A conceptual framework for mapping quatitative trait loci regulating ontogenetic allometry

PLoS ONE

Volumn 2, Issue 11, 2007, Pages

  Li, Hongying ^a   Huang, Zhongwen ^b,c   Gai, Junyi ^b   Wu, Song ^a   Zeng, Yanru ^d   Li, Qin ^a   Wu, Rongling ^a  

^a University of Florida ^*  (United States)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

^c HENAN INSTITUTE OF SCIENCE AND TECHNOLOGY   (China)

^d ZHEJIANG A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALLOMETRY; ARTICLE; COMPUTER ANALYSIS; CONCEPTUAL FRAMEWORK; GENETIC REGULATION; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MAXIMUM LIKELIHOOD METHOD; ONTOGENY; PHENOTYPE; QUANTITATIVE TRAIT LOCUS MAPPING; SOYBEAN; BIOLOGICAL MODEL; COMPUTER SIMULATION; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

GLYCINE MAX;

ALGORITHMS; COMPUTER SIMULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI;

EID: 44249111215     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001245     Document Type: Article

References (64)

1. Kleiber M (1932) Body size and metabolism. Hilgardia 6: 315-353.
2. Calder WA (1984) Size, Function, and Life History. Cambridge, MA: Harvard University Press.
3. West GB, Brown JH, Enquist BJ (1999) A general model for the structure, and allometry of plant vascular srtems. Nature 400: 664-667.
4. Enquist BJ, Niklas KJ (2001) Invariant scaling relations across tree-dominated communities. Nature 410: 655-660.
5. Enquist BJ, Niklas KJ (2002) Global allocation rules for patterns of biomass partitioning across seed plants. Science 295: 1517-1520.
6. West GB, Brown JH (2005) The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization. J Exp Biol 208: 1575-1592.
7. Niklas KJ (2006) A phyletic perspective on the allometry of plant biomass-partitioning patterns and functionally equivalent organ-categories. New Phytologist 171: 27-40.
8. Frankino WA, Zwaan BJ, Stern DL, Brakefield PM (2005) Natural selection and developmental constraints in the evolution of allometries. Science 307: 718-720.
9. Peter RH (1983) The Ecological Implications of Body Size. Cambridge, MA: Cambridge University Press.
10. Niklas KJ (1994) Plant Allometry: The Scaling of Form and Process. Chicago, IL: University of Chicago Press.
11. Savage VM, Gillooly JF, Woodruff WH, West GB, Allen AP, Enquist BJ, Brown JH (2004) The predominance of quarter-power scaling in biology. Fun Eco 118: 257-282.
12. Riisgard HU (1998) No foundation of a "3/4 power scaling law" for respiration in biology. Ecol Iet 1: 71-73.
13. Dodds PS, Rothman DH, Weitz JS (2001) Re-examination of the 3/4-law of metabolism. J Theor Biol 209: 9-27.
14. White CR, Seymour RS (2003) Mammalian basal metabolic rate is proportional to body mass. Proc Natl Acad Sci USA 100: 4046-4049.
15. West GB, Brown JH, Enquist BJ (1997) A general model for the origin of allometric scaling laws in biology. Science 276: 122-126.
16. West GB, Brown JH, Enquist BJ (1999) The fourth dimension of life: Fractal geometry and allometric scaling of organisms. Science 284: 1677-1679.
17. Banavar JR, Maritan A, Rinaldo A (1999) Size and form in efficient transportation networks. Nature 399: 130-132.
18. Banavar JR, Damuth J, Maritan A, Rinaldo A (2002) Supply-demand balance and metabiblic scaling. Proc Natl Acad Sci USA 99: 10506-16509.
19. Stern DL, Emlen DJ (1999) The developmental basis for allometry in insects. Development 126: 1091-1101.
20. Rombough P (2003) Development rate-Modelling developmemal time and temperature. Nature 424: 268-269.
21. Bookstein FL (1991) Morphometric Tools for Landmark Data: Geometry and Biology. NY: Cambridge University Press.
22. Rohlf FJ (1998) On applications of geometric morphometrics to studies of ontogeny and phylogeny. Syst Biol 47: 147-158.
23. Zelditch ML, Swiderski DL, Lundrigan BL (1998) On applications of geometric morphometrics to studies of ontogeny and phylogeny: a repty to Rohlf. Syst Biol 47: 159-167.
24. Zelditch ML, Fink WL (1995) Allometry and developmental integration of body growth in a piranha, Pygocentrus nattereri (Teleostei: Ostariophysi). J Morphol 223: 341-355.
25. Reis RE, Zelditch ML, Fink WL, (1998) Ontogenetic allometry of body shape in the Neotropical catfish Callichthys (Teleostei: Siluriformes). Copeia 1998: 177-182.
26. Wu RL, Lin M (2006) Functional mapping - How to map and study the genetic architecture of dynamic complex traits. Nat Rev Genet 7: 229-237.
27. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789-794.
28. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
29. Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90: 10972-10976.
30. Zeng ZB. (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
31. Lynch M, Walsh B (1998) Genetics and Analysis of Quantitative Traits. Sunderland, MA: Sinauer.
32. Kao C-H, Zeng Z-B, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
33. Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J Roy Stat Soc B 64: 641-656.
34. Yi NJ, Yandell B, Churchill G, Allison D, Eisen EJ, Pomp D (2005) Bayesian model selection for genome-wide epistatic analysis. Genetics 170: 1333-1344.
35. Yi NJ, Shriner D, Banerjee S, Mehta T, Pomp D, Yandel BS (2007) An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects. Genetics 176: 1865-1877.
36. Wu RL, Lin M, Zhao W, Hou W, Zhang B, Zhuge Q, Huang MR, Xu LA (2006) Statistical models for studying the genetic architecture of dynamic complex traits. J Nanjing Forestry Univ 30: 1-12.
37. Jin CF, Fine JP, Yandell BS (2007) A unified semiparametric framework for quantitative trait loci analyses, with application to spike phenotypes. J Am Stat Assoc 102: 56-67.
38. Jiang C Zeng, Z-B (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.
39. Knott SA, Haley CS (2000) Multitrait least squares for quantitative trait loci detection. Genetics 156: 899-911.
40. Vieira C, Pasyukova EG, Zeng ZB, Hackett JB, Lyman RF, Mackay TFC (2000) Genotype environment interaction for quantitative trait loci affecting life span in Drosophila melanogaster. Genetics 154: 213-227.
41. Korol AB, Ronin YI, Itskovich AM, Peng J, Nevo E (2001) Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits. Genetics 157: 1789-1803.
42. Shaw RG, (1987) Maximum-likelihood approaches applied to quantitative genetics of natural populations. Evolution 45: 143-151.
43. Wu RL, Ma CX, Littell RC, Casella G (2002) A statistical model for the genetic origin of allometric scaling laws in biology. J Theor Biol 217: 275-287.
44. Ma CX, Casella G, Littell RC, Khuri AI, Wu RL (2003) Exponential mapping of quantitative traits governing allometric relationships in organisms. J Math Biol 47: 313-324.
45. Wu RL, Hou W (2006) A hyperspace model to decipher the genetic architecture of developmental processes: Allometry meets ontogeny. Genetics 172: 627-637.
46. Long F, Chen YQ, Cheverud JM, Wu RL (2006) Genetic mapping of allometric scaling laws. Genet Res 87: 207-216.
47. Ma CX, Casella G, Wu RL (2002) Functional mapping of quantitative trait loci undelying the character process: A theoretical framework. Genetics 161: 1751-1762.
48. Jiang C, Zeng Z-B (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.
49. Diggle PJ, Heagerty P, Liang KY, Zeger SL (2002) Analysis of Longitudinal Data. Oxford, UK: Oxford University Press.
50. Núñez-Antón V, Zimmerman DL (2000) Modeling nonstationary longitudinal data. Biometrics 56: 699-705.
51. Zimmerman DL, Núñez-Antón V (2001) Parametric modeling of growth curve data: An overview (with discussion). Test 10: 1-73.
52. Louis TA (1982) Finding the observed information matrix when using the EM algorithm. J Roy Stat Soc B 44: 226-233.
53. Wu RL, Ma CX, Lin M, Casella G (2004) A general framework for analyzing the genetic architecture of developmental characteristics. Genetics 166: 1541-1551.
54. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
55. Niklas KJ, Enquist BJ (2001) Invariant scaling relationships for interspecific plant biomass production rates and body size. Proc Natl Acad Sci USA 98: 2922-2927.
56. Zhang WK, Wang YJ, Luo GZ, Zhang JS, He CY, Wu XL, Gai JY, Chen SY (2004) QTL mapping of ten agronomic traits on the soybean (Glycine). Theor Appl Genet 108: 1131-1139.
57. Wu RL, Ma C-X, Casella G (2007) Statistical Genetics of Quantitative Traits: Linkage, Maps, and QTL. NY: Springer-Verlag.
58. Klingenberg CP, Zimmermann M (1992) Static, ontogenctic, and evolutionary allometry: A multivariate comparison in nine species of water striders. Am Nat 140: 601-620.
59. Breuker C, Debat V, Klingenberg CP (2006) Functional evo-devo. Trends Ecol Syst 21: 488-492.
60. Yap JS, Wang C, Wu R (2007) A computational approach for functional mapping of quantitative trait loci that regulate thermal performance curves. PLoS ONE 2(6), e554, doi:10.1371/journal.pone.0000554.
61. von Bertalanffy L (1957) Quantitative laws for metabolism and growth. Quart Rev Biol 32: 217-231.
62. West GB, Brown JH, Enquist BJ (2001) A general model for ontogenetic growth. Nature 413: 628-631.
63. Hou W, Garvan CW, Zhao W, Behnke M, Eyler FD, Wu RL (2005) A generalized molrel for detecting genetic determinants underlying longitudinal traits with unequally spaced measurements and time-dependent correlatd errors. Biostatistics 6: 420-433.
64. Zhao W, Zhu J, Gallo-Meagher M, Wu RL (2004) A unified statistical model for functional mapping of genotype xenvironment interactions for ontogenetic development. Genetics 168: 1751-1762.