Dissecting genetic networks underlying complex phenotypes: The theoretical framework

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Zhang, Fan ^a   Zhai, Hu Qu ^a   Paterson, Andrew H ^b   Xu, Jian Long ^a   Gao, Yong Ming ^a   Zheng, Tian Qing ^a   Wu, Rong Ling ^c   Fu, Bin Ying ^a   Ali, Jauhar ^b   Li, Zhi Kang ^a,d  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b UNIVERSITY OF GEORGIA   (United States)

^c PENN STATE COLLEGE OF MEDICINE   (United States)

^d INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SIMULATION; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DNA FLANKING REGION; GENE FREQUENCY; GENE REGULATORY NETWORK; GENETIC EPISTASIS; GENETIC LINKAGE; GENETIC MODEL; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; HETEROSIS; MATHEMATICAL MODEL; PHENOTYPIC VARIATION; PREDICTION; QUANTITATIVE TRAIT LOCUS; SIGNAL TRANSDUCTION; ALLELE; BIOLOGICAL MODEL; HUMAN; PHENOTYPE;

ALLELES; EPISTASIS, GENETIC; GENE REGULATORY NETWORKS; GENETIC VARIATION; HUMANS; HYBRID VIGOR; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

EID: 79251637003     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014541     Document Type: Article

References (66)

1. Mackay TFC, Lyman RF, Lawrence F (2005) Polygenic mutation in Drosophila melanogaster: Mapping spontaneous mutations affecting sensory bristle number. Genetics 170: 1723-1735.
2. Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10: 565-577.
3. Goddard ME, Hayes BJ (2009) Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10: 381-391.
4. Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145: 453-465.
5. Li ZK, Luo LJ, Mei HW, Wang DL, Shu QY, et al. (2001) Overdominant epistatic loci are the primary genetic basis of Inbreeding Depression and Heterosis in Rice: I. Biomass and grain yield. Genetics 158: 1737-1753.
6. Luo LJ, Li ZK, Mei HW, Shu QY, Tabien R, et al. (2001) Overdominant epistatic loci are the primary genetic basis of Inbreeding Depression and Heterosis in Rice: II. Grain yield components. Genetics 158: 1755-1771.
7. Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, et al. (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Appl Genet 107: 89-101.
8. Mei HW, Li ZK, Shu QY, Guo LB, Wang YP, et al. (2005) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations. Theor Appl Genet 110: 649-659.
9. Hua JP, Xing YZ, Xu CG, Sun XL, Yu SB, et al. (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics 162: 1885-1895.
10. Hua JP, Xing YZ, Wu WR, Xu CG, Sun XL, et al. (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci U S A 100: 2574-2579.
11. Carlborg Ö, Kerje S, Schütz K, Jacobsson L, Jensen P, et al. (2003) A global search reveals epistatic interaction between QTLs for early growth in the chicken. Genome Res 13: 413-421.
12. Kusterer B, Piepho HP, Utz HF, Schön CC, Muminovic J, et al. (2007) Heterosis for biomass-related traits in arabidopsis investigated by quantitative trait loci analysis of the triple testcross design with recombinant inbred lines. Genetics 177: 1839-1850.
13. Malmberg RL, Held S, Waits A, Mauricio R (2005) Epistasis for Fitness-Related Quantitative Traits in Arabidopsis thaliana Grown in the Field and in the Greenhouse. Genetics 171: 2013-2027.
14. Lark KG, Chase K, Adler F, Mansur LM, Orf JH (1995) Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc Natl Acad Sci U S A 92: 4656-4660.
15. Doebley J, Stec A, Gustus C (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141: 333-346.
16. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, et al. (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci U S A 94: 9226-9231.
17. Malmberg RL, Mauricio R (2005) QTL-based evidence for the role of epistasis in evolution. Genet Res 86: 89-95.
18. Li ZK, Arif M, Zhong DB, Fu BY, Xu JL, et al. (2006) Complex genetic networks underlying the defensive system of rice (Oryza sativa L.) to Xanthomonas oryzae pv. oryzae. Proc Natl Acad Sci U S A 103: 7994-7999.
19. Xing Z, Tan F, Hua P, Sun L, Xu G, et al. (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs in the genetic basis of yield traits in rice. Theor Appl Genet 105: 248-257.
20. Melchinger AE, Utz HF, Schön CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149: 383-403.
21. Schön CC, Utz HF, Groh S, Truberg B, Openshaw S, et al. (2004) Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167: 485-498.
22. Xiong L, Zhu JK (2001) Abiotic stress signal transduction in plants: Molecular and genetic perspectives. Physiol Plant 112: 152-166.
23. Santner A, Estelle M (2009) Recent advances and emerging trends in plant hormone signalling. Nature 459: 1071-1078.
24. Wang DL, Zhu J, Li ZK, Paterson AH (1999) Mapping QTLs with epistatic effects and genotype x environment interactions by mixed linear model approaches. Theor Appl Genet 99: 1255-1264.
25. Kao CH, Zeng ZB (2002) Modeling Epistasis of Quantitative Trait Loci Using Cockerham's Model. Genetics 160: 1243-1261.
26. Sanjuán R, Nebot MR (2008) A network model for the correlation between epistasis and genomic complexity. PLoS One 3: e2663.
27. Aylor DL, Zeng ZB (2008) From classical genetics to quantitative genetics to system biology: modeling epistasis. PLoS Genet 4: e1000029.
28. Cooper M, Podlich DW (2002) The E(NK) model: Extending the NK model to incorporate gene-by-environment interactions and epistasis for diploid genomes. Complexity 7: 31-47.
29. Peccoud J, Velden KV, Podlich D, Winkler C, Arthur L, et al. (2004) The selective values of alleles in a molecular network model are context dependent. Genetics 166: 1715-1725.
30. Cooper M, Podlich DW, Smith OS (2005) Gene-to-phenotype models and complex trait genetics. Aust J Agr Sci 56: 895-918.
31. Mather K, Jinks JL (1982) Biometrical genetics. 3rd Edition. London: Chapman and Hall. 396 p.
32. Falconer DS (1981) Introduction to quantitative genetics. 2nd Edition. London, New York: Longman. 340 p.
33. Johannsen W (1909) Elemente der exakten Erblichkeitslehre. Gustav Fischer, Jena.
34. Veitia RA (2003) A sigmoidal transcriptional response: cooperativity, synergy and dosage effects. Biol Rev Camb Philos Soc 78: 149-170.
35. Bennett JH (1954) On the theory of random mating. Ann Eugen 18: 311-317.
36. Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, et al. (2003) QTL x environment interactions in rice. I. Heading date and plant height. Theor Appl Genet 108: 141-153.
37. Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberallin response modulators. Nature 400: 256-261.
38. Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) A mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.
39. Hedden P, Phillips AL (2000) Gibberellin metabolism: new insights revealed by the genes. Trends Plant Sci 5: 523-530.
40. Hedden P (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.
41. Itoh H, Tatsumi T, Sakamoto T, Otomo K, Toyomasu T, et al. (2004) A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase. Plant Mol Biol 54: 533-547.
42. Tong JP, Liu XJ, Zhang SY, Li SQ, Peng XJ, et al. (2007) Identification, genetic characterization, GA response and molecular mapping of Sdt97: a dominant mutant gene conferring semi-dwarfism in rice (Oryza sativa L.) Genet Res 89: 221-230.
43. Li ZK, Fu BY, Gao YM, Xu JL, Ali J, et al. (2005) Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant Mol Biol 59: 33-52.
44. Li Z, Pinson SR, Paterson AH, Park WD, Stansel JW (1997) Genetics of hybrid sterility and hybrid breakdown in an intersubspecific rice (Oryza sativa L.) population. Genetics 145: 1139-1148.
45. Davidson EH, McClay DR, Hood L (2003) Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A 100: 1475-1480.
46. Chesler EJ, Lu L, Wang J, Williams RW, Manly KF (2004) WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nat Neurosci 7: 485-486.
47. Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58: 221-227.
48. Gjuvsland AB, Hayes BJ, Omholt SW, Carlborg O (2007) Statistical epistasis is a feature of gene regulatory networks. Genetics 175: 411-420.
49. Calvo AP, Nicolás C, Lorenzo O, Nicolás G, Rodríguez D (2004) Evidence for positive regulation by gibberellins and ethylene of ACC oxidase expression and activity during transition from dormancy to germination in Fagus sylvatica L. seeds. Journal of Plant Growth Regulation 23: 44-53.
50. Steffens B, Sauter M (2005) Epidermal cell death in rice is regulated by ethylene, gibberellin, and abscisic acid. Plant Physiol 139: 713-721.
51. Falconer DS (1955) Patterns of response in selection experiments with mice. Cold Spring Harb Symp Quant Biol 20: 178-196.
52. Hill WG, Rasbash J (1986) Models of long term artificial selection in finite population. Genet Res 48: 41-50.
53. Hill WG, Caballero A (1992) Artificial selection experiments. Annu Rev Ecol Syst 23: 287-310.
54. Welbergen P, van Dijken FR (1992) Asymmetric response to directional for licking behavior of Drosophila melanogaster males. Behav Genet 22: 113-124.
55. Stanton ML, Roy BA, Thiede DA (2000) Evolution in stressful environments. I. Phenotypic variability, phenotypic selection, and response to selection in five distinct environmental stresses. Evolution 54: 93-111.
56. DeFries JC, Gervais MC, Thomas EA (1978) Response to 30 generations of selection for open field activity in laboratory mice. Behav Genet 8: 3-13.
57. Nevo E (2001) Evolution of genome-phenome diversity under environmental stress. Proc Natl Acad Sci U S A 98: 6233-6240.
58. Vellend M (2005) Species diversity and genetic diversity: parallel processes and correlated patterns. Am Nat 166: 199-215.
59. Zhuang JY, Lin HX, Lu J, Qian HR, Hittalmani S, et al. (1997) Analysis of QTL x environment interaction for yield components and plant height in rice. Theor Appl Genet 95: 799-808.
60. Stern DL, Orgogozo V (2009) Is genetic evolution predictable? Science 323: 746-751.
61. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317: 338-342.
62. Mariani L, Löhning M, Radbruch A, Höfer T (2004) Transcriptional control networks of cell differentiation: insights from helper T lymphocytes. Prog Biophys Mol Biol 86: 45-76.
63. Félix MA, Wagner A (2008) Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity 100: 132-140.
64. Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218: 1-14.
65. Podlich DW, Cooper M (1998) QU-GENE: a simulation platform for quantitative analysis of genetic models. Bioinformatics 14: 632-653.
66. Weir BS (1996) Genetic data analysis II: Methods for discrete population genetic data. 2nd edition. Sunderland, MA: Sinauer Associates. 445 p.