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Bayesian Analysis for Genetic Architectures of Body Weights and Morphological Traits Using Distorted Markers in Japanese Flounder Paralichthys olivaceus

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Abstract

A doubled haploids (DH) population of 160 individuals is constructed by using mitotic gynogenetics for the study of genetic architectures of the body weight and morphological traits in Japanese flounder. Each DH individual is genotyped for 458 SSR markers, 222 of which segregate distortionally. By modifying conditional probabilities of quantitative trait locus (QTL) genotypes on the distorted flanking markers, Bayesian model selection is used to dissect genetic architectures for the traits. As a result, we identify 42 main-effect QTLs on chromosomes 5, 6, 7, 8, 9, 10, 15, 20, 21, 22, and 59 pairs of interacting QTLs. Among these detected QTLs, the largest interacting QTL is between chromosome 6 and chromosome 9 and accounts for 25.196 % of phenotypic variance for body weights and in a similar trend. Also, many QTLs show pleiotropic effects. The QTL on chromosome 9 simultaneously governs seven traits, BL, BH, FL, HL, PFL, HW, and CW. As compared to method using the uncorrected conditional probabilities of QTL genotypes, our method using corrected conditional probabilities can detect more interacting QTLs for the traits.

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References

  • Castaño-Sánchez C, Fuji K, Ozaki A, Hasegawa O, Sakamoto T, Morishima K, Nakayama I, Fujiwara A, Masaoka T, Okamoto H (2010) A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus). BMC Genomics 11:554

    Article  PubMed Central  PubMed  Google Scholar 

  • Cheng L, Liu L, Yu X, Wang D, Tong J (2010) A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers. Anim Genet 41:191–198

    Article  CAS  PubMed  Google Scholar 

  • Coimbra MR, Kobayashi K, Koretsugu S, Hasegawa O, Ohara E, Ozaki A, Sakamoto T, Naruse K, Okamoto N (2003) A genetic linkage map of the Japanese flounder, Paralichthys olivaceus. Aquaculture 220:203–218

    Article  CAS  Google Scholar 

  • Ds F, Tfc M (1996) Introduction to quantitative genetics, 4th edn. Longman, London

    Google Scholar 

  • Fuji K, Kobayashi K, Hasegawa O, Coimbra MRM, Sakamoto T, Okamoto N (2006) Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus). Aquaculture 254:203–210

    Article  CAS  Google Scholar 

  • Guo X, Li Q, Wang QZ, Kong LF (2012) Genetic mapping and QTL analysis of growth-related traits in the Pacific oyster. Mar Biotechnol 14:218–226

    Article  CAS  PubMed  Google Scholar 

  • Hackett C, Broadfoot L (2003) Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90:33–38

    Article  CAS  PubMed  Google Scholar 

  • Hu Z, Xu S (2009) PROC QTL—A SAS procedure for mapping quantitative trait loci. Int J Plant Genom 2009:1–3

    Article  Google Scholar 

  • Kang J-H, Kim W-J, Lee W-J (2008) Genetic linkage map of olive flounder, Paralichthys olivaceus. Int J Biol Sci 4:143

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kao C-H, Zeng Z-B (2002) Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics 160:1243–1261

    PubMed Central  PubMed  Google Scholar 

  • Kass RE, Raftery AE (1995) Bayes factors. J Am Stat Assoc 90:773–795

    Article  Google Scholar 

  • Lallias D, Lapegue S, Hecquet C, Boudry P, Beaumont A (2007) AFLP‐based genetic linkage maps of the blue mussel (Mytilus edulis). Anim Genet 38:340–349

    Article  CAS  PubMed  Google Scholar 

  • Li L, Xiang J, Liu X, Zhang Y, Dong B, Zhang X (2005) Construction of AFLP-based genetic linkage map for Zhikong scallop, Chlamys farreri Jones et Preston and mapping of sex-linked markers. Aquaculture 245:63–73

    Article  CAS  Google Scholar 

  • Liao X, Ma H-Y, Xu G-B, Shao C-W, Tian Y-S, Ji X-S, Yang J-F, Chen S-L (2009) Construction of a genetic linkage map and mapping of a female-specific DNA marker in half-smooth tongue sole (Cynoglossus semilaevis). Mar Biotechnol 11:699–709

    Article  CAS  PubMed  Google Scholar 

  • Liu Z, Karsi A, Li P, Cao D, Dunham R (2003) An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family. Genetics 165:687–694

    PubMed Central  CAS  PubMed  Google Scholar 

  • Liu Y, Liu Y, Liu Y, Zhang X, Si F, Sun Z, Wang G, Wang Y, Yang R, Liu H (2013) Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder. Biologia 68:1221–1228

    CAS  Google Scholar 

  • Lorieux M, Goffinet B, Perrier X, De Leon DG, Lanaud C (1995) Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations. Theor Appl Genet 90:73–80

    Article  CAS  PubMed  Google Scholar 

  • Song W, Pang R, Niu Y, Gao F, Zhao Y, Zhang J, Sun J, Shao C, Liao X, Wang L (2012) Construction of high-density genetic linkage maps and mapping of growth-related quantitative trail loci in the Japanese flounder (Paralichthys olivaceus). PLoS One 7:e50404

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Song W, Miao G, Zhao Y, Niu Y, Pang R, Liao X, Shao C, Chen S (2013) Construction of a microsatellite-based genetic linkage map for half-smooth tongue sole Cynoglossus semilaevis. Zoology 59:1

    Google Scholar 

  • Xu S (1998) Iteratively reweighted least squares mapping of quantitative trait loci. Behav Genet 28:341–355

    Article  CAS  PubMed  Google Scholar 

  • Xu S (2008) Quantitative trait locus mapping can benefit from segregation distortion. Genetics 180:2201–2208

    Article  PubMed Central  PubMed  Google Scholar 

  • Yamamoto E (1999) Studies on sex-manipulation and production of cloned populations in hirame, Paralichthys olivaceus (Temminck et Schlegel). Aquaculture 173:235–246

    Article  Google Scholar 

  • Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, Von Smith R, Yi N (2007) R/qtlbim: QTL with Bayesian interval mapping in experimental crosses. Bioinformatics 23:641–643

    Article  CAS  PubMed  Google Scholar 

  • Yi N, Yandell BS, Churchill GA, Allison DB, Eisen EJ, Pomp D (2005) Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics 170:1333–1344

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yi N, Shriner D, Banerjee S, Mehta T, Pomp D, Yandell BS (2007) An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects. Genetics 176:1865–1877

    Article  PubMed Central  PubMed  Google Scholar 

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Acknowledgments

This work was financially supported by Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Sciences (2014B004 and 2014A04XK01) and the National Natural Science Foundations of China (30972077 and 31172190).

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Authors and Affiliations

  1. Research Centre for Aquatic Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China

    Yan Cui, Hongwei Wang, Haijin Liu & Runqing Yang

  2. School of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China

    Yan Cui & Xuemei Qiu

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  1. Yan Cui
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  2. Hongwei Wang
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  3. Xuemei Qiu
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  4. Haijin Liu
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  5. Runqing Yang
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Correspondence to Runqing Yang.

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Cui, Y., Wang, H., Qiu, X. et al. Bayesian Analysis for Genetic Architectures of Body Weights and Morphological Traits Using Distorted Markers in Japanese Flounder Paralichthys olivaceus . Mar Biotechnol 17, 693–702 (2015). https://doi.org/10.1007/s10126-015-9646-8

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  • DOI: https://doi.org/10.1007/s10126-015-9646-8

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