Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations

<div><p>Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis.</p></div

Average LOD profiles across 1000 simulation runs for the unlinked QTL model.

<p>LOD, LOD_A and LOD_AE are LOD scores for detecting QTL with both average and QEI effects, QTL only with average effect, and QTL only with QEI effects, respectively.</p

Estimated effects and positions of QTL detected in the maize RIL population by single-environment analysis.

<p>Positive effect indicates the allele increasing trait value is from parental line CML444. Negative effect indicates the allele increasing trait value is from parental line SC-Malawi. PVE is the percentage of variance explained by individual QTL.</p><p>Estimated effects and positions of QTL detected in the maize RIL population by single-environment analysis.</p

Predefined chromosomal positions and additive effects of five unlinked QTL.

<p>A, AE₁ and AE₂ represent average additive effect, QEI effect in E₁ and QEI effect in E₂ respectively. PVE, the percentage of variance explained by individual QTL, was calculated under the assumption that the frequencies of two QTL genotypes <i>QQ</i> and <i>qq</i> are equal to 0.5.</p><p>Predefined chromosomal positions and additive effects of five unlinked QTL.</p

Predefined chromosomal positions and additive effects of two linked QTL.

<p>PVE, the percentage of variance explained by individual QTL, was calculated under the assumption that the frequency of genotype <i>QQ</i> is equal to 0.5.</p><p>Predefined chromosomal positions and additive effects of two linked QTL.</p

LOD thresholds of QEI mapping based on empirical formula and simulation method.

<p>(A) BC₁ population and <i>α</i>_<i>g</i> = 0.05. (B) BC₁ population and <i>α</i>_<i>g</i> = 0.01. (C) F₂ population and <i>α</i>_<i>g</i> = 0.05. (D) F₂ population and <i>α</i>_<i>g</i> = 0.01.</p

Average LOD profiles on chromosome 1 across 1000 simulation runs for the linked QTL model.

<p>(A) <i>H</i>² = 0.1. (B) <i>H</i>² = 0.5. (C) <i>H</i>² = 0.8. LOD scores on other chromosomes were not shown because no QTL was defined there. LOD score was close to zero on chromosomes 2 to 6.</p

Power (A) and FDR (B) for linked QTL model.

<p>Power (A) of each QTL was calculated as the proportion of runs where the QTL was identified in a 10 cM support interval. FDR (B), false discovery rate, was calculated as the proportion of false positive QTL to total QTL detected for each model and each heritability level.</p

Power analysis by marker interval for the unlinked QTL model.

<p>Power was calculated as the proportion of runs where QTL on the interval was detected. There were 90 marker intervals defined by the 96 markers evenly distributed on six chromosomes.</p

LOD profiles for MFLW in the maize population by QEI mapping (A) and single-environment analysis (B).

<p>The dash line denotes the LOD threshold of 5.67 in QEI mapping.</p