Statistical method for mapping QTLs for complex traits based on two backcross populations

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.

Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies

“…Zhihong et al ( 2012 ) have also highlighted the advantages of this design, also known as the double backcross design and is used for constituting an immortal mapping population, allowing for across-environment replications, estimation of dominance effects, epistatic effects, and QTL-environment interactions, and thus remedies the drawbacks of a single backcross population. Recent studies on QTL mapping in rice, maize, cotton, and B. napus have shown that dominance and epistasis, especially the additive × additive interaction, play a key role in contributing to heterosis (Stuber et al, 1992 ; Yu et al, 1997 ; Tang et al, 2010 ).…”

Modern quantitative genetics: Dissecting complex polygenic systems into individual genetic factors

“…The first article [1] is a review of statistical approaches for QTL mapping and marker-assisted breeding that were developed by the authors and their group. In subsequent articles, several new QTL mapping methods are proposed for specific experimental designs, including (1) the use of two backcross populations [2], (2) the use of a NCIII design based on recombinant inbred lines [3], and (3) the use of chromosome segment substitution lines [4]; or for specific purposes, namely, (1) to detect epistasis between nuclear genes (QTLs) and the cytoplasm [5], and (2) to map sterile genes (QTLs) with epistasis in remote hybridization of plant [6]. In another article [7], an improved approach for QTL mapping in farm animals based on general pedigrees, termed pedigree transmission disequilibrium test, is proposed; this method performs better than existing statistical methods.…”

Table_10.XLSX

“…A similar design was earlier adopted by Radoev et al (2008) and Basunanda et al (2010) for studying heterosis for seedling biomass and yield traits. Zhihong et al (2012) have also highlighted the advantages of this design, also known as the double backcross design and is used for constituting an immortal mapping population, allowing for across-environment replications, estimation of dominance effects, epistatic effects, and QTL-environment interactions, and thus remedies the drawbacks of a single backcross population. Recent studies on QTL mapping in rice, maize, cotton, and B. napus have shown that dominance and epistasis, especially the additive × additive interaction, play a key role in contributing to heterosis (Stuber et al, 1992;Yu et al, 1997;Tang et al, 2010).…”