Marine Biotechnology

, Volume 13, Issue 1, pp 74–82 | Cite as

Mapping QTL for an Adaptive Trait: The Length of Caudal Fin in Lates calcarifer

  • C. M. Wang
  • L. C. Lo
  • Z. Y. Zhu
  • H. Y. Pang
  • H. M. Liu
  • J. Tan
  • H. S. Lim
  • R. Chou
  • L. Orban
  • G. H. Yue
Original Article


The caudal fin represents a fundamental design feature of fishes and plays an important role in locomotor dynamics in fishes. The shape of caudal is an important parameter in traditional systematics. However, little is known about genes involved in the development of different forms of caudal fins. This study was conducted to identify and map quantitative trait loci (QTL) affecting the length of caudal fin and the ratio between tail length and standard body length in Asian seabass (Lates calcarifer). One F1 family containing 380 offspring was generated by crossing two unrelated individuals. One hundred and seventeen microsatellites almost evenly distributed along the whole genome were genotyped. Length of caudal fin at 90 days post-hatch was measured. QTL analysis detected six significant (genome-wide significant) and two suggestive (linkage-group-wide significant) QTL on seven linkage groups. The six significant QTL explained 5.5–16.6% of the phenotypic variance, suggesting these traits were controlled by multiple genes. Comparative genomics analysis identified several potential candidate genes for the length of caudal fin. The QTL for the length of caudal fin detected for the first time in marine fish may provide a starting point for the future identification of genes involved in the development of different forms of caudal fins in fishes.


Fish Teleosts Tail QTL Evolution 



This study was funded by AVA and the internal fund of the Temasek Life Sciences Laboratory, Singapore. We thank our colleagues for technical assistance and Dr Mamta Chauhan for editing English of this manuscript.


  1. Andersson L, Georges M (2004) Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet 5:202–12PubMedCrossRefGoogle Scholar
  2. Berger W, Meindl A, van de Pol TJ, Cremers FP, Ropers HH, Doerner C, Monaco A, Bergen AA, Lebo R, Warburgh M (1992) Isolation of a candidate gene for Norrie disease by positional cloning. Nat Genet 1:199–203PubMedCrossRefGoogle Scholar
  3. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–31PubMedGoogle Scholar
  4. Boulding EG, Culling M, Glebe B, Berg PR, Lien S, Moen T (2008) Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptive traits in parr from four trans-Atlantic backcrosses. Heredity 101:381–91PubMedCrossRefGoogle Scholar
  5. Calboli FC, Kennington WJ, Partridge L (2003) QTL mapping reveals a striking coincidence in the positions of genomic regions associated with adaptive variation in body size in parallel clines of Drosophila melanogaster on different continents. Evolution 57:2653–2658PubMedGoogle Scholar
  6. Cano JM, Matsuba C, Makinen H, Merila J (2006) The utility of QTL-linked markers to detect selective sweeps in natural populations–a case study of the EDA gene and a linked marker in threespine stickleback. Mol Ecol 15:4613–4621PubMedCrossRefGoogle Scholar
  7. Chao J, Miao RQ, Chen V (2001) Novel roles of kallistatin, a specific tissue kallikrein inhibitor, in vascular remodeling. Biol Chem 382:15–21PubMedCrossRefGoogle Scholar
  8. Cnaani A, Zilberman N, Tinman S, Hulata G, Ron M (2004) Genome-scan analysis for quantitative trait loci in an F2 tilapia hybrid. Mol Genet Genomics 272:162–72PubMedCrossRefGoogle Scholar
  9. Danzmann RG (2006) Linkage analysis package for outcrossed families with male or female exchange of the mapping parent, version 2.3. <∼rdanzman/> software/LINKMFEX.
  10. Flammang BE, Lauder GV (2009) Caudal fin shape modulation and control during acceleration, braking and backing maneuvers in bluegill sunfish, Lepomis macrochirus. J Exp Biol 212:277–86PubMedCrossRefGoogle Scholar
  11. Haidle L, Janssen JE, Gharbi K, Moghadam HK, Ferguson MM, Danzmann RG (2008) Determination of quantitative trait loci (QTL) for early maturation in Rainbow trout (Oncorhynchus mykiss). Mar Biotechnol 10:579–92PubMedCrossRefGoogle Scholar
  12. Imre I, Mclaughlin RL, Noakes DLG (2002) Phenotypic plasticity in brook charr: changes in caudal fin induced by water flow. J Fish Biol 61:1171–81CrossRefGoogle Scholar
  13. Jermstad KD, Bassoni DL, Jech KS, Ritchie GA, Wheeler NC, Neale DB (2003) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactions. Genetics 165:1489–506PubMedGoogle Scholar
  14. Kizil C, Otto GW, Geisler R, Nusslein-Volhard C, Antos CL (2009) Simplet controls cell proliferation and gene transcription during zebrafish caudal fin regeneration. Dev Biol 325:329–40PubMedCrossRefGoogle Scholar
  15. Laforest L, Brown CW, Poleo G, Geraudie J, Tada M, Ekker M, Akimenko MA (1998) Involvement of the sonic hedgehog, patched 1 and bmp2 genes in patterning of the zebrafish dermal fin rays. Development 125:4175–84PubMedGoogle Scholar
  16. Lallias D, Gomez-Raya L, Haley CS, Arzul I, Heurtebise S, Beaumont AR, Boudry P, Lapègue S (2009) Combining two-stage testing and interval mapping strategies to detect QTL for resistance to bonamiosis in the European flat oyster Ostrea edulis. Mar Biotechnol 11:570–84PubMedCrossRefGoogle Scholar
  17. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–81PubMedCrossRefGoogle Scholar
  18. Lauder GV (1989) Caudal fin locomotion in ray-finned fishes: Historical and functional analyses. Am Zool 29:85–102Google Scholar
  19. Leavy TR, Bonner TH (2009) Relationships among swimming ability, current velocity associations, and morphology for freshwater lotic fishes. N Am J Fish Mange 29:72–83CrossRefGoogle Scholar
  20. Leto G, Tumminello FM, Crescimanno M (2004) Cathepsin D expression levels in nongynecological solid tumors: clinical and therapeutic implications. Clin Exp Metastasis 21:91–106PubMedCrossRefGoogle Scholar
  21. Li J, Xie Y, Dai A, Liu L, Li Z (2009) Root and shoot traits responses to phosphorus deficiency and QTL analysis at seedling stage using introgression lines of rice. J Genet Genomics 36:173–83PubMedCrossRefGoogle Scholar
  22. Liu F, Shao Z, Zhang H, Liu J, Wang X, Duan D (2010) QTL Mapping for frond length and width in Laminaria japonica Aresch (Laminarales, Phaeophyta) using AFLP and SSR Markers. Mar Biotech (in press)Google Scholar
  23. Mehta R, Devi K, Mehta HS (1989) Caudal skeleton in some gobiid fishes and its value in systematics. Res bul Panjab Univ 40:29–34Google Scholar
  24. Moghadam HK, Poissant J, Fotherby H, Haidle L, Ferguson MM, Danzmann RG (2007) Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Mol Genet Genomics 277:647–61PubMedCrossRefGoogle Scholar
  25. Naisbitt S, Kim E, Tu JC (1999) Shank, a novel family of postsynaptic density proteins that binds to the NMDA receptor/PSD-95/GKAP complex and cortactin. Neuron 23:569–82PubMedCrossRefGoogle Scholar
  26. Nelson J (2006) Fishes of the world. Wiley, New YorkGoogle Scholar
  27. O’Malley KG, Sakamoto T, Danzmann RG, Ferguson MM (2003) Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J Heredity 94:273–84CrossRefGoogle Scholar
  28. Orr HA, Coyne JA (1992) The genetics of adaptation: a reassessment. Am Nat 140:725–42PubMedCrossRefGoogle Scholar
  29. Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–42PubMedGoogle Scholar
  30. Perry GM, Danzmann RG, Ferguson MM, Gibson JP (2001) Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). Heredity 86:333–41PubMedCrossRefGoogle Scholar
  31. Pillay TVR (1990) Aquaculture principles and practices. Fishing News Books, OxfordGoogle Scholar
  32. Robertson NG, Skvorak AB, Yin Y, Weremowicz S, Johnson KR, Kovatch KA, Battey JF, Bieber FR, Morton CC (1997) Mapping and characterization of a novel cochlear gene in human and in mouse: a positional candidate gene for a deafness disorder, DFNA9. Genomics 46:345–54PubMedCrossRefGoogle Scholar
  33. Rogers SM, Bernatchez L (2007) The genetic architecture of ecological speciation and the association with signatures of selection in natural lake whitefish (Coregonus sp. Salmonidae) species pairs. Mol Biol Evol 24:1423–38PubMedCrossRefGoogle Scholar
  34. Sarropoulou E, Nousdili D, Magoulas A, Kotoulas G (2008) Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol 10:227–333PubMedCrossRefGoogle Scholar
  35. Schultze H, Arratia G (1989) The composition of the caudal skeleton of teleosts (Actinopterygii: Osteichthyes). Zool J Linn Soc 97:189–231CrossRefGoogle Scholar
  36. Seshimo H, Ryuzaki M, Yoshizato K (1997) Specific inhibition of triiodothyronine-induced tadpole tail-fin regression by cathepsin D-inhibitor pepstatin. Dev Biol 59:96–100CrossRefGoogle Scholar
  37. Sheng M, Kim E (2000) The Shank family of scaffold proteins. J Cell Sci 113:1851–6PubMedGoogle Scholar
  38. Sims K Jr, Eble DM, Iovine MK (2009) Connexin43 regulates joint location in zebrafish fins. Dev Biol 327:410–8PubMedCrossRefGoogle Scholar
  39. Slate J (2005) Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Mol Ecol 14:363–79PubMedCrossRefGoogle Scholar
  40. Somorjai IM, Danzmann RG, Ferguson MM (2003) Distribution of temperature tolerance quantitative trait loci in Arctic charr (Salvelinus alpinus) and inferred homologies in rainbow trout (Oncorhynchus mykiss). Genetics 165:1443–56PubMedGoogle Scholar
  41. Tabin CJ (1992) Why we have (only) five fingers per hand: hox genes and the evolution of paired limbs. Development 116:289–96PubMedGoogle Scholar
  42. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–33PubMedCrossRefGoogle Scholar
  43. Van Ooijen JW, Boer MP, Jansen RC (2002) MapQTL 4.0: Software for the calculation of QTL positions on genetic maps. Wageningen (the Netherlands), Plant Research International.Google Scholar
  44. Videler JJ (1993) Fish swimming. Chapman and Hall, LondonGoogle Scholar
  45. Wang CM, Lo LC, Zhu ZY, Yue GH (2006) Genome-scan QTL for growth-related traits in an F1 family from a breeding population of Asian seabass. BMC Genomics 7:274PubMedCrossRefGoogle Scholar
  46. Wang CM, Zhu ZY, Lo LC, Feng F, Lin G, Yang WT, Li J, Yue GH (2007) A microsatellite linkage map of Barramundi, Lates calcarifer. Genetics 175:907–15PubMedCrossRefGoogle Scholar
  47. Wang CM, Lo LC, Zhu ZY, Feng F, Yue GH (2008a) Identification and verification of QTL associated with growth traits in two genetic backgrounds of Barramundi (Lates calcarifer). Anim Genet 39:34–9PubMedCrossRefGoogle Scholar
  48. Wang CM, Lo LC, Zhu ZY, Lin G, Feng F, Li J, Yang WT, Tan J, Chou R, Lim HS, Orban L, Yue GH (2008b) Estimating reproductive success of brooders and heritability of growth traits in Asian seabass using microsatellites. Aquac Res 39:1612–9Google Scholar
  49. White JA, Boffa MB, Jones B, Petkovich M (1994) A zebrafish retinoic acid receptor expressed in the regenerating caudal fin. Development 120:1861–72PubMedGoogle Scholar
  50. White GR, Varley JM, Heighway J (1998) Isolation and characterization of a human homologue of the latrophilin gene from a region of 1p31.1 implicated in breast cancer. Oncogene 31:3513–9Google Scholar
  51. Wills AA, Kidd AR 3 rd, Lepilina A, Poss KD (2008) Fgfs control homeostatic regeneration in adult zebrafish fins. Development 135:3063–70PubMedCrossRefGoogle Scholar
  52. Yue GH, Orban L (2005) A simple and affordable method for high-throughput DNA extraction from animal tissues for polymerase chain reaction. Electrophoresis 26:3081–3PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • C. M. Wang
    • 1
  • L. C. Lo
    • 1
  • Z. Y. Zhu
    • 1
  • H. Y. Pang
    • 1
  • H. M. Liu
    • 1
  • J. Tan
    • 2
  • H. S. Lim
    • 2
  • R. Chou
    • 2
  • L. Orban
    • 3
  • G. H. Yue
    • 1
  1. 1.Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research LinkNational University of SingaporeSingaporeSingapore
  2. 2.Agri-Food & Veterinary Authority of SingaporeSingaporeSingapore
  3. 3.Reproductive Genomics GroupTemasek Life Sciences LaboratorySingaporeSingapore

Personalised recommendations