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Genome-Wide QTL Analysis Identified Significant Associations Between Hypoxia Tolerance and Mutations in the GPR132 and ABCG4 Genes in Nile Tilapia

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Abstract

Exposure to hypoxia induces both acute and chronic stress responses, which plays an important role in health of cultured organisms including growth, reproduction, immunity, and other energy demanding activities. Application of advanced genomic technologies allows rapid identification of hypoxia trait-associated genes and precise selection of superior brood stocks with high tolerance in tilapia. By applying QTL-seq and double-digest restriction-site associated DNA sequencing (ddRAD-seq) techniques, we identified four genome-wide significant quantitative trait loci (QTLs) for hypoxia tolerance and many suggestive QTLs in Nile tilapia. These QTLs explained 6.6–14.7% of the phenotypic variance. Further analysis revealed that single nucleotide polymorphisms (SNPs) in exons of both GPR132 and ABCG4 genes located in genome-wide QTL intervals were significantly associated with hypoxia-tolerant traits. Expression analysis of both genes suggested that they were strong candidate genes involved into hypoxia tolerance in tilapia. Our findings suggest that both QTL-seq and ddRAD-seq techniques can be effectively utilized in QTL mapping of hypoxia traits in fish. Our data supply a basis for further marker-assisted selection of super lines with a high level of tolerance against low oxygen stress in the tilapia.

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References

  • 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 14:139–149

    Article  CAS  PubMed  Google Scholar 

  • Beall CM (2000) Tibetan and Andean patterns of adaptation to high-altitude hypoxia. Hum Biol 72:201–228

    CAS  PubMed  Google Scholar 

  • Boleza KA, Burnett LE, Burnett KG (2001) Hypercapnic hypoxia compromises bactericidal activity of fish anterior kidney cells against opportunistic environmental pathogens. Fish Shellfish Immunol 11:593–610

    Article  CAS  PubMed  Google Scholar 

  • Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan SH, 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 SY, 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 513:375–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen YM, Kao YT, Chen TY (2016) Functional analysis of small ubiquitin-modifier (SUMO) in orange-spotted grouper (Epinephelus coioides). Fish Shellfish Immunol 53:110

    Article  Google Scholar 

  • Chen P, Zuo H, Xiong H, Kolar MJ, Chu Q, Saghatelian A, Siegwart DJ, Wan Y (2017) Gpr132 sensing of lactate mediates tumor-macrophage interplay to promote breast cancer metastasis. Proc Natl Acad Sci U S A 114:580–585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Claireaux G, Webber DM, Lagardere JP, Kerr SR (2000) Influence of water temperature and oxygenation on the aerobic metabolic scope of Atlantic cod (Gadus morhua). J Sea Res 44:257–265

    Article  Google Scholar 

  • 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 272:162–172

    Article  CAS  Google Scholar 

  • Das S, Upadhyaya HD, Bajaj D, Kujur A, Badoni S, Laxmi, Kumar V, Tripathi S, Gowda CLL, 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 22:193–203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Evans JJ, Shoemaker CA, Klesius PH (2003) Effects of sublethal dissolved oxygen stress on blood glucose and susceptibility to Streptococcus agalactiae in Nile tilapia Oreochromis niloticus. J Aquat Anim Health 15:202–208

    Article  Google Scholar 

  • Fernandes MN, Rantin FT (1994) Relationships between oxygen availability and metabolic cost of breathing in Nile tilapia (Oreochromis niloticus): aquacultural consequences. Aquaculture 127:339–346

    Article  Google Scholar 

  • Fisher RA (1922) On the interpretation of χ2 from contingency tables, and the calculation of P. J R Stat Soc 85:87–94

    Article  Google Scholar 

  • Fry, F.J. (1969). Some possible physiological stresses induced by eutrophication. Eutrophication: causes, consequences, correctives. Proceedings of an international symposium on eutrophication, University of Wisconsin, Madison. National Academy of Sciences, Washington, D.C., pp 531–536

  • Gallage S, Katagiri T, Endo M, Futami K, Endo M, Maita M (2016) Influence of moderate hypoxia on vaccine efficacy against Vibrio anguillarum in Oreochromis niloticus (Nile tilapia). Fish Shellfish Immunol 51:271–281

    Article  CAS  PubMed  Google Scholar 

  • Garry MG, Garry DJ (2008) Hypoxia-inducible factor-2α transactivates Abcg2 and promotes cytoprotection in cardiac side population cells. Circ Res 102:1075–1081

    Article  PubMed  Google Scholar 

  • Gracey AY, Troll JV, Somero GN (2001) Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci U S A 98:1993–1998

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Herbert NA, Steffensen JF (2005) The response of Atlantic cod, Gadus morhua, to progressive hypoxia: fish swimming speed and physiological stress. Mar Biol 147:1403–1412

    Article  Google Scholar 

  • Howe AE (2004). The genetic basis of red color in tilapia. MS Thesis, University of New Hampshire, Durham

  • 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 90:4266–4279

    Article  CAS  PubMed  Google Scholar 

  • Jha AR, Zhou D, Brown CD, Kreitman M, Haddad GG, White KP (2016) Shared genetic signals of hypoxia adaptation in Drosophila and in high-altitude human populations. Mol Biol Evol 33:501–517

    Article  CAS  PubMed  Google Scholar 

  • Kai W, Nomura K, Fujiwara A, Nakamura Y, Yasuike M, Ojima N, Masaoka T, Ozaki A, Kazeto Y, Gen K, Nagao J, Tanaka H, Kobayashi T, Ototake M (2014) A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics 15:233

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 6:89

    Article  PubMed  PubMed Central  Google Scholar 

  • Kietzmann T, Mennerich D, Dimova EY (2016) Hypoxia-inducible factors (HIFs) and phosphorylation: impact on stability, localization, and transactivity. Front Cell Dev Biol 4:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Kofler R, Pandey RV, Schlotterer C (2011) PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 27:3435–3436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kronvang B (1993) Nationwide monitoring of nutrients and their ecological effects: state of the Danish aquatic environment. Ambio 22:176–187

    Google Scholar 

  • Lague SL, Speers-Roesch B, Richards JG, Farrell AP (2012) Exceptional cardiac anoxia tolerance in tilapia (Oreochromis hybrid). J Exp Biol 215:1354–1365

    Article  PubMed  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leveelahti L, Leskinen P, Leder EH, Waser W, Nikinmaa M (2011) Responses of threespine stickleback (Gasterosteus aculeatus, L) transcriptome to hypoxia. Comp Biochem Physiol Part D Genomics Proteomics 6:370–381

  • Li BJ, Li HL, Meng Z, Zhang Y, Lin H, Yue GH, Xia JH (2017) Copy number variations in tilapia genomes. Mar Biotechnol 19:11–21

    Article  CAS  PubMed  Google Scholar 

  • 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 14:58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • Martinovic D, Villeneuve DL, Kahl MD, Blake LS, Brodin JD, Ankley GT (2009) Hypoxia alters gene expression in the gonads of zebrafish (Danio rerio). Aquat Toxicol 95:258–272

    Article  CAS  PubMed  Google Scholar 

  • Mcconnell SKJ, Beynon C, Leamon J, Skibinski DOF (2000) Microsatellite marker based genetic linkage maps of Oreochromis aureus and O-niloticus (Cichlidae): extensive linkage group segment homologies revealed. Anim Genet 31:214–218

    Article  CAS  PubMed  Google Scholar 

  • Moen T, Agresti JJ, Cnaani A, Moses H, Famula TR, Hulata G, Gae G, 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 35:893–904

  • Ooijen JW (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 93:343–349

    Article  Google Scholar 

  • Palaiokostas C, Bekaert M, Khan MGQ, 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:e68389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Phang YL, Soga T, Kitahashi T, Parhar IS (2012) Cloning and functional expression of novel cholesterol transporters ABCG1 and ABCG4 in gonadotropin-releasing hormone neurons of the tilapia. Neuroscience 203:39–49

    Article  CAS  PubMed  Google Scholar 

  • Sun Y (2017) FasParser: a package for manipulating sequence data. Zool Res 38:110–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 74:174–183

    Article  CAS  PubMed  Google Scholar 

  • Van Bers NEM, Crooijmans RPMA, Groenen MAM, Dibbits BW, Komen J (2012) SNP marker detection and genotyping in tilapia. Mol Ecol Resour 12:932–941

    Article  PubMed  Google Scholar 

  • Van Ooijen, J. (2009). MapQTL 6.0, software for the mapping of quantitative trait loci in experimental populations of dihaploid species

  • Wang Z, Wan ZY, Bai B, Huang SQ, Chua E, Lee M, Pang HY, Wen YF, Liu P, Liu F, Sun F, Lin G, Ye BQ, Yue GH (2015) Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass. Sci Rep 5:16358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Liu S, Jiang C, Geng X, Zhou T, Li N, Bao L, Li Y, Yao J, Yang Y, Zhong X, Jin Y, Dunham R, Liu Z (2016) Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish. Mol Gen Genomics 292:63–76

    Article  Google Scholar 

  • Welker TL, Mcnulty ST, Klesius PH (2007) Effect of sublethal hypoxia on the immune response and susceptibility of channel catfish, Ictalurus punctatus, to enteric septicemia. J World Aquacult Soc 38:12–23

    Article  Google Scholar 

  • Wulff T, Jokumsen A, Hojrup P, Jessen F (2012) Time-dependent changes in protein expression in rainbow trout muscle following hypoxia. J Proteome 75:2342–2351

    Article  CAS  Google Scholar 

  • Xia JH, Lin G, He X, Liu P, Liu F, Sun F, Tu R, Yue GH (2013) Whole genome scanning and association mapping identified a significant association between growth and a SNP in the IFABP—a gene of the Asian seabass. BMC Genomics 14:295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 432:67–73

    Article  CAS  Google Scholar 

  • 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 5:14168

    Article  CAS  PubMed  Google Scholar 

  • Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329:75–78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang ZP, Wells MC, Boswell MG, Beldorth I, Kirk LM, Wang YL, Wang SL, Savage M, Walter RB, Booth RE (2012) Identification of robust hypoxia biomarker candidates from fin of medaka (Oryzias latipes). Comp Biochem Physiol C Toxicol Pharmacol 155:11–17

    Article  CAS  PubMed  Google Scholar 

  • 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 40:5657–5668

    Article  CAS  PubMed  Google Scholar 

  • Zhong XP, Wang D, Zhang YB, Gui JF (2009) Identification and characterization of hypoxia-induced genes in Carassius auratus blastulae embryonic cells using suppression subtractive hybridization. Comp Biochem Physiol B Biochem Mol Biol 152:161–170

    Article  PubMed  Google Scholar 

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Acknowledgements

We thank two anonymous reviewers for comments on the manuscript. This work was supported by the National Natural Science Foundation of China (No. 31572612), Natural Science Foundation of Guangdong Province, China (No. 2015A030313150), Special Fund for Marine Fisheries-Scientific Research of Guangdong Province (A201501A04), and Modern Agriculture Talents Support Program (2016-2020).

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  1. State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Hong Lian Li, Xiao Hui Gu, Bi Jun Li, Chao Hao Chen, Hao Ran Lin & Jun Hong Xia

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  1. Hong Lian Li
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  2. Xiao Hui Gu
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  3. Bi Jun Li
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JHX and HRL contributed to project conception. Experiment and data analysis was conducted by JHX, HLL, XHG, BJL, and CHC. The manuscript was prepared by JHX and HLL. All authors read and approved the final manuscript.

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Correspondence to Jun Hong Xia.

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All the read data were available at DDBJ database (BioProject Accession: PRJDB5502).

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The authors declare that they have no competing interests.

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Supplementary Table S1

The significant QTL intervals identified by QTL-seq technique. (XLSX 11 kb)

Supplementary Table S2

The primer list used for genotyping and qRT-PCR analysis. (XLSX 9 kb)

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Li, H.L., Gu, X.H., Li, B.J. et al. Genome-Wide QTL Analysis Identified Significant Associations Between Hypoxia Tolerance and Mutations in the GPR132 and ABCG4 Genes in Nile Tilapia. Mar Biotechnol 19, 441–453 (2017). https://doi.org/10.1007/s10126-017-9762-8

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