title: Interactions between markers can be caused by the dominance effect of quantitative trait loci.
abstract: F(2) populations are commonly used in genetic studies of animals and plants. For simplicity, most quantitative trait locus or loci (QTL) mapping methods have been developed on the basis of populations having two distinct genotypes at each polymorphic marker or gene locus. In this study, we demonstrate that dominance can cause the interactions between markers and propose an inclusive linear model that includes marker variables and marker interactions so as to completely control both additive and dominance effects of QTL. The proposed linear model is the theoretical basis for inclusive composite-interval QTL mapping (ICIM) for F(2) populations, which consists of two steps: first, the best regression model is selected by stepwise regression, which approximately identifies markers and marker interactions explaining both additive and dominance variations; second, the interval mapping approach is applied to the phenotypic values adjusted by the regression model selected in the first step. Due to the limited mapping population size, the large number of variables, and multicollinearity between variables, coefficients in the inclusive linear model cannot be accurately determined in the first step. Interval mapping is necessary in the second step to fine tune the QTL to their true positions. The efficiency of including marker interactions in mapping additive and dominance QTL was demonstrated by extensive simulations using three QTL distribution models with two population sizes and an actual rice F(2) population.
authors.affiliation: School of Mathematical Sciences, Beijing Normal University, Beijing 100875, China.
authors.forename: Luyan
authors.initials: L
authors.lastname: Zhang
authors.forename: Huihui
authors.initials: H
authors.lastname: Li
authors.forename: Zhonglai
authors.initials: Z
authors.lastname: Li
authors.forename: Jiankang
authors.initials: J
authors.lastname: Wang
mesh_terms: D000483:Alleles; D005819:Genetic Markers / Q000235:genetics*; D005828:Genetics, Population; D005838:Genotype; D016014:Linear Models; D040641:Quantitative Trait Loci
chemical_list: D005819:Genetic Markers
references.citation: Genetics. 1999 Jul;152(3):1203-16
references.pmid: 10388834
references.citation: Genetics. 2006 Jul;173(3):1693-703
references.pmid: 16624924
references.citation: Genetics. 2006 Aug;173(4):2269-82
references.pmid: 16702423
references.citation: Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9226-31
references.pmid: 11038567
references.citation: Genetics. 2004 Jun;167(2):989-99
references.pmid: 15238547
references.citation: Nat Rev Genet. 2002 Jan;3(1):43-52
references.pmid: 11823790
references.citation: Genetics. 1994 Mar;136(3):1195-207
references.pmid: 8005424
references.citation: Genetics. 2001 Jan;157(1):433-44
references.pmid: 11139523
references.citation: Genetics. 2001 Nov;159(3):1351-64
references.pmid: 11729175
references.citation: Genetics. 2001 Sep;159(1):371-87
references.pmid: 11560912
references.citation: Genetics. 2003 Jul;164(3):1129-38
references.pmid: 12871920
references.citation: Theor Appl Genet. 2008 Jan;116(2):243-60
references.pmid: 17985112
references.citation: Genetics. 2007 May;176(1):611-23
references.pmid: 17339210
references.citation: Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2574-9
references.pmid: 12604771
references.citation: Genetics. 2007 Jan;175(1):361-74
references.pmid: 17110476
references.citation: Genetics. 1989 Jan;121(1):185-99
references.pmid: 2563713
references.citation: Trends Genet. 2002 Jun;18(6):301-7
references.pmid: 12044359
references.citation: Theor Appl Genet. 1994 Oct;89(2-3):305-12
references.pmid: 24177846
references.citation: Genetics. 2009 Mar;181(3):1077-86
references.pmid: 19104078
references.citation: Theor Appl Genet. 1992 Dec;85(4):480-8
references.pmid: 24197463
references.citation: Heredity (Edinb). 1992 Oct;69(4):315-24
references.pmid: 16718932
references.citation: Nat Rev Genet. 2001 Jan;2(1):11-20
references.pmid: 11253063
references.citation: Genetics. 1996 Oct;144(2):805-16
references.pmid: 8889541
references.citation: Nat Rev Genet. 2002 Jan;3(1):11-21
references.pmid: 11823787
references.citation: Genetics. 2005 Mar;169(3):1711-25
references.pmid: 15654105
references.citation: Genetics. 1994 Apr;136(4):1457-68
references.pmid: 8013918
references.citation: Genetics. 1991 Jan;127(1):181-97
references.pmid: 1673106
references.citation: Genetics. 1995 Jul;140(3):1111-27
references.pmid: 7672582
references.citation: Genetics. 2000 May;155(1):391-405
references.pmid: 10790412