Identifying a Long QTL Cluster Across chrLG18 Associated with Salt Tolerance in Tilapia Using GWAS and QTL-seq
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Understanding the genetic mechanism of osmoregulation is important for the improvement of salt tolerance in tilapia. In our previous study, we have identified a major quantitative trait locus (QTL) region located at 23.0 Mb of chrLG18 in a Nile tilapia line by QTL-seq. However, the conservation of these QTLs in other tilapia populations or species is not clear. In this study, we successfully investigated the QTLs associated with salt tolerance in a mass cross population from the GIFT line of Nile tilapia (Oreochromis niloticus) using a ddRAD-seq-based genome-wide association study (GWAS) and in a full-sib family from the Malaysia red tilapia strain (Oreochromis spp) using QTL-seq. Our study confirmed the major QTL interval that is located at nearly 23.0 Mb of chrLG18 in Nile tilapia and revealed a long QTL cluster across chrLG18 controlling for the salt-tolerant trait in both red tilapia and Nile tilapia. This is the first GWAS analysis on salt tolerance in tilapia. Our finding provides important insights into the genetic architecture of salinity tolerance in tilapia and supplies a basis for fine mapping QTLs, marker-assisted selection, and further detailed functional analysis of the underlying genes for salt tolerance in tilapia.
KeywordsNile tilapia Red tilapia Genome-wide association study Salt tolerance QTL-seq
JHX and HRL contributed to project conception. Experiments and data analysis were conducted by DLJ, XHG, BJL, ZXZ, ZNM, and HQ. The manuscript was prepared by JHX and DLJ. All the authors read and approved the final manuscript.
This work was supported by the Science and Technology Program of Guangzhou, China (No. 201804020013, 201803020043), Science and Technology Planning Project of Guangdong Province, China (2017A030303008), and National Natural Science Foundation of China (No. 31572612).
Compliance with Ethical Standards
All experiments in this study were approved by the Animal Care and Use Committee of the School of Life Science at Sun Yat-Sen University and were performed according to the regulations and guidelines established by this committee.
Conflict of Interest
The authors declare that they have no conflict of interest.
- Chen CH, Li BJ, Gu XH, Lin HR, Xia JH (2018) Marker-assisted selection of YY supermales from a genetically improved farmed tilapia-derived strain. Zool Res 0:42Google Scholar
- Hiroi J, Mccormick SD, Ohtani-Kaneko R, Kaneko T (2005a) 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 208:2023–2036CrossRefPubMedGoogle Scholar
- Hiroi J, Mccormick SD, Ohtani-Kaneko R, Kaneko T (2005b) 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 208:2023–2036CrossRefPubMedGoogle Scholar
- Howe AE (2004) The genetic basis of red color in tilapia. MS thesis, Univ of New Hampshire, Durham NHGoogle Scholar
- Maryoung LA, Lavado R, Bammler TK, Gallagher EP, Stapleton PL, Beyer RP, Farin FM, Hardiman G, Schlenk D (2015) Differential gene expression in liver, gill, and olfactory rosettes of coho salmon (Oncorhynchus kisutch) after acclimation to salinity. Mar Biotechnol 17:703–717CrossRefPubMedPubMedCentralGoogle Scholar
- Mccormick SD (2001) Endocrine control of osmoregulation in teleost fish. Am Zool 41:781–794Google Scholar
- Norman JD, Robinson M, Glebe B, Ferguson MM, Danzmann RG (2012) Genomic arrangement of salinity tolerance QTLs in salmonids: a comparative analysis of Atlantic salmon (Salmo salar) with Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss). BMC Genomics 13:Artn 420CrossRefGoogle 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 74:174–183CrossRefPubMedGoogle Scholar
- Van Oojjen JW (2009) MapQTL 6, software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BW, WageningenGoogle Scholar
- Wang H, Misztal I, Aguilar I, Legarra A, Fernando RL, Vitezica Z, Okimoto R, Wing T, Hawken R, Muir WM (2014) Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens. Front Genet 5:134PubMedPubMedCentralGoogle Scholar
- Xia JH, Li HL, Zhang Y, Meng ZN, Lin HR (2017) Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal:1–14Google Scholar
- Zhong XX, Wang XZ, Zhou T, Jin YL, Tan SX, Jiang C, Geng X, Li N, Shi HT, Zeng QF, Yang YJ, Yuan ZH, Bao LS, Liu SK, Tian CX, Peatman E, Li Q, Liu ZJ (2017) Genome-wide association study reveals multiple novel QTL associated with low oxygen tolerance in hybrid catfish. Mar Biotechnol 19:379–390CrossRefPubMedGoogle Scholar