Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)
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. High-density 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.
References
[1]
Oblessuc PR, Tatiana de Campos, Cardoso JMK (2009) Adaptation of fluorescent technique for genotyping with new microsatellite markers in common bean. Pesq agropec bras 44(6): 638–644.
[2]
Gilbey J, Verspoor E, McLay A, Houlihan D (2004) A microsatellite linkage map for Atlantic salmon (Salmo salar). Animal Genetics 35: 98–105.
[3]
Lee BY, Lee WJ, Streelman JT, Carleton KL, Howe AE, et al. (2005) A second-generation genetic linkage map of tilapia (Oreochromis spp.). Genetics 170: 237–244.
[4]
Chistiakov DA, Hellemans B, Haley CS, Law AS, Tsigenopoulos CS, et al. (2005) A microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Genetics. 170: 1821–1826.
[5]
Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, et al. (2006) A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7: 302.
[6]
Senger F, Priat C, Hitte C, Sarropoulou E, Franch R, et al. (2006) The first radiation hybrid map of a perch-like fish: the gilthead seabream (Sparus aurata L). Genomics 87: 793–800.
[7]
Wang CM, Zhu ZY, Lo LC, Feng F, Lin G, et al. (2007) A microsatellite linkage map of Barramundi, Lates calcarifer. Genetics 175: 907–915.
[8]
Kucuktas H, Wang SL, Li P, He CB, Xu P, et al. (2009) Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 181: 1649–1660.
[9]
Xia JH, Feng L, Zhu ZY, Fu JJ, Feng JB, et al. (2010) A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs. BMC Genomics 11: 135.
[10]
Casta？o-Sánchez C, Fuji K, Ozaki A, Hasegawa O, Sakamoto T, et al. (2010) A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). BMC Genomics 11: 554.
[11]
Wang CM, Bai ZY, He XP, Grace L, Xia JH, et al. (2011) A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian sea bass, Lates calcarifer. BMC Genomics 12: 174.
Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238: 1–37.
[14]
Ozaki A, Sakamoto T, Khoo S, Nakamura K, Coimbra M, et al. (2001) Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Mol Genet Genom 265: 23–31.
[15]
Fuji K, Kobayashi K, Hasegawa O, Coimbra M, Sakamoto T, et al. (2006) Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus). Aquaculture 254: 203–210.
[16]
Reid DP, Szanto A, Glebe B, Danzmann R, Ferguson M (2004) QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Heredity 94: 166–172.
[17]
Massault C, Hellemans B, Louro B, Batargias C, Van Houdt J, et al. (2010) QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax. Animal Genetics 41: 337–345.
[18]
Cnaani A, Hallerman EM, Ron M, Weller JI, Indelman M, et al. (2003) Detection of a chromosomal region with two quantitative trait loci, affecting cold tolerance and fish size, in an F-2 tilapia hybrid. Aquaculture 223: 117–128.
[19]
Tripathi N, Hoffmann M, Willing E, Lanz C, Weigel D, et al. (2009) Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation. Proc Biol Sci 276: 2195–2208.
[20]
Chen SL, Tian YS, Xu TJ, Deng H, Liu ST, et al. (2008) Development and characterization for growth rate and disease resistance of disease-resistance population and family in Japanese flounder (Paralichthys olivaceus).. J Fisheries China 32: 665–673.
[21]
Xu TJ, Chen SL, Ji XS, Tian YS, Ma HY (2008) MHC polymorphism and disease resistance to Vibrio anguillarum in 12 selective Japanese flounder (Paralichthys olivaceus) familie. Fish Shell Immunol 25: 213–221.
[22]
Du M, Chen SL, Liang Y, Wang L, Gao FT, et al.. (2011) Polymorphism and balancing selection of MHC class II DAB gene in 7 selective flounder (Paralichthys olivaceus) families. Evidence-Based Complementary and Alternative Medicine 2011: doi:10.1155/2011/613629.
[23]
Coimbra M, Kobayashi K, Koretsugu S, Hasegawa O, Ohara E, et al. (2003) A genetic linkage map of the Japanese flounder, Paralichthys olivaceus. Aquaculture 220: 203–218.
[24]
Kang JH, Kim WJ, Lee WJ (2008) Genetic linkage map of olive flounder, Paralichthys olivaceus. International Journal of Biological Sciences 4: 143–149.
[25]
You EM, Liu KF, Huang SW, Chen M, Groumellec ML, et al. (2010) Construction of integrated genetic linkage maps of the tiger shrimp (Penaeus monodon) using microsatellite and AFLP markers. Animal Genetics 41: 365–376.
[26]
Moen T, Hoyheim B, Munck H, Gomez RL (2004) A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes. Animal Genetics 35: 81–92.
[27]
Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, et al. (2000) A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics 155: 1331–1345.
[28]
Bouza C, Hermida M, Pardo BG, Fernández C, Fortes GG, et al. (2007) A Microsatellite Genetic Map of the Turbot (Scophthalmus maximus). Genetics 177: 2457–2467.
[29]
Reid DP, Smith CA, Rommens M, Blanchard B, Martin-Robichaud D, et al. (2007) A genetic linkage map of Atlantic halibut (Hippoglossus hippoglossus). Genetics 177: 1193–1205.
[30]
Franch R, Louro B, Tsalavouta M, Chatziplis D, Tsigenopoulos CS, et al. (2006) A Genetic Linkage Map of the Hermaphrodite Teleost Fish Sparus aurata L. Genetics. 174: 851–861.
[31]
Kai W, Kikuchi KK, Fujita M, Suetake H, Fujiwara A, et al. (2005) A genetic linkage map for the tiger puffer fish, Takifugu rubripes. Genetics 171: 227–238.
[32]
Kondo M, Nagao E, Mitani H, Shima A (2001) Differences in recombination frequencies during female and male meiosis of the sex chromosomes of medaka, Oryzias latipes. Genet. Res. 78: 23–30.
[33]
Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, et al. (1999) Zebrafish genetic map with 2000 microsatellite markers. Genomics 58: 219–232.
[34]
Rexroad CE, Palti Y, Gahr SA, Vallejo RL (2008) A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genetics 9: 74.
[35]
Zhang LS, Yang CJ, Zhang Y, Li L, Zhang XM, et al. (2007) A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates. Genetica 131: 37–49.
[36]
Li L, Guo XM (2004) AFLP-Based Genetic Linkage Maps of the Pacific Oyster Crassostrea gigas Thunberg. Mar Biotechnol 6: 26–36.
[37]
Young WP, Wheeler PA, Coryell VH, Keim P, Thorgaard GH (1998) A detailed linkage map of rainbow trout produced using doubled haploids. Genetics 148: 1–13.
[38]
Liu ZJ, Karsi A, Li P, Cao D, Dunham R (2003) An AFLP-based genetic linkage map of channel catfish (Icalurus puncatus) constructed by using an interspecific hybrid resource family. Genetics 165: 687–694.
[39]
Cheng L, Liu L, Yu X, Wang D, Tong J (2009) A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers. Animal Genetics 41: 191–198.
[40]
Wang WJ, Wang HP, Yao H, Wallat GK, Tiu LG, et al. (2010) A first genetic linkage map of bluegill sunfish (Lepomis macrochirus) using AFLP markers. Aquacult Int 18: 825–835.
[41]
Zamir D, Tadmor Y (1986) Unequal segregation of nuclear genes in plants. Bot Gaz 147: 355–358.
[42]
Plomion C, O’Malley DM, Durel CE (1995) Genomic analysis in maritime pine (Pinus pinaster). Comparison of two RAPD maps using selfed and open pollinated seeds of the same individual. Theor Appl Genet 90: 1028–1034.
[43]
Nikaido A, Yoshimaru H, Tsumura Y, Suyama Y, Murai M (1999) Segregation distortion of AFLP markers in Cryptomeria japonica. Genes GenetSyst 74: 55–59.
[44]
Faris JD, Laddomada B, Gill BS (1998) Molecular mapping of segregation distortion loci in Aegilops taushii. Genetics 149: 319–327.
[45]
Hubert S, Hedgecock D (2004) Linkage maps of microsatellite DNA markers for the Pacific oyster. Genetics 168: 351–362.
[46]
Liu ZJ (2007) Aquaculture Genome Technologies. Wiley-Blackwell.
[47]
Ma HY, Chen SL, Yang JF, Chen SP, Liu HW (2011) Genetic linkage maps of barfin flounder (Verasper moseri) and spotted halibut (Verasper variegatus) based on AFLP and microsatellite markers. Molecular biology reports 38: 4749–4764.
[48]
Liao XL, Ma HY, Xu GB, Shao CW, Tian YS, et al. (2009) Construction of a genetic linkage map and mapping of a female-specific DNA marker in half-smooth tongue sole (Cynoglossus semilaevis). Mar Biotechnol 11: 699–709.
[49]
Sambrook J, Russell DW (2001) Molercular Cloning: A Laboratory Mamual, 3rd dition. New York: Cold Spring Harkbor Labroatory Press.
[50]
Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry 96: 80–83.
