Marine Biotechnology

, Volume 20, Issue 1, pp 98–107 | Cite as

Identifying a Major QTL Associated with Salinity Tolerance in Nile Tilapia Using QTL-Seq

  • Xiao Hui Gu
  • Dan Li Jiang
  • Yan Huang
  • Bi Jun Li
  • Chao Hao Chen
  • Hao Ran Lin
  • Jun Hong XiaEmail author
Original Article


Selection of new lines with high salinity tolerance allows for economically feasible production of tilapias in brackish water areas. Mapping QTLs and identifying the markers linked to salinity-tolerant traits are the first steps in the improvement of the tolerance in tilapia through marker-assisted selection techniques. By using QTL-seq strategy and linkage-based analysis, two significant QTL intervals (chrLG4 and chrLG18) on salinity-tolerant traits were firstly identified in the Nile tilapia. Fine mapping with microsatellite and SNP markers suggested a major QTL region that located at 23.0 Mb of chrLG18 and explained 79% of phenotypic variation with a LOD value of 95. Expression analysis indicated that at least 10 genes (e.g., LACTB2, KINH, NCOA2, DIP2C, LARP4B, PEX5R, and KCNJ9) near or within the QTL interval were significantly differentially expressed in intestines, brains, or gills under 10, 15, or 20 ppt challenges. Our findings suggest that QTL-seq can be effectively utilized in QTL mapping of salinity-tolerant traits in fish. The identified major QTL is a promising locus to improve our knowledge on the genetic mechanism of salinity tolerance in tilapia.


Single nucleotide polymorphism Salinity tolerance Candidate gene Quantitative trait locus 



We thank two anonymous reviewers for comments on the manuscript. This work was supported by the National Natural Science Foundation of China (No. 31572612); Science and Technology Planning Project of Guangdong Province, China (2017A030303008); and Modern Agriculture Talents Support Program (2016–2020).

Author Contributions

JHX and HRL contributed to project conception. Experiment and data analysis was conducted by XHG, DLJ, HY, CCH, and BJL. The manuscript was prepared by JHX and DLJ. All authors read and approved the final manuscript.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no competing interests.

Supplementary material

10126_2017_9790_MOESM1_ESM.xlsx (12 kb)
Supplementary Table S1 The primer list used for genotyping and qRT-PCR analysis. (XLSX 11 kb)


  1. Aruna A, Nagarajan G, Chang CF (2012) Involvement of corticotrophin-releasing hormone and corticosteroid receptors in the brain-pituitary-gill of tilapia during the course of seawater acclimation. J Neuroendocrinol 24(5):818–830CrossRefPubMedGoogle Scholar
  2. Avarre JC, Dugue R, Alonso P, Diombokho A, Joffrois C, Faivre N, Cochet C, Durand JD (2014) Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes. Mol Ecol Resour 14(1):139–149CrossRefPubMedGoogle Scholar
  3. Bras YL, Dechamp N, Krieg F, Filangi O, Guyomard R, Boussaha M, Bovenhuis H, Pottinger TG, Prunet P, Roy PL (2011) Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss). BMC Genet 12(1):46CrossRefPubMedPubMedCentralGoogle Scholar
  4. Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alfoldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D’Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F (2014) The genomic substrate for adaptive radiation in African cichlid fish. Nature 513(7518):375–381CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bystriansky JS, Richards JG, Schulte PM, Ballantyne JS (2006) Reciprocal expression of gill Na+/K+-ATPase alpha-subunit isoforms alpha1a and alpha1b during seawater acclimation of three salmonid fishes that vary in their salinity tolerance. J Exp Biol 209(10):1848–1858CrossRefPubMedGoogle Scholar
  6. Cnaani A, Zilberman N, Tinman S, Hulata G, Ron M (2004) Genome-scan analysis for quantitative trait loci in an F-2 tilapia hybrid. Mol Gen Genomics 272:162–172CrossRefGoogle Scholar
  7. Das S, Upadhyaya HD, Bajaj D, Kujur A, Badoni S, Laxmi, Kumar V, Tripathi S, Gowda CL, Sharma S, Singh S, Tyagi AK, Parida SK (2015) Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Res 22(3):193–203CrossRefPubMedPubMedCentralGoogle Scholar
  8. Dean DB, Whitlow ZW, Borski RJ (2003) Glucocorticoid receptor upregulation during seawater adaptation in a euryhaline teleost, the tilapia (Oreochromis mossambicus). Gen Comp Endocrinol 132(1):112–118CrossRefPubMedGoogle Scholar
  9. Eknath AE, Hulata G (2009) Use and exchange of genetic resources of Nile tilapia (Oreochromisƒniloticus). Rev Aquac 1(3-4):197–213CrossRefGoogle Scholar
  10. Evans TG (2010) Co-ordination of osmotic stress responses through osmosensing and signal transduction events in fishes. J Fish Biol 76(8):1903–1925CrossRefPubMedGoogle Scholar
  11. Evans D, Claiborne J (2006) The physiology of fishe, 3rd edn. CRC, Boca RatonGoogle Scholar
  12. Evans DH, Piermarini PM, Choe KP (2004) The multifunctional fish gill: dominant site of gas exchange, osmoregulation, acid-base regulation, and excretion of nitrogenous waste. Physiol Rev 85:97CrossRefGoogle Scholar
  13. Farcy E, Serpentini A, Fievet B, Lebel JM (2007) Identification of cDNAs encoding HSP70 and HSP90 in the abalone Haliotis tuberculata: transcriptional induction in response to thermal stress in hemocyte primary culture. Comp Biochem Physiol B Biochem Mol Biol 146(4):540–550CrossRefPubMedGoogle Scholar
  14. Fiol DF, Sanmarti E, Lim AH, Kültz D (2011) A novel GRAIL E3 ubiquitin ligase promotes environmental salinity tolerance in euryhaline tilapia. Biochim Biophys Acta Gen Subj 1810(4):439–445CrossRefGoogle Scholar
  15. Gil J, Peters G (2006) Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. Nat Rev Mol Cell Biol 7(9):667–677CrossRefPubMedGoogle Scholar
  16. Gu XH, Li BJ, Lin HR, Xia JH (2018) Unraveling the associations of the tilapia DNA polymerase delta subunit 3 (POLD3) gene with saline tolerance traits. Aquaculture 485:53–58CrossRefGoogle Scholar
  17. Haupt Y, Bath ML, Harris AW, Adams JM (1993) bmi-1 transgene induces lymphomas and collaborates with myc in tumorigenesis. Oncogene 8(11):3161–3164PubMedGoogle Scholar
  18. Hiroi J, Mccormick SD, Ohtani-Kaneko R, Kaneko T (2005) Functional classification of mitochondrion-rich cells in euryhaline Mozambique tilapia (Oreochromis mossambicus) embryos, by means of triple immunofluorescence staining for Na+/K+-ATPase, Na+/K+/2Cl cotransporter and CFTR anion channel. J Exp Biol 208(11):2023–2036CrossRefPubMedGoogle Scholar
  19. Hiroi J, Yasumasu S, Mccormick SD, Hwang PP, Kaneko T (2008) Evidence for an apical Na-Cl cotransporter involved in ion uptake in a teleost fish. J Exp Biol 211(16):2584–2599CrossRefPubMedGoogle Scholar
  20. Howe AE (2004) The genetic basis of red color in tilapia. M.S. thesis, Univ. of New Hampshire, DurhamGoogle Scholar
  21. Huang CW, Li YH, Hu SY, Chi JR, Lin GH, Lin CC, Gong HY, Chen JY, Chen RH, Chang SJ, Liu FG, Wu JL (2012) Differential expression patterns of growth-related microRNAs in the skeletal muscle of Nile tilapia (Oreochromis niloticus). J Anim Sci 90(12):4266–4279CrossRefPubMedGoogle Scholar
  22. Jacobs JJ, Scheijen B, Voncken JW, Kieboom K, Berns A, van Lohuizen M (1999) Bmi-1 collaborates with c-Myc in tumorigenesis by inhibiting c-Myc-induced apoptosis via INK4a/ARF. Genes Dev 13(20):2678–2690CrossRefPubMedPubMedCentralGoogle Scholar
  23. Kamal AHMM, Mair GC (2005) Salinity tolerance in superior genotypes of tilapia, Oreochromis niloticus, Oreochromis mossambicus and their hybrids. Aquaculture 247(1-4):189–201CrossRefGoogle Scholar
  24. Katagiri T, Kidd C, Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD (2005) A BAC-based physical map of the Nile tilapia genome. BMC Genomics 6(1):89CrossRefPubMedPubMedCentralGoogle Scholar
  25. Kiilerich P, Kristiansen K, Madsen SS (2007) Cortisol regulation of ion transporter mRNA in Atlantic salmon gill and the effect of salinity on the signaling pathway. J Endocrinol 194(2):417–427CrossRefPubMedGoogle Scholar
  26. Kofler R, Pandey RV, Schlotterer C (2011) PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 27(24):3435–3436CrossRefPubMedPubMedCentralGoogle Scholar
  27. Kültz D (2012) The combinatorial nature of osmosensing in fishes. Physiology 27(4):259–275CrossRefPubMedGoogle Scholar
  28. Kultz D, Li J, Gardell A, Sacchi R (2013) Quantitative molecular phenotyping of gill remodeling in a Cichlid fish responding to salinity stress. Mol Cell Proteomics 12(12):3962–3975CrossRefPubMedPubMedCentralGoogle Scholar
  29. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359CrossRefPubMedPubMedCentralGoogle Scholar
  30. Lee K, Adhikary G, Balasubramanian S, Gopalakrishnan R, McCormick T, Dimri GP, Eckert RL, Rorke EA (2008) Expression of Bmi-1 in epidermis enhances cell survival by altering cell cycle regulatory protein expression and inhibiting apoptosis. J Invest Dermatol 128(1):9–17CrossRefPubMedGoogle Scholar
  31. Li BJ, Li HL, Meng Z, Zhang Y, Lin H, Yue GH, Xia JH (2017a) Copy number variations in tilapia genomes. Mar Biotechnol (NY). 19(1):11–21CrossRefPubMedGoogle Scholar
  32. Li HL, Gu XH, Li BJ, Chen CH, Lin HR, Xia JH (2017b) Genome-wide QTL analysis identified significant associations between hypoxia tolerance and mutations in the GPR132 and ABCG4 genes in Nile tilapia. Mar Biotechnol (NY) 19(5):441–453CrossRefGoogle Scholar
  33. Liu ZJ, Cordes JF (2004) DNA marker technologies and their applications in aquaculture genetics. Aquaculture 242(1-4):735–736CrossRefGoogle Scholar
  34. Liu F, Sun F, Li J, Xia JH, Lin G, Tu RJ, Yue GH (2013) A microsatellite-based linkage map of salt tolerant tilapia (Oreochromis mossambicus x Oreochromis spp.) and mapping of sex-determining loci. BMC Genomics 14(1):58CrossRefPubMedPubMedCentralGoogle Scholar
  35. Lorin-Nebel C, Avarre JC, Faivre N, Wallon S, Charmantier G, Durand JD (2012) Osmoregulatory strategies in natural populations of the black-chinned tilapia Sarotherodon melanotheron exposed to extreme salinities in West African estuaries. J Comp Physiol B 182(6):771–780CrossRefPubMedGoogle Scholar
  36. McConnell SK, Beynon C, Leamon J, Skibinski DO (2000) Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed. Anim Genet 31(3):214–218CrossRefPubMedGoogle Scholar
  37. McCormick SD (2001) Endocrine control of osmoregulation in teleost fish. Am Zool 41:781–794Google Scholar
  38. Mccormick SD, Regish A, O’Dea MF, Shrimpton JM (2008) Are we missing a mineralocorticoid in teleost fish? Effects of cortisol, deoxycorticosterone and aldosterone on osmoregulation, gill Na+,K+ -ATPase activity and isoform mRNA levels in Atlantic salmon. Gen Comp Endocrinol 157(1):35–40CrossRefPubMedGoogle Scholar
  39. Mccormick SD, Regish AM, Christensen AK (2009) Distinct freshwater and seawater isoforms of Na+/K+-ATPase in gill chloride cells of Atlantic salmon. J Exp Biol 212(24):3994–4001CrossRefPubMedGoogle Scholar
  40. Moen T, Agresti JJ, Cnaani A, Moses H, Famula TR, Hulata G, Gall GAE, May B (2004) A genome scan of a four-way tilapia cross supports the existence of a quantitative trait locus for cold tolerance on linkage group 23. Aquac Res 35(9):893–904CrossRefGoogle Scholar
  41. Norman JD, Danzmann RG, Glebe B, Ferguson MM (2011) The genetic basis of salinity tolerance traits in Arctic charr (Salvelinus alpinus). BMC Genet 12(1):81CrossRefPubMedPubMedCentralGoogle Scholar
  42. Norman JD, Robinson M, Glebe B, Ferguson MM, Danzmann RG (2012) Genomic arrangement of salinity tolerance QTL in salmonids: a comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss). BMC Genomics 13(1):420CrossRefPubMedPubMedCentralGoogle Scholar
  43. Norman JD, Ferguson MM, Danzmann RG (2014) Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes. Physiol Genomics 46(4):123–137CrossRefPubMedGoogle Scholar
  44. Palaiokostas C, Bekaert M, Khan MG, Taggart JB, Gharbi K, McAndrew BJ, Penman DJ (2013) Mapping and validation of the major sex-determining region in Nile tilapia (Oreochromis niloticus L.) using RAD sequencing. PLoS One 8(7):e68389CrossRefPubMedPubMedCentralGoogle Scholar
  45. Rengmark, A.H. and F. Lingaas (2007) Genomic structure of the Nile tilapia (Oreochromis niloticus) transferrin gene and a haplotype associated with saltwater tolerance. Aquaculture, 272:146–155Google Scholar
  46. Richards JG, Semple JW, Bystriansky JS, Schulte PM (2003) Na+/K+-ATPase alpha-isoform switching in gills of rainbow trout (Oncorhynchus mykiss) during salinity transfer. J Exp Biol 206(24):4475–4486CrossRefPubMedGoogle Scholar
  47. Sakamoto T, McCormick SD (2006) Prolactin and growth hormone in fish osmoregulation. Gen Comp Endocrinol 147(1):24–30CrossRefPubMedGoogle Scholar
  48. Seale AP, Fiess JC, Hirano T, Cooke IM, Grau EG (2006) Disparate release of prolactin and growth hormone from the tilapia pituitary in response to osmotic stimulation. Gen Comp Endocrinol 145(3):222–231CrossRefPubMedGoogle Scholar
  49. Smith HW (1930) The absorption and excretion of water and salts by marine teleosts. Am J Physiol 93:480Google Scholar
  50. Stauffer JR Jr, Van DK, Hocutt CH (1984) Effects of salinity on preferred and lethal temperatures of the blackchin tilapia, Sarotherodon melanotheron. Water Resour Bull 20(5):771–775CrossRefGoogle Scholar
  51. Streelman JT, Kocher TD (2002) Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia. Physiol Genomics 9(1):1–4CrossRefPubMedGoogle Scholar
  52. Sun YB (2017) FasParser: a package for manipulating sequence data. Zool Res 38(2):110–112CrossRefPubMedPubMedCentralGoogle Scholar
  53. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74(1):174–183CrossRefPubMedGoogle Scholar
  54. Thomsen DS, Anders K, Nielsen EE, Larsen PF, Olsvik PA, Volker L (2008) Interpopulation differences in expression of candidate genes for salinity tolerance in winter migrating anadromous brown trout (Salmo trutta L.) BMC Genet 9:12PubMedPubMedCentralGoogle Scholar
  55. Tipsmark CK, Madsen SS, Seidelin M, Christensen AS, Cutler CP, Cramb G (2002) Dynamics of Na(+),K(+),2Cl(−) cotransporter and Na(+),K(+)-ATPase expression in the branchial epithelium of brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). J Exp Zool 293(2):106–118CrossRefPubMedGoogle Scholar
  56. Tipsmark CK, Kiilerich P, Nilsen TO, Ebbesson LO, Stefansson SO, Madsen SS (2008) Branchial expression patterns of claudin isoforms in Atlantic salmon during seawater acclimation and smoltification. Am J Physiol Regul Integr Comp Physiol 294(5):R1563–R1574CrossRefPubMedGoogle Scholar
  57. Van Bers NE, Crooijmans RP, Groenen MA, Dibbits BW, Komen J (2012) SNP marker detection and genotyping in tilapia. Mol Ecol Resour 12(5):932–941CrossRefPubMedGoogle Scholar
  58. Van Ooijen JW, 2009. MapQTL 6.0, software for the mapping of quantitative trait loci in experimental populations of dihaploid speciesGoogle Scholar
  59. Van Ooijen JW (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 93(05):343–349CrossRefGoogle Scholar
  60. Wang X, Kultz D (2017) Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish. Proc Natl Acad Sci U S A 114(13):E2729–E2738CrossRefPubMedPubMedCentralGoogle Scholar
  61. Watanabe W, Kuo C-M, Huang M-C (1985a) Salinity tolerance of Nile tilapia (Oreochromis niloticus) spawned and hatched at various salinities. Aquaculture 48(2):159–176CrossRefGoogle Scholar
  62. Watanabe WO, Kuo C-M, Huang M-C (1985b) The ontogeny of salinity tolerance in the tilapias Oreochromis aureus, O. niloticus, and an O. mossambicus × O. niloticus hybrid, spawned and reared in freshwater. Aquaculture 47(4):353–367CrossRefGoogle Scholar
  63. Xia JH, Wan ZY, Ng ZL, Wang L, Fu GH, Lin G, Liu F, Yue GH (2014) Genome-wide discovery and in silico mapping of gene-associated SNPs in Nile tilapia. Aquaculture 432:67–73CrossRefGoogle Scholar
  64. Xia JH, Bai Z, Meng Z, Zhang Y, Wang L, Liu F, Jing W, Wan ZY, Li J, Lin H, Yue GH (2015) Signatures of selection in tilapia revealed by whole genome resequencing. Sci Rep 5:14168CrossRefPubMedGoogle Scholar
  65. Xu Z, Gan L, Li T, Xu C, Chen K, Wang X, Qin JG, Chen L, Li E (2015) Transcriptome profiling and molecular pathway analysis of genes in association with salinity adaptation in Nile tilapia Oreochromis niloticus. PLoS One 10(8):e0136506CrossRefPubMedPubMedCentralGoogle Scholar
  66. Yan B, Guo JT, Zhao LH, Zhao JL (2012) MiR-30c: a novel regulator of salt tolerance in tilapia. Biochem Biophys Res Commun 425(2):315–320CrossRefPubMedGoogle Scholar
  67. Yue GH (2014) Recent advances of genome mapping and marker-assisted selection in aquaculture. Fish Fish 15(3):376–396CrossRefGoogle Scholar
  68. Yue GH, Lin H, Li J (2016) Tilapia is the fish for next-generation aquaculture. Int J Marine Sci Ocean Technol 3:11–13Google Scholar
  69. Zhang R, Zhang LL, Ye X, Tian YY, Sun CF, Lu MX, Bai JJ (2013) Transcriptome profiling and digital gene expression analysis of Nile tilapia (Oreochromis niloticus) infected by Streptococcus agalactiae. Mol Biol Rep 40(10):5657–5668CrossRefPubMedGoogle Scholar
  70. Zhang M, Sun Y, Liu Y, Qiao F, Chen L, Liu W-T, Du Z, Li E (2016) Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference. Aquaculture 454:72–80CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China

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