Abstract
The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects. Here, we propose a two-step approach to dissect all genetic effects of QTL and digenic interactions on a whole genome without sacrificing statistical power based on an augmented TTC (aTTC) design. Because the aTTC design has more transformation combinations than do the NCIII and TTC designs, it greatly enriches the QTL mapping for studying heterosis. When the basic population comprises recombinant inbred lines (RIL), we can use the same materials in the NCIII design for aTTC-design QTL mapping with transformation combination Z1, Z2, and Z4 to obtain genetic effect of QTL and digenic interactions. Compared with RIL-based TTC design, RIL-based aTTC design saves time, money, and labor for basic population crossed with F1. Several Monte Carlo simulation studies were carried out to confirm the proposed approach; the present genetic parameters could be identified with high statistical power, precision, and calculation speed, even at small sample size or low heritability. Additionally, two elite rice hybrid datasets for nine agronomic traits were estimated for real data analysis. We dissected the genetic effects and calculated the dominance degree of each QTL and digenic interaction. Real mapping results suggested that the dominance degree in Z2 that mainly characterize heterosis showed overdominance and dominance for QTL and digenic interactions. Dominance and overdominance were the major genetic foundations of heterosis in rice.
Highlights
Heterosis, or hybrid vigor, describes the superior performance of heterozygous hybrid plants over their homozygous parental inbred lines [1,2,3]
Hua et al [23] investigated the genetic components conditioning the heterosis of yield and yield component traits in an elite rice hybrid using an immortalized F2 population with modified composite interval mapping (CIM) and two-way analysis of variance (ANOVA) methods and found that heterotic effects at the single-locus level and a dominance × dominance interaction at the two-locus level could adequately explain the genetic basis of heterosis
Based on the augmented TTC (aTTC) design, this paper developed a quantitative trait locus (QTL) mapping method that fit for many base populations (RIL, F2, and Double Haploid (DH)); by employing multiple data set transformations (Z1i, Z2i, Z3i, Z4i, Z5i, and Z6i), many types of main and epistatic effects can be dissected
Summary
Hybrid vigor, describes the superior performance of heterozygous hybrid plants over their homozygous parental inbred lines [1,2,3]. Hua et al [23] investigated the genetic components conditioning the heterosis of yield and yield component traits in an elite rice hybrid using an immortalized F2 population with modified composite interval mapping (CIM) and two-way ANOVA methods and found that heterotic effects at the single-locus level and a dominance × dominance interaction at the two-locus level could adequately explain the genetic basis of heterosis. In 2008, Garcia et al [25] developed a multiple-interval mapping model for the NCIII design that provided a platform to simultaneously estimate the number, genomic positions, augmented additive and dominance effects, and digenic interactions (aa + dd and ad + da) of QTL This method was used to reanalyze the datasets by Stuber et al [12], who found that additive × additive effect (aa) epistatic effects of QTL could be the main cause for the heterosis in rice. We further applied the proposed method to real data analysis
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