Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

et al. (2012) Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus). PLoS ONE 7(11): e50404. doi:10.1371/journal.pone.0050404 Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus ) Wentao Song 0 Renyi Pang 0 Yuze Niu 0 Fengtao Gao 0 Yongwei Zhao 0 Jing Zhang 0 Jian Sun 0 Changwei Shao 0 Xiaolin Liao 0 Lei Wang 0 Yongsheng Tian 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 were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. Highdensity genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS. - Funding: The work was supported by grants from the National Major Basic Research Program (2010CB126303), the State 863 High-Technology R&D Project (2012AA092208; 2012AA092203) of China, and the Taishan Scholar Project of Shandong Province. The funders had an important role in study design and the decision to publish. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Genetic linkage mapping has become a critically important tool in many areas of genetic research. In order to perform a useful linkage study, it is necessary to genotype and map large numbers of the available genetic markers on the mapping families. Microsatellites comprise an excellent opportunity for genomic mapping due to their abundance in most vertebrate genomes, as well as their genomic distribution pattern, high polymorphism rate and ease of typing, all of which are determinable 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 [1]. Genetic linkage maps based on microsatellite markers have been produced for economically important fish species, including salmon [2], tilapia [3], European sea bass [4], rainbow trout [5], sea bream [6], Barramundi [7], catfish [8], grass carp [9], Japanese flounder [10] and Asian sea bass [11]. The traditional methods of genetic improvement of quantitative traits have relied mainly on phenotype and pedigree information [12], which are both commonly influenced by environmental factors. It is generally accepted that 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 the genetic markers associated with QTL can be used in MAS breeding programs to identify and select individuals carrying the desired traits. QTL mapping in commercial fishes is still in its infancy [13]. The QTL for growth, disease resistance and stress response have been mapped in only a few species to date, such as disease resistance in rainbow trout [14] and Japanese flounder [15], body weight in salmon [16] and European seabass [17], cold tolerance in tilapia [18], and color variation in the guppy [19]. Japanese flounder (Paralichthys olivaceus) is a marine fish which is economically important as a food, and has been widely cultured in Asian countries such as China, Japan and Korea. It is mostly distributed along the coast of China, where it has been cultured for approximately 20 years due to its favourable traits such a fast growth rate, good adaptability to temperature and disease resistance in a variety of cultivation conditions. With extensive cultivation, however, farming of the Japanese flounder has also been confronted with certain problems, including a high mortality rate as well as a decline in growth. In order to further increase the productivity of Japanese flounder farming, it is thus essential to carry out both classic selective breeding and MAS. Recently, a number of genetic studies in this species have been reported. Fuji et al. [15] found a single major genetic locus associated with lymphocystis disease resistance in the Japanese flounder and succeeded in commercially producing a lymphocystis diseaseresistant strain by MAS. A large number of flounder families have been developed and disease resistance-related MHC gene markers identified in the Japanese flounder in China [2022]. Furthermore, three genetic linkage maps have been published for P. olivaceus [2324] [10]. In these maps, the second generation genetic linkage map of the Japanese flounder constructed by Castan o-Sanchez is the most dense, having 1375 markers. However, the male and female maps have only 235 and 184 unique positions, with average intervals of 5.0 cM and 4.4 cM, respectively. In this study, a high-density microsatellite genetic linkage map containing 1487 markers and growth-related QTL are reported for the first time for the Japanese flounder. The female and male maps have 1242 and 1215 unique positions, respectively, (...truncated)