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The Statistical Power of Inclusive Composite Interval Mapping in Detecting Digenic Epistasis Showing Common F 2 Segregation Ratios F
Author(s) -
Zhang Luyan,
Li Huihui,
Wang Jiankang
Publication year - 2012
Publication title -
journal of integrative plant biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.734
H-Index - 83
eISSN - 1744-7909
pISSN - 1672-9072
DOI - 10.1111/j.1744-7909.2012.01110.x
Subject(s) - epistasis , inclusive composite interval mapping , quantitative trait locus , population , biology , heritability , genetics , doubled haploidy , statistics , evolutionary biology , mathematics , gene mapping , gene , demography , sociology , chromosome
Epistasis is a commonly observed genetic phenomenon and an important source of variation of complex traits, which could maintain additive variance and therefore assure the long‐term genetic gain in breeding. Inclusive composite interval mapping (ICIM) is able to identify epistatic quantitative trait loci (QTLs) no matter whether the two interacting QTLs have any additive effects. In this article, we conducted a simulation study to evaluate detection power and false discovery rate (FDR) of ICIM epistatic mapping, by considering F 2 and doubled haploid (DH) populations, different F 2 segregation ratios and population sizes. Results indicated that estimations of QTL locations and effects were unbiased, and the detection power of epistatic mapping was largely affected by population size, heritability of epistasis, and the amount and distribution of genetic effects. When the same likelihood of odd (LOD) threshold was used, detection power of QTL was higher in F 2 population than power in DH population; meanwhile FDR in F 2 was also higher than that in DH. The increase of marker density from 10 cM to 5 cM led to similar detection power but higher FDR. In simulated populations, ICIM achieved better mapping results than multiple interval mapping (MIM) in estimation of QTL positions and effect. At the end, we gave epistatic mapping results of ICIM in one actual population in rice ( Oryza sativa L.).