a trait of interest is required for QTL identification. Information on genetic markers associated with QTL can be used in MAS breeding programs to identify and select individuals carrying desired traits. QTL mapping in commercial fishes is still in its infancy [12]. QTL for growth, disease resistance and stress response have been mapped in only a few species, such as Asian sea bass [10], rainbow trout [13], tilapia [14], salmon [15], Japanese flounder [16], guppy [17] and European seabass [18]. Half-smooth tongue sole (Cynoglossus semilaevis) is a commercially valuable flatfish that is widely distributed in Chinese coastal waters. Due to its appealing taste, commercial value, easy domestication and natural resource depletion, half-smooth tongue sole has been selected as a promising species for aquaculture [19]. It has been one of the most popular marine species used in aquaculture in China, together with turbot (Scophthalmus maximus), olive flounder (Paralichthys olivaceus), Spotted halibut (Verasper variegatus), and barfin flounder (Verasper moseri). Based on chromosome karyotype analysis, the karyotype of half-smooth tongue sole was determined to be 2 n = 42 t, NF = 42 [20]. After further study based on G-banding patterns analysis, it was confirmed that, in addition to having 20 euchromosome pairs, there was a pair of sex chromosomes (chromosome Z and W), and sex in this species is determined by a WZ/ZZ chromosomal system [20]. In addition, half-smooth tongue sole females grow two to three times larger and faster than males. Therefore, these characteristics suggest that half-smooth tongue sole has great potential for the production of all-female stock, as well as for studying the mechanisms of both genome evolution and sex determination [19]. Half-smooth tongue sole breeding is still in its infancy. Breeding efforts are complicated by the fact that most traits of economic significance exhibit quantitative inheritance [21]. Half-smooth tongue sole breeding community lacks a detailed genetic linkage map to facilitate the breeding process. Recently, number of genetic studies in this species have been reported, including microsatellite markers [2228] and female-specific DNA markers [29], the construction of BAC libraries [30], molecular marker-assisted sex control [31], the characterization of certain sex-related genes [32] and artificial gynogenesis [33]. Furthermore, a low-density genetic linkage map was first constructed for half-smooth tongue sole by Liao et al. [19]. However, as a result this map has provided very little information on the genomic organization of this important marine species. Like other aquaculture species, the production of half-smooth tongue sole is often affected by outbreaks of deadly infectious diseases caused by bacteria, viruses or protozoan pathogens. To accelerate the genetic improvement needed to achieve large (...truncated)