FAO. The State of World Fisheries and Aquaculture 2020. Rome: Sustainability in action; 2020.
Guyon R, Rakotomanga M, Azzouzi N, Coutanceau JP, Bonillo C, D'Cotta H, Pepey E, Soler L, Rodier-Goud M, D'Hont A, et al. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. BMC Genomics. 2012;13:222.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ponzoni RW, Nguyen NH, Khaw HL, Hamzah A, Bakar KRA, Yee HY. Genetic improvement of Nile tilapia (Oreochromis niloticus) with special reference to the work conducted by the WorldFish Center with the GIFT strain. Rev Aquac. 2011;3(1):27–41.
Article
Google Scholar
Portner HO. Oxygen- and capacity-limitation of thermal tolerance: a matrix for integrating climate-related stressor effects in marine ecosystems. J Exp Biol. 2010;213(6):881–93.
Article
PubMed
Google Scholar
Fitzgibbon QP, Strawbridge A, Seymour RS. Metabolic scope, swimming performance and the effects of hypoxia in the mulloway, Argyrosomus japonicus (Pisces : Sciaenidae). Aquaculture. 2007;270(1–4):358–68.
Article
Google Scholar
Mengistu SB, Mulder HA, Benzie JAH, Komen H. A systematic literature review of the major factors causing yield gap by affecting growth, feed conversion ratio and survival in Nile tilapia (Oreochromis niloticus). Rev Aquac. 2020;12(2):524–41.
Article
Google Scholar
Michiels C. Physiological and pathological responses to hypoxia. Am J Pathol. 2004;164(6):1875–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Majmundar AJ, Wong WHJ, Simon MC. Hypoxia-inducible factors and the response to hypoxic stress. Mol Cell. 2010;40(2):294–309.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nikinmaa M, Rees BB. Oxygen-dependent gene expression in fishes. Am J Physiol Regul Integr Comp Physiol. 2005;288(5):R1079–90.
Article
CAS
PubMed
Google Scholar
Xiao W. The hypoxia signaling pathway and hypoxic adaptation in fishes. Sci China Life Sci. 2015;58(2):148–55.
Article
CAS
PubMed
Google Scholar
Zhu CD, Wang ZH, Yan BA. Strategies for hypoxia adaptation in fish species: a review. J Comp Physiol B. 2013;183(8):1005–13.
Article
CAS
PubMed
Google Scholar
Du SNN, Mahalingam S, Borowiec BG, Scott GR. Mitochondrial physiology and reactive oxygen species production are altered by hypoxia acclimation in killifish (Fundulus heteroclitus). J Exp Biol. 2016;219(8):1130–8.
PubMed
Google Scholar
Zhong X, Wang X, Zhou T, Jin Y, Tan S, Jiang C, Geng X, Li N, Shi H, Zeng Q, et al. Genome-wide association study reveals multiple novel QTL associated with low oxygen tolerance in hybrid catfish. Mar Biotechnol. 2017;19(4):379–90.
Article
CAS
Google Scholar
Wang XZ, Liu SK, Jiang C, Geng X, Zhou T, Li N, Bao LS, Li Y, Yao J, Yang YJ, et al. Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish. Mol Gen Genomics. 2017;292(1):63–76.
Article
CAS
Google Scholar
Anttila K, Dhillon RS, Boulding EG, Farrell AP, Glebe BD, Elliott JAK, Wolters WR, Schulte PM. Variation in temperature tolerance among families of Atlantic salmon (Salmo salar) is associated with hypoxia tolerance, ventricle size and myoglobin level. J Exp Biol. 2013;216(7):1183–90.
Article
CAS
PubMed
Google Scholar
Li HL, Gu XH, Li BJ, Chen CH, Lin HR, Xia JH. Genome-wide QTL analysis identified significant associations between hypoxia tolerance and mutations in the GPR132 and ABCG4 genes in Nile Tilapia. Mar Biotechnol. 2017;19(5):441–53.
Article
CAS
Google Scholar
Aquaculture Genomics G, Breeding W, Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, et al. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics. 2017;18(1):191.
Article
Google Scholar
Brennan RS, Healy TM, Bryant HJ, Van La M, Schulte PM, Whitehead A. Integrative population and physiological genomics reveals mechanisms of adaptation in killifish. Mol Biol Evol. 2018;35(11):2639–53.
CAS
PubMed
Google Scholar
Yoshida GM, Lhorente JP, Correa K, Soto J, Salas D, Yanez JM. Genome-wide association study and cost-efficient genomic predictions for growth and fillet yield in Nile Tilapia (Oreochromis niloticus). G3. 2019;9(8):2597–607.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mandic M, Todgham AE, Richards JG. Mechanisms and evolution of hypoxia tolerance in fish. Proc Biol Sci. 2009;276(1657):735–44.
CAS
PubMed
Google Scholar
Almeida-Val VM, Val AL, Duncan WP, Souza FC, Paula-Silva MN, Land S. Scaling effects on hypoxia tolerance in the Amazon fish Astronotus ocellatus (Perciformes: Cichlidae): contribution of tissue enzyme levels. Comp Biochem Physiol B Biochem Mol Biol. 2000;125(2):219–26.
Article
CAS
PubMed
Google Scholar
Sloman KA, Wood CM, Scott GR, Wood S, Kajimura M, Johannsson OE, Almeida-Val VM, Val AL. Tribute to R. G. Boutilier: the effect of size on the physiological and behavioural responses of oscar, Astronotus ocellatus, to hypoxia. J Exp Biol. 2006;209(Pt 7):1197–205.
Article
PubMed
Google Scholar
Ishibashi Y, Inoue K, Nakatsukasa H, Ishitani Y, Miyashita S, Murata O. Ontogeny of tolerance to hypoxia and oxygen consumption of larval and juvenile red sea bream, Pagrus major. Aquaculture. 2005;244(1–4):331–40.
Article
Google Scholar
Burleson ML, Wilhelm DR, Smatresk NJ. The influence of fish size on the avoidance of hypoxia and oxygen selection by largemouth bass. J Fish Biol. 2001;59(5):1336–49.
Google Scholar
Robb T, Abrahams MV. Variation in tolerance to hypoxia in a predator and prey species: an ecological advantage of being small? J Fish Biol. 2003;62(5):1067–81.
Article
Google Scholar
Vejrik L, Matejickova I, Juza T, Frouzova J, Seda J, Blabolil P, Ricard D, Vasek M, Kubecka J, Riha M, et al. Small fish use the hypoxic pelagic zone as a refuge from predators. Freshw Biol. 2016;61(6):899–913.
Article
CAS
Google Scholar
Nilsson GE, Ostlund-Nilsson S. Does size matter for hypoxia tolerance in fish? Biol Rev. 2008;83(2):173–89.
Article
PubMed
Google Scholar
Abdel-Tawwab M, Monier MN, Hoseinifar SH, Faggio C. Fish response to hypoxia stress: growth, physiological, and immunological biomarkers. Fish Physiol Biochem. 2019;45(3):997–1013.
Article
CAS
PubMed
Google Scholar
Abdel-Tawwab M, Hagras AE, Elbaghdady HAM, Monier MN. Effects of dissolved oxygen and fish size on Nile tilapia, Oreochromis niloticus (L.): growth performance, whole-body composition, and innate immunity. Aquacult Int. 2015;23(5):1261–74.
Article
CAS
Google Scholar
Wang XJ, Dasari S, Nowakowski GS, Lazaridis KN, Wieben ED, Kadin ME, Feldman AL, Boddicker RL. Retinoic acid receptor alpha drives cell cycle progression and is associated with increased sensitivity to retinoids in T-cell lymphoma. Oncotarget. 2017;8(16):26245–55.
Article
PubMed
PubMed Central
Google Scholar
Hale LA, Tallafuss A, Yan YL, Dudley L, Eisen JS, Postlethwait JH. Characterization of the retinoic acid receptor genes raraa, rarab and rarg during zebrafish development. Gene Expr Patterns. 2006;6(5):546–55.
Article
CAS
PubMed
Google Scholar
Harrison C, Wabbersen T, Shepherd IT. In vivo visualization of the development of the enteric nervous system using a Tg(−8.3bphox2b:Kaede) transgenic Zebrafish. Genesis. 2014;52(12):985–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tian Y, Wen HS, Qi X, Zhang XY, Li Y. Identification of mapk gene family in Lateolabrax maculatus and their expression profiles in response to hypoxia and salinity challenges. Gene. 2019;684:20–9.
Article
CAS
PubMed
Google Scholar
Marques IJ, Leito JTD, Spaink HP, Testerink J, Jaspers RT, Witte F, van Den Berg S, Bagowski CP. Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts. J Comp Physiol B. 2008;178(1):77–92.
Article
CAS
PubMed
Google Scholar
Maitland ML, Lou XJ, Ramirez J, Desai AA, Berlin DS, McLeod HL, Weichselbaum RR, Ratain MJ, Altman RB, Klein TE. Vascular endothelial growth factor pathway. Pharmacogenet Genomics. 2010;20(5):346–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurihara T, Westenskow PD, Friedlander M. Hypoxia-inducible factor (HIF)/vascular endothelial growth factor (VEGF) signaling in the retina. Adv Exp Med Biol. 2014;801:275–81.
Article
PubMed
Google Scholar
Hakuno F, Takahashi SI. IGF1 receptor signaling pathways. J Mol Endocrinol. 2018;61(1):T69–86.
Article
CAS
PubMed
Google Scholar
Husain A, Chiu YT, Ho DW, Sze KM, Chan LK, Tsui YM, Wong CC, Ng IO. EFNA3, a key functional mediator of hypoxic microenvironment in hepatocellular carcinoma. Cancer Res. 2018;78(13 Suppl):Abstract nr 2431.
Li H, Zhou L, Dai J. Retinoic acid receptor-related orphan receptor RORalpha regulates differentiation and survival of keratinocytes during hypoxia. J Cell Physiol. 2018;233(1):641–50.
Article
CAS
PubMed
Google Scholar
Romain CV, Paul P, Lee S, Qiao J, Chung DH. Targeting aurora kinase A inhibits hypoxia-mediated neuroblastoma cell tumorigenesis. Anticancer Res. 2014;34(5):2269–74.
CAS
PubMed
PubMed Central
Google Scholar
Obirikorang KA, Acheampong JN, Duodu CP, Skov PV. Growth, metabolism and respiration in Nile tilapia (Oreochromis niloticus) exposed to chronic or periodic hypoxia. Comp Biochem Physiol A Mol Integr Physiol. 2020;248:110768.
Article
CAS
PubMed
Google Scholar
Roze T, Christen F, Amerand A, Claireaux G. Trade-off between thermal sensitivity, hypoxia tolerance and growth in fish. J Therm Biol. 2013;38(2):98–106.
Article
Google Scholar
Mandic M, Regan MD. Can variation among hypoxic environments explain why different fish species use different hypoxic survival strategies? J Exp Biol. 2018;221(21):jeb161349.
Article
PubMed
Google Scholar
Kwong JQ, Huo JZ, Bround MJ, Boyer JG, Schwanekamp JA, Ghazal N, Maxwell JT, Jang YC, Khuchua Z, Shi K, et al. The mitochondrial calcium uniporter underlies metabolic fuel preference in skeletal muscle. Jci Insight. 2018;3(22):e121689.
Article
PubMed Central
Google Scholar
Sprague J, Bayraktaroglu L, Clements D, Conlin T, Fashena D, Frazer K, Haendel M, Howe DG, Mani P, Ramachandran S, et al. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 2006;34(Database issue):D581–5.
Article
CAS
PubMed
Google Scholar
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, et al. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res. 2014;42(Database issue):D802–9.
Article
CAS
PubMed
Google Scholar
Teumer A, Qi Q, Nethander M, Aschard H, Bandinelli S, Beekman M, Berndt SI, Bidlingmaier M, Broer L, Group CLW, et al. Genomewide meta-analysis identifies loci associated with IGF-I and IGFBP-3 levels with impact on age-related traits. Aging Cell. 2016;15(5):811–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chun AY, Estrada K, Luan J, Kutalik Z, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014;46(11):1173–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Couto Alves A, De Silva NMG, Karhunen V, Sovio U, Das S, Taal HR, Warrington NM, Lewin AM, Kaakinen M, Cousminer DL, et al. GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI. Sci Adv. 2019;5(9):eaaw3095.
Article
PubMed
PubMed Central
CAS
Google Scholar
Seabury CM, Oldeschulte DL, Saatchi M, Beever JE, Decker JE, Halley YA, Bhattarai EK, Molaei M, Freetly HC, Hansen SL, et al. Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC Genomics. 2017;18(1):386.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mengistu SB, Mulder HA, Benzie JA, Khaw HL, Megens H-J, Trinh TQ, Komen H. Genotype by environment interaction between aerated and non-aerated ponds and the impact of aeration on genetic parameters in Nile tilapia (Oreochromis niloticus). Aquaculture. 2020;529:735704.
Article
CAS
Google Scholar
Ponzoni RW, Khaw HL, Nguyen NH, Hamzah A. Inbreeding and effective population size in the Malaysian nucleus of the GIFT strain of Nile tilapia (Oreochromis niloticus). Aquaculture. 2010;302(1–2):42–8.
Article
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. In: Babraham bioinformatics. Cambridge: Babraham Institute; 2010.
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garrison E, Marth G: Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:12073907. 2012.
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Villasenor Alva JA, Estrada EG. A generalization of Shapiro–Wilk’s test for multivariate normality. Commun Stat Theory Methods. 2009;38(11):1870–83.
Article
Google Scholar
McDonald JH. Handbook of biological statistics, vol. 2. Baltimore: Sparky House Publishing; 2009.
Google Scholar
Neerchal NK, Morel J, Huang X, Moluh A. A stepwise algorithm for generalized linear mixed models, vol. 2014. Washington, DC: SAS Global Forum; 2014. p. 1822–2014.
Google Scholar
Gondro C, van der Werf J, Hayes B. Genome-wide association studies and genomic prediction. Volume 1019. Springer: Humana Press; 2013.
Gao XY, Becker LC, Becker DM, Starmer JD, Province MA. Avoiding the high Bonferroni penalty in genome-wide association studies. Genet Epidemiol. 2010;34(1):100–5.
PubMed
PubMed Central
Google Scholar
Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012;44(7):821–U136.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu B, Pankow JS. Fast and accurate genome-wide association test of multiple quantitative traits. Comput Math Methods Med. 2018;2018:2564531.
PubMed
PubMed Central
Google Scholar
Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, et al. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nat Med. 2015;21(9):1018–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu JZ, Tozzi F, Waterworth DM, Pillai SG, Muglia P, Middleton L, Berrettini W, Knouff CW, Yuan X, Waeber G, et al. Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat Genet. 2010;42(5):436–U475.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee CH, Cook S, Lee JS, Han B. Comparison of two meta-analysis methods: inverse-variance-weighted average and weighted sum of Z-scores. Genomics Inform. 2016;14(4):173–80.
Article
PubMed
PubMed Central
Google Scholar
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The Ensembl variant effect predictor. Genome Biol. 2016;17(1):122.
Article
PubMed
PubMed Central
CAS
Google Scholar
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–13.
Article
CAS
PubMed
Google Scholar