Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations

Li, Huihui; Ribaut, Jean-Marcel; Li, Zhonglai; Wang, Jiankang

doi:10.1007/s00122-007-0663-5

Cited by 307 publications

(207 citation statements)

References 37 publications

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“…This avoidance would result in a larger residual variance, further a lower power of QTL detection and poorer precision (little larger in standard deviation) in estimated QTL effects and positions [41]. The two dimensional scanning methods, which consider both main and epistatic effects of pair QTL simultaneously with genetic background controlling, such as the mixed model approach of Wang et al [23] and inclusive composite interval mapping (ICIM) of Li et al [42], are alternative methods. However, the genetic design matrix should be reconstructed (Table 1) and the genetic parameter should be correctly explained [14][15][16]24,30,41].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

Zhang

2012

Chin. Sci. Bull.

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Heterosis represents one of the most revolutionary advancements in crop improvement. In the genetic dissection of heterosis, NCIII design is one of the most powerful and widely used mating schemes. However, the methodologies for quantitative trait loci (QTL) detection in the design were mostly based on composite interval mapping. Therefore, in this study, our purpose was to develop a statistical method for mapping epistatic QTL associated with heterosis in the RIL-based NCIII design. First, we derivated the expectations of two classical linear transformations, Z 1 and Z 2 , while a quantitative trait was controlled by two QTL with digenic epistasis and arbitrary linkage under the F ∞ and F 2 metric models. Then, we constructed an epistatic genetic model that includes all markers on the whole genome simultaneously, and estimated all the parameters in the model by the empirical Bayes approach. Finally, a series of Monte Carlo simulation experiments was carried out to confirm the proposed approach. The results show that: (1) all the augmented genetic parameters for main-effect QTL could be rightly identified with satisfactory statistical power and precision; (2) the statistical powers in the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; (3) it is more difficult to detect epistatic QTL than to detect main-effect QTL; (4) statistical power is higher in the RIL-based NCIII design than in the F 2 -based NCIII design, especially in the detection of the augmented epistatic effect that consists of two pure epistatic effects in opposite directions.empirical Bayes, epistasis, NCIII design, heterosis, quantitative trait locus, recombinant inbred line Citation:He X H, Hu Z L, Zhang Y M. Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design.

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Section: Discussionmentioning

confidence: 99%

Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

Zhang

2012

Chin. Sci. Bull.

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“…QTLs exhibiting significant effects (LOD [ 3) in more than one experiment (in map positions close to the same or directly neighbouring markers) were selected for interpretation. The ICIM method (Li et al 2008) was used to find first-order QTL-QTL interaction effects. As the method is restricted to the analysis of homozygous lines, heterozygotes were treated as missing genotypes for codominant markers and as dominant homozygotes otherwise.…”

Section: Genotyping and Linkage Analysismentioning

confidence: 99%

“…Full advantage was taken of the availability of the two populations. Besides additive QTL effects, found by the application of Windows QTL Cartographer 2.0 (2007) software, both types of epistasis were analysed: the QTL by genetic background interaction by a comparison of additive QTL effects found, and the first-order QTL-QTL interaction by the recently developed inclusive composite interval mapping (ICIM) method (Li et al 2008). …”

Section: Introductionmentioning

confidence: 99%

QTL for yield components and protein content: a multienvironment study of two pea (Pisum sativum L.) populations

et al. 2011

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Quantitative trait loci for yield, yield components and seed protein content were investigated on the basis of experiments performed with two populations of pea (Pisum sativum L.) lines derived from linked crosses between lines Wt11238, Wt3557 and Wt10245 with contrasting characteristics. The yield-related traits were defined as components giving the grain yield in a multiplicative way. The aim was to clarify the genetic architecture of the relation between seed yield, its components and protein content, with a possible inclusion of the role of epistasis in this explanation. To take full advantage of the availability of the two populations, additive QTL effects and both types of epistasis were analysed: the QTL by genetic background interaction and the first-order QTL-QTL interaction. The two hybrid populations differed with respect to the prevailing gene action, which in the Wt11238 9 Wt3557 progeny was mainly additive, while in the Wt10245 9 Wt11238 progeny mainly epistatic. Some loci with previously reported, large, repeatable, but contradictory effects on yield and protein content were confirmed. New loci with alleles coming from the protein-rich Wt11238 line, positive for yield components, were identified. It was found that the first order QTL-QTL interaction events were more frequent for the loci showing the QTL by genetic background interaction.

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“…In the present study, three mapping methods which can analyze epistatic effect were employed to detect QTLs for GL, LWR, CGR, CD, GT, AC and GC in head rice. The three methods were composite interval mapping in QTLMapper 2.0 software (Wang et al, 1999) based on mixed linear model (MCIM), inclusive composite interval mapping in QTL IciMapping 3.0 software (Li et al, 2008) based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR). The QTL mapping results obtained by the three genetic statistical models were compared and the highly reliable QTLs were determined.…”

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confidence: 99%

QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models

et al. 2013

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QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length (GL), grain length to width ratio (LWR), chalk grain rate (CGR), chalkiness degree (CD), gelatinization temperature (GT), amylose content (AC) and gel consistency (GC) of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM), inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR). Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously, two by two methods simultaneously, and 23 by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 28 by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142 pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 23.78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.

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Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations

Cited by 307 publications

References 37 publications

Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

QTL for yield components and protein content: a multienvironment study of two pea (Pisum sativum L.) populations

QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models

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