title: Mapping of epistatic quantitative trait loci in four-way crosses.
abstract: Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL in a 4WC population are built on the single-QTL genetic model. This simple genetic model fails to take into account QTL interactions, which play an important role in the genetic architecture of complex traits. In this paper, therefore, we attempted to develop a statistical method to detect epistatic QTL in 4WC population. Conditional probabilities of QTL genotypes, computed by the multi-point single locus method, were used to sample the genotypes of all putative QTL in the entire genome. The sampled genotypes were used to construct the design matrix for QTL effects. All QTL effects, including main and epistatic effects, were simultaneously estimated by the penalized maximum likelihood method. The proposed method was confirmed by a series of Monte Carlo simulation studies and real data analysis of cotton. The new method will provide novel tools for the genetic dissection of complex traits, construction of QTL networks, and analysis of heterosis.
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
authors.forename: Xiao-Hong
authors.initials: XH
authors.lastname: He
authors.forename: Hongde
authors.initials: H
authors.lastname: Qin
authors.forename: Zhongli
authors.initials: Z
authors.lastname: Hu
authors.forename: Tianzhen
authors.initials: T
authors.lastname: Zhang
authors.forename: Yuan-Ming
authors.initials: YM
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D020090:Chromosome Segregation / Q000235:genetics; D003198:Computer Simulation; D032561:Cotton Fiber; D003433:Crosses, Genetic; D004843:Epistasis, Genetic; D005819:Genetic Markers; D003368:Gossypium / Q000235:genetics*; D009010:Monte Carlo Method; D040641:Quantitative Trait Loci / Q000235:genetics*; D018401:Sample Size
chemical_list: D005819:Genetic Markers
references.citation: Genetics. 2001 Sep;159(1):371-87
references.pmid: 11560912
references.citation: Genetics. 1995 Dec;141(4):1657-9
references.pmid: 8601503
references.citation: Genetics. 2009 Mar;181(3):1101-13
references.pmid: 19139143
references.citation: Heredity (Edinb). 2005 Jul;95(1):96-104
references.pmid: 15931238
references.citation: Genetics. 1996 Oct;144(2):805-16
references.pmid: 8889541
references.citation: Genetics. 2007 Apr;175(4):1955-63
references.pmid: 17277367
references.citation: Genetics. 1994 Apr;136(4):1457-68
references.pmid: 8013918
references.citation: Genetics. 1995 Mar;139(3):1421-8
references.pmid: 7768449
references.citation: Trends Genet. 2007 Feb;23(2):60-6
references.pmid: 17188398
references.citation: Heredity (Edinb). 2006 Feb;96(2):139-49
references.pmid: 16304603
references.citation: Genetics. 1994 Nov;138(3):871-81
references.pmid: 7851782
references.citation: Genetics. 1999 Jul;152(3):1203-16
references.pmid: 10388834
references.citation: Genetica. 1997;101(1):47-58
references.pmid: 9465409
references.citation: J Theor Biol. 2005 Aug 7;235(3):350-64
references.pmid: 15882697
references.citation: Heredity (Edinb). 1998 Aug;81 ( Pt 2):214-24
references.pmid: 9750263
references.citation: Heredity (Edinb). 2008 Jul;101(1):39-47
references.pmid: 18461088
references.citation: Genetics. 1995 Mar;139(3):1455-61
references.pmid: 7768453
references.citation: Behav Genet. 1998 Sep;28(5):341-55
references.pmid: 9926616
references.citation: Genetics. 1994 Apr;136(4):1447-55
references.pmid: 8013917
references.citation: Nat Genet. 2005 Jan;37(1):13-4
references.pmid: 15624016
references.citation: Theor Appl Genet. 1993 Feb;85(8):946-52
references.pmid: 24196144
references.citation: Genetics. 1989 Jan;121(1):185-99
references.pmid: 2563713
references.citation: Proc Natl Acad Sci U S A. 1987 Apr;84(8):2363-7
references.pmid: 3470801
references.citation: Theor Appl Genet. 2006 Jul;113(2):206-24
references.pmid: 16791688
references.citation: Genetics. 1994 Dec;138(4):1293-300
references.pmid: 7896107
references.citation: Theor Appl Genet. 1993 Feb;85(8):953-60
references.pmid: 24196145
references.citation: Anim Genet. 2006 Dec;37(6):543-53
references.pmid: 17121599
references.citation: Genetics. 1998 Mar;148(3):1373-88
references.pmid: 9539450
references.citation: Heredity (Edinb). 2009 Oct;103(4):346-54
references.pmid: 19491924
references.citation: Genetics. 1998 Jun;149(2):1069-80
references.pmid: 9611214
references.citation: Heredity (Edinb). 2003 Jun;90(6):459-67
references.pmid: 12764421
references.citation: Genetics. 2008 Jun;179(2):1045-55
references.pmid: 18505874
references.citation: Biometrics. 2007 Jun;63(2):513-21
references.pmid: 17688503
references.citation: Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9226-31
references.pmid: 11038567
references.citation: Physiol Genomics. 2006 Jun 16;26(1):46-54
references.pmid: 16782841
references.citation: Nat Rev Genet. 2004 Aug;5(8):618-25
references.pmid: 15266344
references.citation: Genet Res. 2000 Jun;75(3):345-55
references.pmid: 10893870
references.citation: Theor Appl Genet. 1992 Dec;85(4):480-8
references.pmid: 24197463
references.citation: Genetics. 2007 Jan;175(1):411-20
references.pmid: 17028346
references.citation: Heredity (Edinb). 1992 Oct;69(4):315-24
references.pmid: 16718932
references.citation: Genetics. 2005 May;170(1):465-80
references.pmid: 15781696
references.citation: Genetics. 1994 Mar;136(3):1195-207
references.pmid: 8005424
references.citation: Genetics. 2007 Nov;177(3):1815-25
references.pmid: 18039883
references.citation: Theor Appl Genet. 2008 Oct;117(6):883-94
references.pmid: 18604518