title: Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems.
abstract: BACKGROUND
  Every phenotypic trait can be viewed as a "system" in which a group of interconnected components function synergistically to yield a unified whole. Once a system's components and their interactions have been delineated according to biological principles, we can manipulate and engineer functionally relevant components to produce a desirable system phenotype.
  
  
  RESULTS
  We describe a conceptual framework for mapping quantitative trait loci (QTLs) that control complex traits by treating trait formation as a dynamic system. This framework, called systems mapping, incorporates a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function through genes, and provides a quantitative and testable platform for assessing the interplay between gene action and development. We applied systems mapping to analyze biomass growth data in a mapping population of soybeans and identified specific loci that are responsible for the dynamics of biomass partitioning to leaves, stem, and roots.
  
  
  CONCLUSIONS
  We show that systems mapping implemented by design principles of biological systems is quite versatile for deciphering the genetic machineries for size-shape, structural-functional, sink-source and pleiotropic relationships underlying plant physiology and development. Systems mapping should enable geneticists to shed light on the genetic complexity of any biological system in plants and other organisms and predict its physiological and pathological states.
authors: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China. rwu@hes.hmc.psu.edu
authors: Rongling
authors: R
authors: Wu
authors: Jiguo
authors: J
authors: Cao
authors: Zhongwen
authors: Z
authors: Huang
authors: Zhong
authors: Z
authors: Wang
authors: Junyi
authors: J
authors: Gai
authors: Eduardo
authors: E
authors: Vallejos
references: Nature. 2010 Apr 15;464(7291):1039-42
references: 20393561
references: Nature. 2001 Oct 11;413(6856):628-31
references: 11675785
references: Plant Methods. 2010 Jun 02;6:13
references: 20525184
references: Genetics. 1989 Jan;121(1):185-99
references: 2563713
references: Science. 2008 Nov 7;322(5903):881-8
references: 18988837
references: J Stat Plan Inference. 2009 Mar 1;139(3):978-989
references: 20160841
references: Theor Appl Genet. 2004 Apr;108(6):1131-9
references: 15067400
references: Genetics. 2008 Jun;179(2):1045-55
references: 18505874
references: Nat Rev Genet. 2009 Aug;10(8):565-77
references: 19584810
references: Science. 2002 Mar 1;295(5560):1664-9
references: 11872830
references: Science. 1999 Jun 4;284(5420):1677-9
references: 10356399
references: Nature. 2002 Mar 21;416(6878):326-30
references: 11907579
references: Nat Genet. 2010 Jun;42(6):541-4
references: 20495565
references: PLoS One. 2007 Nov 28;2(11):e1245
references: 18043752
references: Science. 2002 Mar 1;295(5560):1662-4
references: 11872829
references: Science. 1997 Apr 4;276(5309):122-6
references: 9082983
references: Nat Rev Genet. 2006 Mar;7(3):229-37
references: 16485021
references: Science. 2006 Mar 31;311(5769):1936-9
references: 16527928
references: Stat Med. 2002 Aug 15;21(15):2199-214
references: 12210633
references: Science. 2004 Apr 16;304(5669):445-8
references: 15031436
references: Genetics. 1995 Nov;141(3):1189-97
references: 8582623
references: Nat Genet. 2009 Apr;41(4):494-7
references: 19305410
references: PLoS Genet. 2008 Oct;4(10):e1000231
references: 18949033
references: Genetics. 2002 Aug;161(4):1751-62
references: 12196415
references: Science. 2000 Jul 7;289(5476):85-8
references: 10884229
references: Nat Rev Genet. 2003 Feb;4(2):145-51
references: 12560811
references: Biol Rev Camb Philos Soc. 2010 May;85(2):207-16
references: 19930171
references: Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19910-4
references: 19066216
references: Trends Plant Sci. 2006 Dec;11(12):610-7
references: 17092760
references: Genetics. 2002 Feb;160(2):779-92
references: 11861578
references: PLoS One. 2009;4(2):e4318
references: 19183806
references: Biometrics. 2002 Sep;58(3):601-11
references: 12229995
references: J Am Stat Assoc. 2008 Dec 1;103(484):1570-1583
references: 19956350
references: Genetics. 1994 Apr;136(4):1457-68
references: 8013918