Abstract
In the past two decades, various statistical approaches have been developed to identify quantitative trait locus with experimental organisms. In this chapter, we introduce several commonly used QTL mapping methods for intercross and backcross populations. Important issues related to QTL mapping, such as threshold and confidence interval calculations are also discussed. We list and describe five public domain QTL software packages commonly used by biologists.
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Sax, K. (1923) The association of size differences with seed-coat pattern and pigmentation Phaseolus Vulgaris. Genetics 8: 552–560.
Lander, ES, Botstein, D. (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199.
Haley, CS, Knott, SA. (1992) A simple regression method for mapping quantitative trait in line crosses using flanking markers. Heredity 69: 315–324.
Kao, CH, Zeng, ZB. (1997) General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics 53, 653–665.
Kao, CH, Zeng, ZB, Teasdale, RD. (1999) Multiple interval mapping for quantitative trait loci. Genetics 152: 1203–1216.
Zeng, ZB. (1993) Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc Nat Acad Sci USA 90: 10972–10976.
Zeng, ZB. (1994) Precision mapping of quantitative traits loci. Genetics 136: 1457–1468.
Jansen, RC, Stam, P. (1994) High resolution of quantitative traits into multiple quantitative trait in line crosses using flanking markers. Heredity 69: 315–324.
Satagopan, JM, Yandell, BS, Newton, MA, et al. (1996) A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics 144: 805–816.
Sillanpää, MJ, Arjas, E. (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373–1388.
Stephens, DA, Fisch, RD. (1998) Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Biometrics 54: 1334–1347.
Yi, N, Xu, S. (2000) Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 155: 1391–1403.
Yi, N, Xu, S. (2001) Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics 157: 1759–1771.
Hoeschele, I. (2001) Mapping quantitative trait loci in outbred pedigrees. In: Balding, D, Bishop, M, Cannings, O, (eds) Handbook of Statistical Genetics, Wiley and Sons, New York, pp. 599–644.
Yi, N. (2004) A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci. Genetics 167: 967–975.
Churchill, GA, Doerge, RW. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963–971.
Zou, F, Fine, JP, Hu, J, et al. (2004) An efficient resampling method for assessing genome-wide statistical significance in mapping quantitative trait loci. Genetics 168: 2307–2316.
Stoehr, JP, Nadler, ST, Schueler, KL, et al. (2000) Genetic obesity unmasks nonlinear interactions between murine type 2 diabetes susceptibility loci. Diabetes 49: 1946–1954.
Lan, H, Kendziorski, CM, Haag, JD, et al. (2001) Genetic loci controlling breast cancer susceptibility in the Wistar-Kyoto rat. Genetics 157: 331–339.
Ott, J (1999) Analysis of Human Genetic Linkage. The Johns Hopkins University Press, Baltimore, MD.
Lynch, M, Walsh, B. (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
Liu, BH. (1998) Statistical Genomics: Linkage, Mapping, and QTL Analysis. CRC Press, Boca Raton, FL
Dempster, AP, Laird, NM, Rubin, DB. (1997) Maximum likelihood from incomplete data via the EM algorithm. J R Stat. Soc. Series B 39: 1–38.
Knapp, SJ, Bridges, WC, Birkes, D. (1990) Mapping quantitative trait loci using molecular marker linkage maps. Theor. Appl. Genet. 79: 583–592.
Martinez, O, Curnow, RN. (1992) Estimating the locations and sizes of the effects of quantitative trait loci using flanking markers. Theor. Appl. Genet. 85: 480–488.
Xu, SZ. (1998) Iteratively reweighted least squares mapping of quantitative trait loci. Behav. Genet. 28: 341–355.
Dupuis, J, Siegmund, D. (1999) Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics 151: 373–386.
Rebai, A, Goffinet, B, Mangin, B, et al. (1994) Detecting QTLs with diallel schemes. In: van Ooijen JW, Jansen, J. (eds) Biometrics in plant breeding: applications of molecular markers. 9th meeting of the EUCARPIA, Wageningen, The Netherlands.
Rebai, A, Goffinet, B, Mangin, B. (1995) Comparing power of different methods for QTL detection. Biometrics 51: 87–99.
Piepho, HP. (2001) A quick method for computing approximate thresholds for quantitative trait loci detection. Genetics 157: 425–432.
Zou, F, Yandell, BS, Fine, JP. (2001) Statistical issues in the analysis of quantitative traits in combined crosses. Genetics 158: 1339–1346.
Zou, F, Fine, JP. (2002) Note on a partial empirical likelihood. Biometrika 89: 958–961.
Zou, F, Xu, ZL, Vision, TJ. (2006) Assessing the significance of quantitative trait loci in replicated mapping populations. Genetics 174: 1063–1068.
Churchill, GA, Doerge, RW. (2008) Naive application of permutation testing leads to inflated type I error rates. Genetics. 178: 609–610.
Manichaikul, A, Dupuis, J, Sen, S, et al. (2006) Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus. Genetics 174: 481–489.
Mangin, B, Goffinet, B, Rebai, A. (1994) Constructing confidence intervals for QTL location. Genetics 138: 1301–1308.
Visscher, PM, Thompson, R, Haley, CS, (1996) Confidence intervals in QTL mapping by bootstrapping. Genetics 143: 1013–1020.
Zeng, ZB. (2000). Unpublished notes on Statistical model for mapping Quantitative trait loci. North Carolina State University, Raleigh, NC.
Zeng, ZB, Kao, CH, Basten, CJ. (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74: 279–289.
Broman, KW, Speed, TP. (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses. J. R. Stat. Soc. Series B 64: 641–656.
Green, PJ. (1995) Reversible jump Markov Chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711–732.
Ven, RV. (2004) Reversible-Jump Markov Chain Monte Carlo for quantitative trait loci mapping. Genetics 167: 1033–1035.
Godsill, SJ. (2001) On the relationship between Markov chain Monte Carlo methods for model uncertainty. J. Comput. Graph. Stat. 10: 230–248.
Godsill, SJ. (2003) Proposal densities, and product space methods. In: Green, PJ, Hjort, NL, Richardson, S, (eds) Highly Structured Stochastic Systems. Oxford University Press, London/New York/Oxford.
George, EI, McCulloch, RE, (1993) Variable selection via gibbs sampling. J. Am. Stat. Assoc. 88: 881–889.
Wang, H, Zhang, YM, Li, X, et al. (2005) Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170: 465–480.
Yi, N, Shriner, D. (2008) Advances in Bayesian multiple QTL mapping in experimental 11 designs. Heredity 100: 240–252.
Bernardo, R. (1994) Prediction of maize single-cross performance using RFLPs and information from related hybrids. Crop Science 34: 20–25.
Liu, Y, Zeng, ZB. (2000) A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines. Genet. Res. 75: 345–355.
Draper, NR, Smith, H. (1998) Applied Regression Analysis. John Wiley & Sons, New York.
Visscher, PM, Haley, CS, Knott, SA. (1996) Mapping QTLs for binary traits in backcross and F-2 populations. Genet. Res. 68: 55–63.
Xu, S, Atchley, WR. (1995) A random model approach to interval mapping of quantitative genes. Genetics 141: 1189–1197.
McIntyre, LM, Coffman, C, Doerge, RW. (2000) Detection and location of a single binary trait locus in experimental populations. Genet. Res. 78: 79–92.
Rao, SQ, Li, X. (2000) Strategies for genetic mapping of categorical traits. Genetica 109: 183–197.
Broman, KW. (2003) Quantitative trait locus mapping in the case of a spike in the phenotype distribution. Genetics 163: 1169–1175.
Mackay, TF, Fry, JD. (1996) Polygenic mutation in Drosophila melanogaster: genetic interactions between selection lines and candidate quantitative trait loci. Genetics 144: 671–688.
Shepel, LA, Lan, H, Haag, JD, et al. (1998) Genetic identification of multiple loci that control breast cancer susceptibility in the rat. Genetics 149: 289–299.
Hackett, CA, Weller, JI. (1995) Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics 51: 1254–1263.
Diao, G, Lin, DY, Zou, F. (2004) Mapping quantitative trait loci with censored observations. Genetics 168: 1689–1698.
Kruglyak, L, Lander, ES, (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139: 1421–1428.
Poole, TM, Drinkwater, NR, (1996) Two genes abrogate the inhibition of murine hepatocarcinogenesis by ovarian hormones. Proc Nat Acad Sci USA 93: 5848–5853.
Zou, F, Fine, JP, Yandell, BS. (2002) On empirical likelihood for a semiparametric mixture model. Biometrika 89: 61–75.
Jin, C, Fine, JP, Yandell, B. (2007) A unified semiparametric framework for QTL mapping, with application to spike phenotypes. J Am Stat Assoc 102: 56–57.
Fine, JP, Zou, F, Yandell, BS. (2004) Nonparametric estimation of mixture models, with application to quantitative trait loci. Biostatistics 5: 501–513.
Huang, C, Qin, J, Zou, F. (2007) Empirical likelihood-based inference for genetic mixture models. Can J Stat 35: 563–574.
Lange, C., Whittaker, J. C. (2001). Mapping quantitative trait loci using generalized estimating equations. Genetics 159: 1325–1337.
Symons, RCA, Daly, MJ, Fridlyand, J, et al. (2002) Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E5-v-abl transgenic mice. Proc Nat Acad Sci USA 99: 11299–11304.
Diao, G, Lin, DY. (2005) Semiparametric methods for mapping quantitative rait loci with censored data. Biometrics 61: 789–798.
Epstein, MP, Lin, X, Boehnke, M, (2003) A Tobit variance-component method for linkage analysis of censored trait data. Am J Hum Genet 72: 611–620.
Lincoln, SE, Daly, MJ, Lander, ES. (1993) A tutorial and reference manual. 3rd edn. Technical Report Whitehead Institute for Biomedical Research.
Basten, CJ, Weir, BS, Zeng, ZB. (1997) QTL Cartographer: A Reference Manual and Tutorial for QTL Mapping. North Carolina State University, Raleigh, NC.
Manly, KF, Cudmore, JRH, Meer, JM. (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12: 930–932.
Manly, KF, Olson, JM, (1999) Overview of QTL mapping software and introduction to Map Manager QT. Mamm Genome 10: 327–334.
Broman, KW, Wu, H, Sen, S, et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890.
Yandell, BS, Mehta, T, Banerjee, S, et al. (2007) R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics 23: 641–643.
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Zou, F. (2009). QTL Mapping in Intercross and Backcross Populations. In: DiPetrillo, K. (eds) Cardiovascular Genomics. Methods in Molecular Biology™, vol 573. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-247-6_9
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DOI: https://doi.org/10.1007/978-1-60761-247-6_9
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