Abstract
Most important agronomic and quality traits of crops are quantitative in nature. The genetic variations in such traits are usually controlled by sets of genes called quantitative trait loci (QTLs), and the interactions between QTLs and the environment. It is crucial to understand the genetic architecture of complex traits to design efficient strategies for plant breeding. In the present study, a new experimental design and the corresponding statistical method are presented for QTL mapping. The proposed mapping population is composed of double backcross populations derived from backcrossing both homozygous parents to DH (double haploid) or RI (recombinant inbreeding) lines separately. Such an immortal mapping population allows for across-environment replications, and can be used to estimate dominance effects, epistatic effects, and QTL-environment interactions, remedying the drawbacks of a single backcross population. In this method, the mixed linear model approach is used to estimate the positions of QTLs and their various effects including the QTL additive, dominance, and epistatic effects, and QTL-environment interaction effects (QE). Monte Carlo simulations were conducted to investigate the performance of the proposed method and to assess the accuracy and efficiency of its estimations. The results showed that the proposed method could estimate the positions and the genetic effects of QTLs with high efficiency.
Highlights
In crop breeding, most target traits are quantitative traits, known as complex traits
A total of 200 Monte Carlo simulations for double backcross populations with double haploid (DH) × P1 and DH × P2 progenies were conducted under three different environments to investigate the statistical properties of the proposed method in detecting QTL positions, estimating QTL effects, and predicting QTL × environment (QE) interactions
When a traditional temporary BC population derived from crossing F1 with one of its parents is used to map QTLs for complex traits, it is impossible to obtain different phenotypes of each genotype in different environments
Summary
Most target traits are quantitative traits, known as complex traits. The F2 population is temporary, the individuals differ from each other in their genetic constitution, and they cannot be duplicated unless somatic cell cloning is applied It is not possible in a QTL study to conduct multiple environmental experiments with an F2 population to analyze QTL × environment (QE) interactions. Since DH and RI populations are homozygous, their marker data can be used repeatedly with phenotypes of quantitative traits observed in different locations and years under various experimental designs. These populations cannot be used to analyze dominance effects and some types of dominance-related epistatic effects, which play important roles in hybrid heterosis. Monte Carlo simulations were carried out to assess the performance of the method
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