Mapping complex traits as a dynamic system

Physics of Life Reviews

Volumn 13, Issue , 2015, Pages 155-185

  Sun, Lidan ^a,b   Wu, Rongling ^a,b  

^a BEIJING FORESTRY UNIVERSITY   (China)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Complex trait; Functional mapping; Genetic mapping; Network mapping; Quantitative trait loci; Systems mapping

Indexed keywords

BIOLOGY; DIFFERENTIAL EQUATIONS; DNA SEQUENCES; MACHINERY; MAPPING;

COMPLEX TRAITS; FUNCTIONAL MAPPING; GENETIC MAPPING; NETWORK MAPPING; QUANTITATIVE TRAIT LOCUS;

COMPLEX NETWORKS;

ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; CHROMOSOMAL MAPPING; GENETICS; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; HUMAN; PHENOTYPE; PLANT; QUANTITATIVE TRAIT LOCUS; SYSTEMS BIOLOGY;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENE-ENVIRONMENT INTERACTION; GENOTYPE; HUMANS; MODELS, GENETIC; PHENOTYPE; PLANTS; QUANTITATIVE TRAIT LOCI; SYSTEMS BIOLOGY;

EID: 84930482469     PISSN: 15710645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plrev.2015.02.007     Document Type: Review

References (198)

1. Agrawal A.A. Community genetics: new insights into community ecology by integrating population genetics. Ecology 2003, 84:543-544.
2. Alonso-Blanco C., Aarts M.G., Bentsink L., Keurentjes J.J., Reymond M., Vreugdenhil D., et al. What has natural variation taught us about plant development, physiology, and adaptation?. Plant Cell 2009, 21:1877-1896.
3. An P., Winkler C.A. Host genes associated with HIV/AIDS: advances in gene discovery. Trends Genet 2010, 26:119-131.
4. Antoniadis P., Fdida S., Griffin C., Jin Y., Kesidis G. Distributed medium access control with conditionally altruistic users. EURASIP J Wirel Commun Netw 2013, 2013:202.
5. Baghalian K., Hajirezaei M.R., Schreiber F. Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. Plant Cell 2014, 26:3847-3866.
6. Bailey J.K., Schweitzer J.A., Ubeda F., Koricheva J., LeRoy C.J., Madritch M.D., et al. From genes to ecosystems: synthesizing the effects of plant genetic factors across systems. Philos Trans R Soc B 2009, 364:1607-1616.
7. Barton N.H., Keightley P.D. Multifactorial genetics: understanding quantitative genetic variation. Nat Rev Genet 2002, 3:11-21.
8. Bateson P., Barker D., Clutton-Brock T., Deb D., D'Udine B., Foley R.A., et al. Developmental plasticity and human health. Nature 2004, 430:419-421.
9. Beerenwinkel S., Pachter L., Sturmfels B., Elena S.F., Lenski R.E. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol 2007, 2007(7):60.
10. Benfey P.N., Mitchell-Olds T. From genotype to phenotype: systems biology meets natural variation. Science 2008, 320:495-497.
11. Biscarini F., Bovenhuis H., van der Poel J., Rodenburg T.B., Jungerius A.P., van Arendonk J.A. Across-line SNP association study for direct and associative effects on feather damage in laying hens. Behav Genet 2010, 2010(40):715-727.
12. Bo W.H., Fu G.F., Wang Z., Xu F., Shen Y., Xu J.C., et al. Systems mapping: how to map genes for biomass allocation towards an ideotype. Brief Bioinform 2014, 15:660-669.
13. Bonhoeffer S., May R.M., Shaw G.M., Nowk M.A. Virus dynamics and drug therapy. Proc Natl Acad Sci USA 1997, 94:6971-6976.
14. Bonneau R., Facciotti M.T., Reiss D.J., Schmid A.K., Pan M., Kaur A., et al. A predictive model for transcriptional control of physiology in a free living cell. Cell 2007, 131:1354-1365.
15. Broman K.W., Speed T.P. A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J R Stat Soc B 2002, 64:641-656.
16. Buckler E.S., Holland J.B., Bradbury P.J., Acharya C.B., Brown P.J., Browne C., et al. The genetic architecture of maize flowering time. Science 2009, 325:714-718.
17. Calarco J.P., Borges F., Donoghue M.T., Van Ex F., Jullien P.E., Lopes T., et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012, 515:194-205.
18. Chen J.L., Reynolds J.F. A coordination model of whole-plant carbon allocation in relation to water stress. Ann Bot 1997, 80:45-55.
19. Cheverud J.M., Hager R., Roseman C., Fawcett G., Wang B., Wolf J.B. Genomic imprinting effects on adult body composition in mice. Proc Natl Acad Sci USA 2008, 105:4253-4258.
20. Civelek M., Lusis A.J. Systems genetics approaches to understand complex traits. Nat Rev Genet 2014, 15:34-48.
21. Cockerham C.C. An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 1954, 39:859-882.
22. Cui Y.H., Wu R. Statistical model for characterizing epistatic control of triploid endosperm triggered by maternal and offspring QTLs. Genet Res 2005, 86:65-75.
23. Cui Y.H., Wu R. Mapping genome-genome epistasis: a multi-dimensional model. Bioinformatics 2005, 21:2447-2455.
24. Cui Y.H., Casella G., Wu R. Mapping quantitative trait locus interactions from the maternal and offspring genomes. Genetics 2004, 167:1017-1026.
25. 2 design. Genomics 2006, 87:543-551.
26. Cui Y.H., Wu J.G., Shi C.H., Zhu J., Littell R.C., Wu R. Modeling epistatic effects of embryo and endosperm QTL on seed development. Genet Res 2006, 87:61-71.
27. Das K., Li J.H., Fu G.F., Wang Z., Li R., Wu R. Dynamic semiparametric Bayesian models for genetic mapping of complex trait with irregular longitudinal data. Stat Med 2012, 32:509-523.
28. Dawber T.R., Meadors G.F., Moore F.E. Epidemiological approaches to heart disease: the Framingham study. Am J Publ Health 1951, 41:279-286.
29. de Koning D.-J., Bovenhuis H., Van Arendonk J.A.M. On the detection of imprinted quantitative trait loci in experimental crosses of outbred species. Genetics 2002, 161:931-938.
30. Dunlap J.C. Molecular bases for circadian clocks. Cell 1999, 96:271-290.
31. Eichten S.R., Swanson-Wagner R.A., Schnable J.C., Waters A.J., Hermanson P.J., et al. Heritable epigenetic variation among maize inbreds. PLoS Genet 2011, 7(11):e1002372.
32. El-Soda M., Malosetti M., Zwaan B.J., Koornneef M., Aarts M.G. Genotype × environment interaction QTL mapping in plants: lessons from Arabidopsis. Trends Plant Sci 2014, 19:390-398.
33. Falconer D.S., Mackay T.F.C. Introduction to quantitative genetics 1996, Longman, Harlow, UK. 4th ed.
34. Fan J., Li R. Variable selection via nonconcave penalized likelihood and it oracle properties. J Am Stat Assoc 2001, 96:1348-1360.
35. Fan J., Li R. New estimation and model selection procedures for semiparametric modeling in longitudinal data analysis. J Am Stat Assoc 2004, 99:710-723.
36. Fan J., Lv J. Sure independence screening for ultrahigh dimensional feature space (with discussion). J R Stat Soc Ser B 2008, 70:849-911.
37. Fan J., Zhang J. Two-step estimation of functional linear models with applications to longitudinal data. J R Stat Soc B 2000, 62:303-322.
38. Fan J., Huang T., Li R. Analysis of longitudinal data with semiparametric estimation of covariance function. J Am Stat Assoc 2007, 35:632-641.
39. Feinberg A.P. Phenotypic plasticity and the epigenetics of human disease. Nature 2007, 447:433-440.
40. Feinberg A.P., Irizarry R.A. Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci USA 2010, 107(Suppl 1):1757-1764.
41. Feng P., Navaratna M. Modelling periodic oscillations during somitogenesis. Math Biosci Eng 2007, 4:661-673.
42. Fisher R.A. The correlation between relatives on the supposition of Mendelian inheritance. Trans R Soc Edinb 1918, 52:399-433.
43. Frank S.A. Age-specific acceleration of cancer. Curr Biol 2004, 14:242-246.
44. Frayling T.M., Timpson N.J., Weedon M.N., Zeggini E., Freathy R.M., Lindgren C.M., et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 2007, 316:889-894.
45. Friesen M.L., Sachs J.L., von Porter S.S., Wettberg E.J., Stark S.C., Martinez-Romero E. Microbially mediated plant functional traits. Annu Rev Ecol Evol Syst 2011, 42:23-36.
46. Fu G.F., Luo J., Berg A., Wang Z., Li J.H., Das K., et al. A dynamic model for functional mapping of biological rhythms. J Biol Dyn 2010, 4:1-10.
47. Fu G.F., Wang Z., Li J.H., Wu R. A mathematical framework for functional mapping of complex systems using delay differential equations. J Theor Biol 2011, 289:206-216.
48. Gagneur J., Stegle O., Zhu C., Jakob J., Tekkedil M.M., Aiyar R.S., et al. Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype. PLoS Genet 2013, 9(9):e1003803.
49. Gallego M., Eide E.J., Woolf M.F., Virshup D.M., Forger D.B. An opposite role for tau in circadian rhythms revealed by mathematical modeling. Proc Natl Acad Sci USA 2006, 103:10618-10623.
50. Genard M., Dauzat J., Franck N., et al. Carbon allocation in fruit trees: from theory to modelling. Trees Struc Func 2008, 22:269-282.
51. Goldbeter A. Biochemical oscillations and cellular rhythms: the molecular bases of periodic and chaotic behaviour 1996, Cambridge University Press, Cambridge.
52. Goldbeter A. Computational approaches to cellular rhythms. Nature 2002, 420:238-245.
53. Gorbacheva V.Y., Kondratov R.V., Zhang R., Cherukuri S., Gudkov A.V., Takahashi J.S., et al. Circadian sensitivity to the chemotherapeutic agent cyclophosphamide depends on the functional status of the CLOCK/BMAL1 transactivation complex. Proc Natl Acad Sci USA 2005, 102:3407-3412.
54. Guo Y.Q., Luo J.T., Wang J.X., Wang Y.Q., Wu R. How to compute which genes control drug resistance dynamics. Drug Discov Today 2011, 16:334-339.
55. Hansen T.F. The evolution of genetic architecture. Annu Rev Ecol Evol Syst 2006, 37:123-157.
56. Hansen T.F., Wagner G.P. Epistasis and the mutation load: a measurement-theoretical approach. Genetics 2001, 158:477-485.
57. Hayes B.J., Pryce J., Chamberlain A.J., Bowman P.J., Goddard M.E. Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genet 2010, 6(9):e1001139.
58. He Q.L., Berg A., Li Y., Vallejos C.E., Wu R. Modeling genes for plant structure, development and evolution: functional mapping meets plant ontology. Trends Genet 2010, 26:39-46.
59. Hermans C., Hammond J.P., White P.J., Verbruggen N. How do plants respond to nutrient shortage by biomass allocation?. Trends Plant Sci 2006, 11:610-617.
60. Hersch-Green E.I., Turley N.E., Johnson M.TJ. Community genetics: what have we accomplished and where should we be going?. Philos Trans R Soc B 2011, 366:1453-1460.
61. Hill W.G. Understanding and using quantitative genetic variation. Philos Trans R Soc Lond B, Biol Sci 2010, 365:73-85.
62. Hindorff LA, MacArthur J (European Bioinformatics Institute), Morales J (European Bioinformatics Institute), Junkins HA, Hall PN, Klemm AK et al. A catalog of published genome-wide association studies. Accessed December 27, 2014. http://www.genome.gov/gwastudies.
63. Holland J.B. Genetic architecture of complex traits in plants. Curr Opin Plant Biol 2007, 10:156-161.
64. Hou W., Liu T., Li Y., Li Q., Li J., Das K., et al. Multilocus genomics of outcrossing plant populations. Theor Pop Biol 2009, (76):68-76.
65. Huang J.Z., Liu N., Pourahmadi M., Liu L. Covariance selection and estimation via penalized normal likelihood. Biometrika 2006, 93:85-98.
66. Imielinski M., Belta C. Exploiting the pathway structure of metabolism to reveal high-order epistasis. BMC Syst Biol 2008, 2:40.
67. Imumorin I.G., Kim E.H., Lee Y.M., De Koning D.J., van Arendonk J.A., De Donato M., et al. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits. Front Genet 2011, 2:44.
68. Jin C., Fine J.P., Yandell B.S. A unified semiparametric framework for QTL analyses, with application to spike phenotypes. J Am Stat Assoc 2007, 102:56-67.
69. Johannes F., Colot V., Jansen R.C. Epigenome dynamics: a quantitative genetics perspective. Nat Rev Genet 2008, 9:883-890.
70. Johannes F., Porcher E., Teixeira F.K., Saliba-Colombani V., Simon M., Agier N., et al. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 2009, 5:e1000530.
71. Kao C.H., Zeng Z.B., Teasdale R.D. Multiple interval mapping for quantitative trait loci. Genetics 1999, 152:1203-1216.
72. Karlebach G., Shamir R. Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 2008, 9:770-780.
73. Kloeden P.E., Platen E. Numerical solution of stochastic differential equations 1999, Springer-Verlag, New York.
74. Knott S.A., Marklund L., Haley C.S., Andersson K., Davies W., Ellegren H., et al. Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics 1998, 149:1069-1080.
75. Kolenbrander P.E., Egland P.G., Diaz P.I., Palmer R.J. Genome-genome interactions: bacterial communities in initial dental plaque. Trends Microbiol 2005, 13:11-15.
76. Labrecque G., Belanger P.M. Biological rhythms in the absorption, distribution, metabolism and excretion of drugs. Pharmacol Ther 1991, 52:95-107.
77. Lambrechts L. Dissecting the genetic architecture of host-pathogen specificity. PLoS Pathog 2010, 6(8):e1001019.
78. Lander E.S., Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989, 121:185-199.
79. Lawson H.A., Cheverud J.M., Wolf J.B. Genomic imprinting and parent-of-origin effects on complex traits. Nat Rev Genet 2013, 14:609-617.
80. Leach R.J., O'Neill R.G., Fitzpatrick J.L., Williams J.L., Glass E.J. Quantitative trait loci associated with the immune response to a bovine respiratory syncytial virus vaccine. PLoS ONE 2012, 7(3):e33526.
81. Legewie S., Herzel H., Westerhoff H.V., Blüthgen N. Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol 2008, 4:190.
82. Lettre G., Jackson A.U., Gieger C., Schumacher F.R., Berndt S.I., Sanna S., et al. Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet 2008, 40:584-591.
83. Li J.H., Das K., Fu G., Li R., Wu R. The Bayesian lasso for genome-wide association studies. Bioinformatics 2012, 27:516-523.
84. Li J.H., Li Q., Hou W., Han K., Li Y., Wu S., et al. An algorithmic model for constructing a linkage and linkage disequilibrium map in open-pollinated progeny populations. Genet Res 2009, 91:9-21.
85. Li J.H., Zhong W., Li R., Wu R. A fast algorithm for detecting gene-gene interactions in genome-wide association studies. Ann Appl Stat 2014, 8:2292-2318.
86. Li N., McMurry T., Berg A., Wang Z., Berceli S.A., Wu R. Functional clustering of periodic transcriptional profiles through ARMA(p, q). PLoS ONE 2010, 5(4):e9894.
87. Li X., Sui Y.H., Liu T., Wang J., Li Y., Lin Z., et al. A model for family-based case-control studies of genetic imprinting and epistasis. Brief Bioinform 2014, 15:1069-1079.
88. Li Y., Wu R. Modeling host-cancer genetic interactions with multilocus sequence data. J Comp Sci Syst Biol 2009, 2:24-43.
89. Li Y., Wu R. Functional mapping of growth and development. Biol Rev 2010, 85:207-216.
90. Li Y.C., Coelho C.M., Liu T., Wu S., Zeng Y., Li Y., et al. A statistical strategy to estimate maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development. PLoS ONE 2008, 3:e3131.
91. Liu G.D., Kong L., Wang Z., Wu R. Systems mapping of metabolic genes through control theory. Adv Drug Deliv Rev 2013, 65:918-928.
92. Liu T., Todhunter R.J., Wu S., Hou W., Mateescu R., Zhang Z., et al. A random model for mapping imprinted quantitative trait loci in a structured pedigree: an implication for mapping canine hip dysplasia. Genomics 2007, 90:276-284.
93. Lovell J.T., Juenger T.E., Michaels S.D., Lasky J.R., Platt A., Richards J.H., et al. Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation. Proc Biol Sci 2013, 280:20131043.
94. Lu Q., Cui Y., Wu R. A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family. BMC Genet 2004, 5:20.
95. Lu T., Liang H., Li H., Wu H. High dimensional ODEs coupled with mixed-effects modeling techniques for dynamic gene regulatory network identification. J Am Stat Assoc 2011, 106:1242-1258.
96. Lucek K., Haesler M.P., Sivasundar A. When phenotypes do not match genotypes-unexpected phenotypic diversity and potential environmental constraints in Icelandic stickleback. J Hered 2012, 103:579-584.
97. Lynch M., Walsh B. Genetics and analysis of quantitative traits 1998, Sinauer Associates, Sunderland, MA.
98. Ma C.X., Casella G., Wu R. Functional mapping of quantitative trait loci underlying the character process: a theoretical framework. Genetics 2002, 161:1751-1762.
99. Mackay T.F.C. The genetic architecture of quantitative traits. Annu Rev Genet 2001, 35:303-339.
100. Mackay T.F.C. Epistasis and quantitative traits: using model organisms to study gene-gene interactions. Nat Rev Genet 2014, 15:22-33.
101. Mackay T.F.C., Stone E.A., Ayroles J.F. The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 2009, 10:565-577.
102. Manichaikul A., Moon J.Y., Sen S., Yandell B.S., Broman K.W. A model selection approach for the identification of quantitative trait loci in experimental crosses. Genetics 2009, 181:1077-1086.
103. Mather K., Jinks J.L. Biometrical genetics, the study of continuous variation 1982, Chapman and Hall, London. 3rd ed.
104. Maynard-Smith J., Price G.R. The logic of animal conflict. Nature 1973, 246:15.
105. McConnaughay K.D.M., Coleman J.S. Biomass allocation in three plants: ontogeny or optimality? A test along three resource gradients. Ecology 1999, 80:2581-2593.
106. McMullen M.D., Byrne P.F., Snook M.E., Wiseman B.R., Lee E.A., Wildstrom N.W., et al. Quantitative trait loci and metabolic pathways. Proc Natl Acad Sci USA 1998, 95:1996-2000.
107. McNamara J.M. Towards a richer evolutionary game theory. J R Soc Interface 2013, 10:20130544.
108. Merilä J., Hendry A.P. Climate change, adaptation, and phenotypic plasticity: the problem and the evidence. Evol Appl 2014, 7:1-14.
109. Muller G.B. Evo-devo: extending the evolutionary synthesis. Nat Rev Genet 2007, 8:943-949.
110. Myles S., Peiffer J., Brown P.J., Ersoz E.S., Zhang Z., Costich D.E., et al. Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 2009, 21:2194-2202.
111. Nash J. Equilibrium points in n-person games. Proc Natl Acad Sci USA 1950, 36:48-49.
112. Nettleton D., Doerge R.W. Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics 2000, 56:52-58.
113. Nicholson J.K., Holmes E., Lindon J., Wilson I.D. The challenges of modeling mammalian biocomplexity. Nat Biotechnol 2004, 22:1268-1274.
114. Nowak M.A., Sigmund K. Evolutionary dynamics of biological games. Science 2004, 303:793-799.
115. Ober U., Ayroles J.F., Stone E.A., Richards S., Zhu D., Gibbs R.A., et al. Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet 2012, 8(5):e1002685.
116. Ohdo S., Koyanagi S., Suyama H., Higuchi S., Aramaki H. Changing the dosing schedule minimizes the disruptive effects of interferon on clock function. Nat Med 2001, 7:356-360.
117. Pavlicev M., Wagner G.P. A model of developmental evolution: selection, pleiotropy and compensation. Trends Ecol Evol 2012, 27:316-322.
118. Plomin R., Haworth C.M., Davis O.S. Common disorders are quantitative traits. Nat Rev Genet 2009, 10:872-878.
119. Ramsay J.O., Hooker G., Campbell D., Cao J. Parameter estimation for differential equations: a generalized smoothing approach (with discussion). J R Stat Soc Ser B 2007, 69:741-796.
120. Reik W., Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet 2001, 2:21-32.
121. Rice S.H. A general population genetic theory for the evolution of developmental interactions. Proc Natl Acad Sci USA 2002, 99:15518-15523.
122. Richards E.J. Natural epigenetic variation in plant species: a view from the field. Curr Opin Plant Biol 2011, 14:204-209.
123. Richards C.L., Bossdorf O., Pigliucci M. What role does heritable epigenetic variation play in phenotypic evolution?. Bioscience 2010, 60:232-237.
124. Rosen J.B. Existence and uniqueness of equilibrium points for concave n-person games. Econometrica 1965, 33:520-534.
125. Samoilov M.S., Price G., Arkin A.P. From fluctuations to phenotypes: the physiology of noise. Sci STKE 2006, 2006(366):re17.
126. Scheiner S.M. Genetics and evolution of phenotypic plasticity. Annu Rev Ecol Syst 1993, 24:35-68.
127. Schlichting C.D., Smith H. Phenotypic plasticity: linking molecular mechanisms with evolutionary outcomes. Evol Ecol 2002, 16:189-211.
128. Schneider M.K., Law R., Illian J.B. Quantification of neighbourhood-dependent plant growth by Bayesian hierarchical modeling. J Ecol 2006, 94:310-321.
129. Sen S., Churchill G.A. A statistical framework for quantitative trait mapping. Genetics 2001, 159:371-387.
130. Shaw K.L., Parsons Y.M., Lesnick S.C. QTL analysis of a rapidly evolving speciation phenotype in the Hawaiian cricket Laupala. Mol Ecol 2007, 16:2879-2892.
131. Sillanpää M.J., Pikkuhookana P., Abrahamsson S., Knürr T., Fries A., Lerceteau E., et al. Simultaneous estimation of multiple quantitative trait loci and growth curve parameters through hierarchical Bayesian modeling. Heredity 2012, 108:134-146.
132. Slatkin M. Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat Rev Genet 2008, 9:477-485.
133. Stam P. Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J 2003, 3:739-744.
134. Stich B., Yu J., Melchinger A.E., Piepho H.-P., Utz H.F., Maurer H.P., et al. Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 2007, 176:563-570.
135. Strauss S.Y., Irwin R.E. Ecological and evolutionary consequences of multispecies plant-animal interactions. Annu Rev Ecol Evol Syst 2004, 35:435-466.
136. Strauss S.Y., Sahli H., Conner J.K. Toward a more trait-centered approach to diffuse (co)evolution. New Phytol 2005, 165:81-90.
137. Sui Y., Wu W., Wang Z., Wang J., Wang Z., Wu R. A case-control design for testing and estimating epigenetic effects on complex diseases. Brief Bioinform 2014, 15:319-326.
138. Sun L., Zhu X., Bo W., Xu F., Cheng T., Zhang Q., et al. An open-pollinated design for mapping imprinting genes in natural populations. Brief Bioinform 2014.
139. Thornley J.H.M., Johnson I.R. Plant and crop modelling: a mathematical approach to plant and crop physiology 1990, Clarendon Press, Oxford.
140. Tveito A., Winther R. Introduction to partial differential equations: a computational approach 1999, Springer-Verlag, New York.
141. van Eeuwijk FA, Bink M.C., Chenu K., Chapman S.C. Detection and use of QTL for complex traits in multiple environments. Curr Opin Plant Biol 2010, 13:193-205.
142. Varshney R.K., Kudapa H., Pazhamala L., Chitikineni A., Thudi M., Bohra M., et al. Translational genomics in agriculture: some examples in grain legumes. Crit Rev Plant Sci 2015, 34:169-194.
143. Verdugo A., Rand R. Hopf bifurcation in a DDE model of gene expression. Commun Nonlinear Sci Numer Simul 2008, 13:235-242.
144. Via S., Lande R. Genotype-environment interaction and the evolution of phenotypic plasticity. Evolution 1985, 39:505-522.
145. Via S., Gomulkiewicz R., De Jong G., Scheiner S.M., Schlichting C.D., Van Tienderen P.H. Adaptive phenotypic plasticity: consensus and controversy. Trends Ecol Evol 1995, 10:212-217.
146. Wagner G.P., Zhang J. The pleiotropic structure of the genotype-phenotype map: the evolvability of complex adaptations. Nat Rev Genet 2011, 12:204-213.
147. Walpole J., Papin J.A., Peirce S.M. Multiscale computational models of complex biological systems. Annu Rev Biomed Eng 2013, 15:137-154.
148. Wang C.G., Wang Z., Luo J.T., Li Q., Li Y., Ahn K., et al. A model for transgenerational imprinting variation in complex traits. PLoS ONE 2010, 5(7):e11396.
149. Wang C.G., Wang Z., Prows D.R., Wu R. A computational framework for the inheritance of genomic imprinting for complex traits. Brief Bioinform 2012, 13:34-45.
150. Wang X.F., Xu C.W., Wu R., Larkins B.A. Genetic dissection of complex endosperm traits. Trends Plant Sci 2009, 14:391-398.
151. Wang Y.Q., Wang N.T., Wang Z., Han H., Wu R. Genetic dissection of complex traits: from functional mapping to systems mapping. J Biometr Biostat 2012, 3:e119.
152. Wang Y.Q., Wang N.T., Wang J.X., Wang Z., Wu R. Delivering systems pharmacogenomics towards precision medicine through mathematics. Adv Drug Deliv Rev 2013, 65:905-911.
153. Wang Z., Wang Z.H., Wang J.X., Sui Y.H., Zhang J., Liao D.P., et al. A quantitative genetic and epigenetic model of complex traits. BMC Bioinform 2012, 13:274.
154. Wang Z., Pang X.M., Lv Y.F., Xu F., Zhou T., Li X., et al. A dynamic framework for quantifying the genetic architecture of phenotypic plasticity. Brief Bioinform 2013, 14:82-95.
155. Wang Z., Wang Y.Q., Wang N.T., Wang J.X., Wang Z.H., Wu R. Towards a comprehensive picture of the genetic landscape of complex traits. Brief Bioinform 2014, 15:30-42.
156. Wang Z.H., Wang Z., Fu G.F., Luo J.T., Wu R. Stochastic modeling of systems mapping for drug response. Adv Drug Deliv Rev 2013, 65:912-917.
157. Waters A.J., Makarevitch I., Eichten S.R. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 2011, 23:4221-4233.
158. Weedon M.N., Frayling T.M. Reaching new heights: insights into the genetics of human stature. Trends Genet 2008, 24:595-603.
159. Weibull J.W. Evolutionary game theory 1997, MIT Press.
160. Weinig C., Stinchcombe J.R., Schmitt J. QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments. Mol Ecol 2003, 12:1153-1163.
161. West G.B., Brown J.H., Enquist B.J. A general model for the origin of allometric scaling laws in biology. Science 1997, 276:122-126.
162. West G.B., Brown J.H., Enquist B.J. A general model for the structure and allometry of plant vascular systems. Nature 1999, 400:664-667.
163. West G.B., Brown J.H., Enquist B.J. The fourth dimension of life: fractal geometry and allometric scaling of organisms. Science 1999, 284:1677-1679.
164. Whitham T.G., Bailey J.K., Schweitzer J.A., Shuster S.M., Bangert R.K., LeRoy C.J., et al. A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet 2006, 7:510-523.
165. Whitham T.G., Difazio S.P., Schweitzer J.A., Shuster S.M., Allan G.J., Bailey J.K., et al. Extending genomics to natural communities and ecosystems. Science 2008, 320:492-495.
166. Whitham T.G., Martinsen G.D., Young W., Gehring C.A., Schweitzer J.A., Shuster S.M., et al. Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 2003, 84:559-573.
167. Wilson D.S. Evolution on the level of communities. Science 1976, 192:1358-1360.
168. Wolf J.B. The geometry of phenotypic evolution in developmental hyperspace. Proc Natl Acad Sci USA 2002, 99:15849-15851.
169. Wolf J.B., Mutic J.J., Kover P.X. Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana. Philos Trans R Soc B 2011, 366:1358-1367.
170. Wright S. Systems of mating. Parts I-V. Genetics 1921, 6:111-178.
171. Wu J.S., Zhu J., Zeng Y.R., Wu R. Functional mapping of norm reactions to environmental signals. Genet Res 2007, 89:27-38.
172. Wu R. Simulated optimal structure of a photosynthetic system: implications for the breeding of forest crop ideotype. Can J For Res 1993, 23:1631-1638.
173. Wu R. Detecting epistatic genetic variance with a clonally replicated design: models for low- vs. high-order nonallelic interaction. Theor Appl Genet 1996, 93:102-109.
174. Wu R., Lin M. Functional mapping - how to map and study the genetic architecture of dynamic complex traits. Nat Rev Genet 2006, 7:229-237.
175. Wu R., Zeng Z.-B. Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 2001, 157:899-909.
176. Wu R., Cao J.G., Huang Z.W., Wang Z., Gai J.Y., Vallejos E. Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems. BMC Syst Biol 2011, 5:84.
177. Wu R., Grisson J.E., McKe S.E., O'Malley D.M. Phenotypic plasticity of fine roots and increased plant growth in pines. BMC Ecol 2004, 4:14.
178. Wu R., Lou X.-Y., Ma C.-X., Wang X.L., Larkins B.A., Casella G. An improved genetic model generates high-resolution mapping of QTL for protein quality in maize endosperm. Proc Natl Acad Sci USA 2002, 99:11281-11286.
179. Wu R., Ma C.-X., Casella G. Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 2002, 160:779-792.
180. Wu R., Ma C.-X., Gallo-Meagher M., Littell R.C., Casella G. Statistical methods for dissecting triploid endosperm traits using molecular markers: an autogamous model. Genetics 2002, 162:875-892.
181. Wu R., Ma C.-X., Lin M., Casella G. A general framework for analyzing the genetic architecture of developmental characteristics. Genetics 2004, 166:1541-1551.
182. Wu R., Ma C.-X., Painter I., Zeng Z.-B. Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theor Popul Biol 2001, 61:349-363.
183. Wu W.B., Pourahmadi M. Nonparametric estimation of large covariance matrices of longitudinal data. Biometrika 2003, 90:831-844.
184. Wu W.M., Feng S.S., Wang Y., Wang N., Hao H., Wu R. Systems mapping of genes controlling chemotherapeutic drug efficiency for cancer stem cells. Drug Discov Today 2014, 19:1125-1130.
185. Xun X., Cao J., Mallick B., Maity A., Carroll R.J. Parameter estimation of partial differential equation models. J Am Stat Assoc 2013, 108:1009-1020.
186. Xu S. Estimating polygenic effects using markers of the entire genome. Genetics 2003, 163:789-801.
187. Xu S., Atchley W.R. Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 1996, 143:1417-1424.
188. Yang R., Xu S. Bayesian shrinkage analysis of quantitative trait loci for dynamic traits. Genetics 2007, 176:1169-1185.
189. Yao F., Müller H.G., Wang J.-L. Functional data analysis for sparse longitudinal data. J Am Stat Assoc 2005, 100:577-590.
190. Yap J., Fan J., Wu R. Nonparametric modeling of covariance structure in functional mapping of quantitative trait loci. Biometrics 2009, 65:1068-1077.
191. Yi N., Shriner D., Banerjee S., Mehta T., Pomp D., Yandell B.S. Efficient strategies for Bayesian mapping of genome-wide interacting QTL. Genetics 2007, 176:1865-1877.
192. Yin D.N., Zhu X.L., Jiang L.B., Zhang J., Zeng Y.R., Wu R. A reciprocal cross design to map the genetic architecture of complex traits in apomictic plants. New Phytol 2015, 205:1360-1367.
193. Young M.W., Kay S.A. Time zones: a comparative genetics of circadian clocks. Nat Rev Genet 2001, 2:702-715.
194. Zeng Z.-B. Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc Natl Acad Sci USA 1993, 90:10972-10976.
195. Zhao W., Hou W., Littell R.C., Wu R. Structured antedependence models for functional mapping of multivariate longitudinal quantitative traits. Stat Methods Mol Genet Biol 2005, 4(1).
196. Zhu S., Wang Z., Wang J.X., Wang Y.Q., Wang N.T., Xu M., et al. A quantitative model of transcriptional differentiation driving host-pathogen interactions. Brief Bioinform 2013, 14:713-723.
197. Zimmerman D.L., Nunez-Anton V. Parametric modeling of growth curve data: an overview (with discussion). Test 2001, 10:1-73.
198. Zou F., Nie L., Wright F.A., Sen P.K. A robust QTL mapping procedure. J Stat Plan Inference 2009, 139:978-989.