Heterosis for biomass-related traits in Arabidopsis investigated by quantitative trait loci analysis of the triple testcross design with recombinant inbred lines

The dominance model for heterosis explains culm length genetics in a hybrid sorghum variety

Heterosis helps increase the biomass of many crops; however, while models for its mechanisms have been proposed, it is not yet fully understood. Here, we use a QTL analysis of the progeny of a high-biomass sorghum F₁ hybrid to examine heterosis. Five QTLs were identified for culm length and were explained using the dominance model. Five resultant homozygous dominant alleles were used to develop pyramided lines, which produced biomasses like the original F₁ line. Cloning of one of the uncharacterised genes (Dw7a) revealed that it encoded a MYB transcription factor, that was not yet proactively used in modern breeding, suggesting that combining classic dw1or dw3, and new (dw7a) genes is an important breeding strategy. In conclusion, heterosis is explained in this situation by the dominance model and a combination of genes that balance the shortness and early flowering of the parents, to produce F₁ seed yields.

Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design

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.

Genomic architecture of biomass heterosis in Arabidopsis

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include WUSCHEL, ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative Arabidopsis hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in Arabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.

Identification of Heterosis-Associated Stable QTLs for Ear-Weight-Related Traits in an Elite Maize Hybrid Zhengdan 958 by Design III

Heterosis plays a decisive role in maize production worldwide, but its genetic basis remains unclear. In this study, we explored heterosis for ear-weight (EW)-related traits using a North Carolina Experiment III design (Design III) population derived from the elite maize hybrid Zhengdan 958. Quantitative trait loci (QTL) analysis was conducted based on phenotypic data collected from five environments using a high-density linkage map that consisted of 905 single nucleotide polymorphisms (SNP). A total of 38 environmentally stable QTLs were detected, and the numbers for the Z₁ and Z₂ populations were 18 and 20, respectively. All environmentally stable QTLs for Z₂ were characterized by the overdominance effect (OD), which indicated that overdominance was one of the most important contributors to the heterosis of EW-related traits. Consistent with the significant positive correlations between EW-related traits, 9 genomic regions with overlapped QTLs for different traits were found and were located on chromosomes 1 (1), 3 (2), 4 (3), 7 (1), 8 (1), and 9 (1). Compared to previous reports, we found that the genomic regions for heterosis were not always congruent between different hybrids, which suggested that the combination of heterotic loci in different hybrids was genotype-dependent. Collectively, these data provided further evidence that the potential utilization of QTLs for heterosis may be feasible by pyramiding if we treat the QTLs as inherited units.

Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize

Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.

Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F2 Population

Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an "immortalized F2" population composed of 105 hybrids produced by intercrossing recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance (epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F1 hybrid.

Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design

Heterosis refers to the phenomenon in which an F₁ hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F₁ hybrids. To understand the genetic basis of heterosis, here we used a subset of F₁ hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH, and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F₁ hybrids in the population could significantly increase the power to detect dominance-related effects, and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype, and fewer QTL were from MPH than from other dependent variables.

Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis

Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.

Analysis of heterosis and quantitative trait loci for kernel shape related traits using triple testcross population in maize

Kernel shape related traits (KSRTs) have been shown to have important influences on grain yield. The previous studies that emphasize kernel length (KL) and kernel width (KW) lack a comprehensive evaluation of characters affecting kernel shape. In this study, materials of the basic generations (B73, Mo17, and B73 × Mo17), 82 intermated B73 × Mo17 (IBM) individuals, and the corresponding triple testcross (TTC) populations were used to evaluate heterosis, investigate correlations, and characterize the quantitative trait loci (QTL) for six KSRTs: KL, KW, length to width ratio (LWR), perimeter length (PL), kernel area (KA), and circularity (CS). The results showed that the mid-parent heterosis (MPH) for most of the KSRTs was moderate. The performance of KL, KW, PL, and KA exhibited significant positive correlation with heterozygosity but their Pearson’s R values were low. Among KSRTs, the strongest significant correlation was found between PL and KA with R values was up to 0.964. In addition, KW, PL, KA, and CS were shown to be significant positive correlation with 100-kernel weight (HKW). 28 QTLs were detected for KSRTs in which nine were augmented additive, 13 were augmented dominant, and six were dominance × additive epistatic. The contribution of a single QTL to total phenotypic variation ranged from 2.1% to 32.9%. Furthermore, 19 additive × additive digenic epistatic interactions were detected for all KSRTs with the highest total R² for KW (78.8%), and nine dominance × dominance digenic epistatic interactions detected for KL, LWR, and CS with the highest total R² (55.3%). Among significant digenic interactions, most occurred between genomic regions not mapped with main-effect QTLs. These findings display the complexity of the genetic basis for KSRTs and enhance our understanding on heterosis of KSRTs from the quantitative genetic perspective.

Interacted QTL mapping in partial NCII design provides evidences for breeding by design

The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F₁ crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F₁ hybrids, and all these F₁ phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F₁ hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.

Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C↔R, B↔S) separated by similar geographic distances (Italy↔Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F1 and F2, and backcross lines. One of these population pairs (C↔R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C↔R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B↔S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.

QTL mapping for combining ability in different population-based NCII designs: a simulation study

The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and heterosis. A series of Monte Carlo simulation experiments with QTL mapping were then conducted for the base population performance, testcross population phenotypic values and the general combining ability (GCA), specific combining ability (SCA) and Hmp (midparental heterosis) datasets. The results indicated that: (i) increasing the number of testers did not necessarily enhance the QTL detection power for GCA, but it was significantly related to the QTL effect. (ii) The QTLs identified in the base population may be different from those from GCA dataset. Similar phenomena can be seen from QTL detected in SCA and Hmp datasets. (iii) The QTL detection power for GCA ranked in the order of DH(RIL) based > F2 based > BC based NCII design, when the heritability was low. The recombinant inbred lines (RILs) (or DHs) allows more recombination and offers higher mapping resolution than other populations. Further, their testcross progeny can be repeatedly generated and phenotyped. Thus, RIL based (or DH based) NCII design was highly recommend for combining ability QTL analysis. Our results expect to facilitate selecting elite parental lines with high combining ability and for geneticists to research the genetic basis of combining ability.

Dominance and epistasis are the main contributors to heterosis for plant height in rice

The genetic basis of heterosis has been debated for over 100 years regarding whether dominance or overdominance plays a more important role and the answer is still unclear. The major limitation to assess the contribution of a single locus has been the genetic background noise due to genome-wide segregation of multiple loci. To dissect the genetic basis of heterosis at a single locus for plant height, we developed a set of 202 chromosome segment substitution lines (CSSLs) of an elite hybrid, Shanyou 63, the best hybrid rice in China in the 1990s. Fifteen CSSLs had varied plant heights within lines. A total of 15 partial dominance QTLs for plant height were detected in these 15 CSSL-F2 populations. All hybrids between the 15 CSSLs and the recurrent parent, Zhenshan 97, were shorter than the corresponding CSSLs, but taller than Zhenshan 97. These indicated that these 15 QTLs were also heterosis loci (HLs) contributed to heterosis acted in dominance. Each HL contributed from -7.4 to 14.4% of midparent heterosis. Additive by additive (AA) and additive by dominance (AD) interactions were detected in the Tetra-F2 population segregating at the four major QTLs with the largest effects on plant height. Substantial negative AA effects were detected between two major QTLs QPH7.2 and QPH7.3, which increased heterosis in the study. Thus we concluded that dominance and epistasis are the major genetic basis of plant height heterosis, which could explain the better parent heterosis in Shanyou 63.

Hybrid breeding in wheat: technologies to improve hybrid wheat seed production

Global food security demands the development and delivery of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. There are several options for boosting wheat yields, but most offer only small yield increases. Wheat is an inbred plant, and hybrids hold the potential to deliver a major lift in yield and will open a wide range of new breeding opportunities. A series of technological advances are needed as a base for hybrid wheat programmes. These start with major changes in floral development and architecture to separate the sexes and force outcrossing. Male sterility provides the best method to block self-fertilization, and modifying the flower structure will enhance pollen access. The recent explosion in genomic resources and technologies provides new opportunities to overcome these limitations. This review outlines the problems with existing hybrid wheat breeding systems and explores molecular-based technologies that could improve the hybrid production system to reduce hybrid seed production costs, a prerequisite for a commercial hybrid wheat system.

Extensive genomic characterization of a set of near-isogenic lines for heterotic QTL in maize (Zea mays L.)

Background

Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture underlying complex phenotypes, and several QTL related to heterosis were detected. However, such analyses generally lacked the statistical power required for the detailed characterization of individual QTL. Currently, QTL introgression into near-isogenic materials is considered the most effective strategy to this end, despite such materials inevitably contain a variable, unknown and undesired proportion of non-isogenic genome.

An introgression program based on residual heterozygous lines allowed us to develop five pairs of maize (Zea mays L.) near-isogenic lines (NILs) suitable for the fine characterization of three major heterotic QTL previously detected. Here we describe the results of the detailed genomic characterization of these NILs that we undertook to establish their genotypic structure, to verify the presence of the expected genotypes within target QTL regions, and to determine the extent and location of residual non-isogenic genomic regions.

Results

The SNP genotyping approach allowed us to determine the parent-of-origin allele for 14,937 polymorphic SNPs and to describe in detail the genotypic structure of all NILs. The correct introgression was confirmed for all target QTL in the respective NIL and several non-isogenic regions were detected genome-wide. Possible linkage drag effects associated to the specific introgressed regions were observed. The extent and position of other non-isogenic regions varied among NIL pairs, probably deriving from random segregating sections still present at the separation of lineages within pairs.

Conclusions

The results of this work strongly suggest that the actual isogenicity and the genotypic architecture of near-isogenic materials should be monitored both during the introgression procedure and on the final materials as a paramount requisite for a successful mendelization of target QTL. The information here gathered on the genotypic structure of NILs will be integrated in future experimental programs aimed at the fine mapping and isolation of major heterotic QTL, a crucial step towards the understanding of the molecular bases of heterosis in maize.

Progress toward understanding heterosis in crop plants

Although heterosis, or hybrid vigor, is widely exploited in agriculture, a complete description of its molecular underpinnings has remained elusive despite extensive investigation. It appears that there is not a single, simple explanation for heterosis. Instead, it is likely that heterosis arises in crosses between genetically distinct individuals as a result of a diversity of mechanisms. Heterosis generally results from the action of multiple loci, and different loci affect heterosis for different traits and in different hybrids. Hence, multigene models are likely to prove most informative for understanding heterosis. Complementation of allelic variation, as well as complementation of variation in gene content and gene expression patterns, is likely to be an important contributor to heterosis. Epigenetic variation has the potential to interact in hybrid genotypes via novel mechanisms. Several other intriguing hypotheses are also under investigation. In crops, heterosis must be considered within the context of the genomic impacts of prior selection for agronomic traits.

Hybrid breeding in autogamous cereals

Hybrid breeding in autogamous cereals has a long history of attempts with moderate success. There is a vast amount of literature investigating the potential problems and solutions, but until now, market share of hybrids is still a niche compared to line varieties. Our aim was to summarize the status quo of hybrid breeding efforts for the autogamous cereals wheat, rice, barley, and triticale. Furthermore, the research needs for a successful hybrid breeding in autogamous cereals are intensively discussed. To our opinion, the basic requirements for a successful hybrid breeding in autogamous cereals are fulfilled. Nevertheless, optimization of the existing hybridization systems is urgently required and should be coupled with the development of clear male and female pool concepts. We present a quantitative genetic framework as a first step to compare selection gain of hybrid versus line breeding. The lack of precise empirical estimates of relevant quantitative genetic parameters, however, is currently the major bottleneck for a robust evaluation of the potential of hybrid breeding in autogamous cereals.

Genetic composition of yield heterosis in an elite rice hybrid

Heterosis refers to the superior performance of hybrids relative to the parents. Utilization of heterosis has contributed tremendously to the increased productivity in many crops for decades. Although there have been a range of studies on various aspects of heterosis, the key to understanding the biological mechanisms of heterotic performance in crop hybrids is the genetic basis, much of which is still uncharacterized. In this study, we dissected the genetic composition of yield and yield component traits using data of replicated field trials of an "immortalized F(2)" population derived from an elite rice hybrid. On the basis of an ultrahigh-density SNP bin map constructed with population sequencing, we calculated single-locus and epistatic genetic effects in the whole genome and identified components pertaining to heterosis of the hybrid. The results showed that the relative contributions of the genetic components varied with traits. Overdominance/pseudo-overdominance is the most important contributor to heterosis of yield, number of grains per panicle, and grain weight. Dominance × dominance interaction is important for heterosis of tillers per plant and grain weight and has roles in yield and grain number. Single-locus dominance has relatively small contributions in all of the traits. The results suggest that cumulative effects of these components may adequately explain the genetic basis of heterosis in the hybrid.

Hybrid breeding in autogamous cereals

Hybrid breeding in autogamous cereals has a long history of attempts with moderate success. There is a vast amount of literature investigating the potential problems and solutions, but until now, market share of hybrids is still a niche compared to line varieties. Our aim was to summarize the status quo of hybrid breeding efforts for the autogamous cereals wheat, rice, barley, and triticale. Furthermore, the research needs for a successful hybrid breeding in autogamous cereals are intensively discussed. To our opinion, the basic requirements for a successful hybrid breeding in autogamous cereals are fulfilled. Nevertheless, optimization of the existing hybridization systems is urgently required and should be coupled with the development of clear male and female pool concepts. We present a quantitative genetic framework as a first step to compare selection gain of hybrid versus line breeding. The lack of precise empirical estimates of relevant quantitative genetic parameters, however, is currently the major bottleneck for a robust evaluation of the potential of hybrid breeding in autogamous cereals.

An Evaluation of Arabidopsis thaliana Hybrid Traits and Their Genetic Control

Heterosis is an important phenomenon in agriculture. However, heterosis often greatly varies among hybrids and among traits. To investigate heterosis across a large number of traits and numerous genotypes, we evaluated 12 life history traits on parents and hybrids derived from five Arabidopsis thaliana ecotypes (Col, Ler-0, Cvi, Ws, and C24) by using a complete diallel analysis containing 20 hybrids. Parental contributions to heterosis were hybrid and trait specific with a few reciprocal differences. Most notably, C24 generated hybrids with flowering time, biomass, and reproductive traits that often exceeded high-parent values. However, reproductive traits of C24 and Col hybrids and flowering time traits of C24 and Ler hybrids had no heterosis. We investigated whether allelic variation at flowering time genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) could explain the genotype- and trait-specific contribution of C24 to hybrid traits. We evaluated both Col and Ler lines introgressed with various FRI and FLC alleles and hybrids between these lines and C24. Hybrids with functional FLC differed from hybrids with nonfunctional FLC for 21 of the 24 hybrid-trait combinations. In most crosses, heterosis was fully or partially explained by FRI and FLC. Our results describe the genetic diversity for heterosis within a sample of A. thaliana ecotypes and show that FRI and FLC are major factors that contribute to heterosis in a genotype and trait specific fashion.

Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns

We conducted a comparative analysis of the root metabolome of six parental maize inbred lines and their 14 corresponding hybrids showing fresh weight heterosis. We demonstrated that the metabolic profiles not only exhibit distinct features for each hybrid line compared with its parental lines, but also separate reciprocal hybrids. Reconstructed metabolic networks, based on robust correlations between metabolic profiles, display a higher network density in most hybrids as compared with the corresponding inbred lines. With respect to metabolite level inheritance, additive, dominant and overdominant patterns are observed with no specific overrepresentation. Despite the observed complexity of the inheritance pattern, for the majority of metabolites the variance observed in all 14 hybrids is lower compared with inbred lines. Deviations of metabolite levels from the average levels of the hybrids correlate negatively with biomass, which could be applied for developing predictors of hybrid performance based on characteristics of metabolite patterns.

A complete solution for dissecting pure main and epistatic effects of QTL in triple testcross design

Epistasis plays an important role in genetics, evolution and crop breeding. To detect the epistasis, triple test cross (TTC) design had been developed several decades ago. Classical procedures for the TTC design use only linear transformations Z(1), Z(2) and Z(3), calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC design have been developed, these approaches do not provide a complete solution for dissecting pure main and epistatic effects. In this study, therefore, we developed a two-step approach to estimate all pure main and epistatic effects in the F(2)-based TTC design under the F(2) and F(∞) metric models. In the first step, with Z(1) and Z(2) the augmented main and epistatic effects in the full genetic model that simultaneously considered all putative QTL on the whole genome were estimated using empirical Bayes approach, and with Z(3) three pure epistatic effects were obtained using two-dimensional genome scans. In the second step, the three pure epistatic effects obtained in the first step were integrated with the augmented epistatic and main effects for the further estimation of all other pure effects. A series of Monte Carlo simulation experiments has been carried out to confirm the proposed method. The results from simulation experiments show that: 1) the newly defined genetic parameters could be rightly identified with satisfactory statistical power and precision; 2) the F(2)-based TTC design was superior to the F(2) and F(2:3) designs; 3) with Z(1) and Z(2) the statistical powers for the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; and 4) with Z(3) the estimation of pure epistatic effects required large sample size and family replication number. The extension of the proposed method in this study to other base populations was further discussed.

Predicting breed composition using breed frequencies of 50,000 markers from the US Meat Animal Research Center 2,000 Bull Project

Knowledge of breed composition can be useful in multiple aspects of cattle production, and can be critical for analyzing the results of whole genome-wide association studies currently being conducted around the world. We examine the feasibility and accuracy of using genotype data from the most prevalent bovine genome-wide association studies platform, the Illumina BovineSNP50 array (Illumina Inc., San Diego, CA), to estimate breed composition for individual breeds of cattle. First, allele frequencies (of Illumina-defined allele B) of SNP on the array for each of 16 beef cattle breeds were defined by genotyping a large set of more than 2,000 bulls selected in cooperation with the respective breed associations to be representative of their breed. With these breed-specific allele frequencies, the breed compositions of approximately 2,000 two-, three-, and four-way cross (of 8 breeds) cattle produced at the US Meat Animal Research Center were predicted by using a simple multiple regression technique or Mendel (http://www.genetics.ucla.edu/software/mendel) and their genotypes from the Illumina BovineSNP50 array, and were then compared with pedigree-based estimates of breed composition. The accuracy of marker-based breed composition estimates was 89% when using either estimation method for all breeds except Angus and Red Angus (averaged 79%), based on comparing estimates with pedigree-based average breed composition. Accuracy increased to approximately 88% when these 2 breeds were combined into an aggregate Angus group. Additionally, we used a subset of these markers, approximately 3,000 that populate the Illumina Bovine3K (Illumina Inc.), to see whether breed composition could be estimated with similar accuracy when using this reduced panel of SNP makers. When breed composition was estimated using only SNP in common with the Bovine 3K array, accuracy was slightly reduced to 83%. These results suggest that SNP data from these arrays could be used to estimate breed composition in most US beef cattle in situations where pedigree is not known (e.g., multiple-sire natural service matings, non-source-verified animals in feedlots or at slaughter). This approach can aid analyses that depend on knowledge of breed composition, including identification and adjustment of breed-based population stratification, when performing genome-wide association studies on populations with incomplete pedigrees. In addition, SNP-based breed composition estimates may facilitate fitting cow germplasm to the environment, managing cattle in the feedlot, and tracing disease cases back to the geographic region or farm of origin.

Dissecting genetic networks underlying complex phenotypes: the theoretical framework

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many 'downstream' loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and "co-adapted" gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.

Gene actions at loci underlying several quantitative traits in two elite rice hybrids

To understand the gene activities controlling nine important agronomic quantitative traits in rice, we applied a North Carolina design 3 (NC III design) analysis to recombinant inbred lines (RILs) in highly heterotic inter- (IJ) and intra-subspecific (II) hybrids by performing the following tasks: (1) investigating the relative contribution of additive, dominant, and epistatic effects for performance traits by generation means analysis and variance component estimates; (2) detecting the number, genomic positions, and genetic effects of QTL for phenotypic traits; and (3) characterizing their mode of gene action. Under an F∞-metric, generation means analysis and variance components estimates revealed that epistatic effects prevailed for the majority of traits in the two hybrids. QTL analysis identified 48 and 66 main-effect QTL (M-QTL) for nine traits in IJ and II hybrids, respectively. In IJ hybrids, 20 QTL (41.7%) showed an additive effect of gene actions, 20 (41.7%) showed partial-to-complete dominance, and 8 (16.7%) showed overdominance. In II hybrids, 34 QTL (51.5%) exhibited additive effects, 14 (21.2%) partial-to-complete dominance, and 18 (27.3%) overdominance. There were 153 digenic interactions (E-QTL) in the IJ hybrid and 252 in the II hybrid. These results suggest that additive effects, dominance, overdominance, and particularly epistasis attribute to the genetic basis of the expression of traits in the two hybrids. Additionally, we determined that the genetic causes of phenotypic traits and their heterosis are different. In the plants we studied, the phenotypic traits investigated and their heterosis were conditioned by different M-QTL and E-QTL, respectively, and were mainly due to non-allelic interactions (epistasis).

High congruency of QTL positions for heterosis of grain yield in three crosses of maize

The genetic basis of heterosis in maize has been investigated in a number of studies but results have not been conclusive. Here, we compare quantitative trait loci (QTL) mapping results for grain yield, grain moisture, and plant height from three populations derived from crosses of the heterotic pattern Iowa Stiff Stalk Synthetic x Lancaster Sure Crop, investigated with the Design III, and analyzed with advanced statistical methods specifically developed to examine the genetic basis of mid-parent heterosis (MPH). In two populations, QTL analyses were conducted with a joint fit of linear transformations Z (1) (trait mean across pairs of backcross progenies) and Z (2) (half the trait difference between pairs of backcross progenies) to estimate augmented additive and augmented dominance effects of each QTL, as well as their ratio. QTL results for the third population were obtained from the literature. For Z (2) of grain yield, congruency of QTL positions was high across populations, and a large proportion of the genetic variance (~70%) was accounted for by QTL. This was not the case for Z (1) or the other two traits. Further, almost all congruent grain yield QTL were located in the same or an adjacent bin encompassing the centromere. We conclude that different alleles have been fixed in each heterotic pool, which in combination with allele(s) from the opposite heterotic pool lead to high MPH for grain yield. Their positive interactions very likely form the base line for the superior performance of the heterotic pattern under study.

Comparative mapping of quantitative trait loci involved in heterosis for seedling and yield traits in oilseed rape (Brassica napus L.)

Little is known about the genetic control of heterosis in the complex polyploid crop species oilseed rape (Brassica napus L.). In this study, two large doubled-haploid (DH) mapping populations and two corresponding sets of backcrossed test hybrids (THs) were analysed in controlled greenhouse experiments and extensive field trials for seedling biomass and yield performance traits, respectively. Genetic maps from the two populations, aligned with the help of common simple sequence repeat markers, were used to localise and compare quantitative trait loci (QTL) related to the expression of heterosis for seedling developmental traits, plant height at flowering, thousand seed mass, seeds per silique, siliques per unit area and seed yield. QTL were mapped using data from the respective DH populations, their corresponding TH populations and from mid-parent heterosis (MPH) data, allowing additive and dominance effects along with digenic epistatic interactions to be estimated. A number of genome regions containing numerous heterosis-related QTL involved in different traits and at different developmental stages were identified at corresponding map positions in the two populations. The co-localisation of per se QTL from the DH population datasets with heterosis-related QTL from the MPH data could indicate regulatory loci that may also contribute to fixed heterosis in the highly duplicated B. napus genome. Given the key role of epistatic interactions in the expression of heterosis in oilseed rape, these QTL hotspots might harbour genes involved in regulation of heterosis (including fixed heterosis) for different traits throughout the plant life cycle, including a significant overall influence on heterosis for seed yield.

Variation of the parental genome contribution in segregating populations derived from biparental crosses and its relationship with heterosis of their Design III progenies

The variation of the parental genome contribution (PGC) and its relationship with the genetic architecture of heterosis have received little attention. Our objectives were to (1) derive formulas for the variance of PGC in selfing, backcross (BC) or intermated generations produced from biparental crosses of homozygous parents, (2) investigate the correlation [Formula: see text] of the PGC [Formula: see text] estimated by a set M of markers, with Z (2) (half the trait difference between each pair of BC progenies) in the Design III, and (3) interpret experimental results on this correlation with regard to the genetic basis of heterosis. Under all mating systems, the variance of PGC is smaller in species with a larger number and more uniform length of chromosomes. It decreases with intermating and backcrossing but increases under selfing. The ratio of variances of PGC in F(1)DH (double haploids), F(2) and BC(1) populations is 4:2:1, but it is smaller in advanced selfing generations than expected for quantitative traits. Thus, altering the PGC by marker-assisted selection for the genetic background is more promising (i) in species with a smaller number and/or shorter chromosomes and (ii) in F(2) than in progenies of later selfing generations. The correlation [Formula: see text] depends on the linkage relationships between M and the QTL influencing Z(2) as well as the augmented dominance effects [Formula: see text] of the QTL, which include dominance and additive x additive effects with the genetic background, and sum up to mid-parent heterosis. From estimates of [Formula: see text] as well as QTL studies, we conclude that heterosis for grain yield in maize is caused by the action of numerous QTL distributed across the entire genome with positive [Formula: see text] effects.

QTL analysis of early stage heterosis for biomass in Arabidopsis

The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F (1) hybrid exhibited 44% heterosis for biomass. Mid-parent heterosis in the RILs ranged from -31 to 99% for dry weight and from -58 to 143% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.

Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population

The genetic basis of heterosis for grain yield and its components was investigated at the single- and two-locus levels using molecular markers with an immortalized F(2) (IF(2)) population, which was developed by pair crosses among recombinant inbred lines (RILs) derived from the elite maize hybrid Yuyu22. Mid-parent heterosis of each cross in the IF(2) population was used to map heterotic quantitative trait loci. A total of 13 heterotic loci (HL) were detected. These included three HL for grain yield, seven for ear length, one for ear row number and two for 100-kernel weight. A total of 143 digenic interactions contributing to mid-parent heterosis were detected at the two-locus level involving all three types of interactions (additive x additive = AA, additive x dominance = AD or DA, dominance x dominance = DD). There were 25 digenic interactions for grain yield, 36 for ear length, 31 for ear row number and 51 for 100-kernel weight. Altogether, dominance effects of HL at the single-locus level as well as AA interactions played an important role in the genetic basis of heterosis for grain yield and its components in Yuyu22.

The genetics of inbreeding depression

Inbreeding depression - the reduced survival and fertility of offspring of related individuals - occurs in wild animal and plant populations as well as in humans, indicating that genetic variation in fitness traits exists in natural populations. Inbreeding depression is important in the evolution of outcrossing mating systems and, because intercrossing inbred strains improves yield (heterosis), which is important in crop breeding, the genetic basis of these effects has been debated since the early twentieth century. Classical genetic studies and modern molecular evolutionary approaches now suggest that inbreeding depression and heterosis are predominantly caused by the presence of recessive deleterious mutations in populations.

Research on inbreeding in the 'omic' era

Developments in molecular and systems biology have enabled novel approaches to be used in the study of inbreeding. Mechanistic and functional studies using 'omic' technologies can increase the understanding of the consequences of inbreeding, from the level of DNA to that of population growth. This gives added power to unravelling the causes of inbreeding depression, results that we suggest will be useful in animal and plant breeding and in evolutionary and conservation biology. First results from 'omic' investigations of inbreeding indicate that inbreeding affects cellular processes that are also observed with aging and exposure to environmental stress. Here, we discuss recent achievements from applications of 'omic' techniques in research on inbreeding and propose new avenues that can be addressed by their use.

Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations

Two mapping populations of a cross between the Arabidopsis thaliana accessions Col-0 and C24 were cultivated and analyzed with respect to the levels of 181 metabolites to elucidate the biological phenomenon of heterosis at the metabolic level. The relative mid-parent heterosis in the F(1) hybrids was <20% for most metabolic traits. The first mapping population consisting of 369 recombinant inbred lines (RILs) and their test cross progeny with both parents allowed us to determine the position and effect of 147 quantitative trait loci (QTL) for metabolite absolute mid-parent heterosis (aMPH). Furthermore, we identified 153 and 83 QTL for augmented additive (Z(1)) and dominance effects (Z(2)), respectively. We identified putative candidate genes for these QTL using the aracyc database (http://www.arabidopsis.org/biocyc), and calculated the average degree of dominance, which was within the dominance and over-dominance range for most metabolites. Analyzing a second population of 41 introgression lines (ILs) and their test crosses with the recurrent parent, we identified 634 significant differences in metabolite levels. Nine per cent of these effects were classified as over-dominant, according to the mode of inheritance. A comparison of both approaches suggested epistasis as a major contributor to metabolite heterosis in Arabidopsis. A linear combination of metabolite levels was shown to significantly correlate with biomass heterosis (r = 0.62).

Additive and over-dominant effects resulting from epistatic loci are the primary genetic basis of heterosis in rice

A set of 148 F9 recombinant inbred lines (RILs) was developed from the cross of an indica cultivar 93-11 and japonica cultivar DT713, showing strong F1 heterosis. Subsequently, two backcross F1 (BCF1) populations were constructed by backcrossing these 148 RILs to two parents, 93-11 and DT713. These three related populations (281BCF1 lines, 148 RILs) were phenotyped for six yield-related traits in two locations. Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations. A total of 42 main-effect quantitative trait loci (M-QTLs) and 109 epistatic effect QTL pairs (E-QTLs) were detected in the three related populations using the mixed model approach. By comparing the genetic effects of these QTLs detected in the RILs, BCF1 performance and mid-parental heterosis (HMP), we found that, in both BCF1 populations, the QTLs detected could be classified into two predominant types: additive and over-dominant loci, which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs. Further, we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations. All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.

Mapping an overdominant quantitative trait locus for heterosis of body weight in mice

The genetic basis of heterosis has not been elucidated. Previously, a congenic mouse strain with a 44-Mb genomic region of proximal chromosome 2 containing the allele derived from wild Mus musculus castaneus at Pbwg1, a quantitative trait locus (QTL) for body weight and growth, has been developed. In this study, to fine-map and characterize body weight QTLs on the congenic region, QTL analysis of body weight at 1, 3, 6, and 10 weeks after birth was performed on a population of 265 F(2) intercross mice between the developed congenic strain and its background strain C57BL/6J. A significant QTL (named Pbwg1.10) affecting body weight at 6 and 10 weeks of age was identified within an approximately 21-Mb support interval. Surprisingly, Pbwg1.10 had an overdominance effect and caused heterosis for body weight. This result supported the overdominance hypothesis explaining heterosis.

Unraveling epistasis with triple testcross progenies of near-isogenic lines

Libraries of near-isogenic lines (NILs) are a powerful plant genetic resource to map quantitative trait loci (QTL). Nevertheless, QTL mapping with NILs is mostly restricted to genetic main effects. Here we propose a two-step procedure to map additive-by-additive digenic epistasis with NILs. In the first step, a generation means analysis of parents, their F(1) hybrid, and one-segment NILs and their triple testcross (TTC) progenies is used to identify in a one-dimensional scan loci exhibiting QTL-by-background interactions. In a second step, one-segment NILs with significant additive-by-additive background interactions are used to produce particular two-segment NILs to test for digenic epistatic interactions between these segments. We evaluated our approach by analyzing a random subset of a genomewide Arabidopsis thaliana NIL library for growth-related traits. The results of our experimental study illustrated the potential of the presented two-step procedure to map additive-by-additive digenic epistasis with NILs. Furthermore, our findings suggested that additive main effects as well as additive-by-additive digenic epistasis strongly influence the genetic architecture underlying growth-related traits of A. thaliana.

Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids

Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter- (IJ) and intrasubspecific (II) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F1 and its two parents of each hybrid were evaluated for nine important traits, including grain yield and eight other yield-related traits. A total of 76 quantitative trait loci (QTL) for the IJ hybrid and 41 QTL for the II hybrid were detected in the RI population, midparent heterosis of two backcross populations, and two independent sets of data by summation (L1 + L2) and by subtraction (L1 - L2) of two backcross populations (L1 and L2). The variance explained by each QTL ranged from 2.6 to 58.3%. In the IJ hybrid, 42% (32) of the QTL showed an additive effect, 32% (24) a partial-to-complete dominant effect, and 26% (20) an overdominant effect. In the II hybrid, 32% (13) of the QTL demonstrated an additive effect, 29% (12) a partial-to-complete dominant effect, and 39% (16) an overdominant effect. There were 195 digenic interactions detected in the IJ hybrid and 328 in the II hybrid. The variance explained by each digenic interaction ranged from 2.0 to 14.9%. These results suggest that the heterosis in these two hybrids is attributable to the orchestrated outcome of partial-to-complete dominance, overdominance, and epistasis.

Genetic expectations of quantitative trait loci main and interaction effects obtained with the triple testcross design and their relevance for the analysis of heterosis

Interpretation of experimental results from quantitative trait loci (QTL) mapping studies on the predominant type of gene action can be severely affected by the choice of statistical model, experimental design, and provision of epistasis. In this study, we derive quantitative genetic expectations of (i) QTL effects obtained from one-dimensional genome scans with the triple testcross (TTC) design and (ii) pairwise interactions between marker loci using two-way analyses of variance (ANOVA) under the F(2)- and the F(infinity)-metric model. The theoretical results show that genetic expectations of QTL effects estimated with the TTC design are complex, comprising both main and epistatic effects, and that genetic expectations of two-way marker interactions are not straightforward extensions of effects estimated in one-dimensional scans. We also demonstrate that the TTC design can partially overcome the limitations of the design III in separating QTL main effects and their epistatic interactions in the analysis of heterosis and that dominance x additive epistatic interactions of individual QTL with the genetic background can be estimated with a one-dimensional genome scan. Furthermore, we present genetic expectations of variance components for the analysis of TTC progeny tested in a split-plot design, assuming digenic epistasis and arbitrary linkage.

Genetic analysis of heterosis for yield and yield components in rapeseed (Brassica napus L.) by quantitative trait locus mapping

The main objective in this research was the genetic analysis of heterosis in rapeseed at the QTL level. A linkage map comprising 235 SSR and 144 AFLP markers covering 2045 cM was constructed in a doubled-haploid population from a cross between the cultivar "Express" and the resynthesized line "R53." In field experiments at four locations in Germany 250 doubled-haploid (DH) lines and their corresponding testcrosses with Express were evaluated for grain yield and three yield components. The heterosis ranged from 30% for grain yield to 0.7% for kernel weight. QTL were mapped using three different data sets, allowing the estimation of additive and dominance effects as well as digenic epistatic interactions. In total, 33 QTL were detected, of which 10 showed significant dominance effects. For grain yield, mainly complete dominance or overdominance was observed, whereas the other traits showed mainly partial dominance. A large number of epistatic interactions were detected. It was concluded that epistasis together with all levels of dominance from partial to overdominance is responsible for the expression of heterosis in rapeseed.

From genotype to phenotype: systems biology meets natural variation

The promise that came with genome sequencing was that we would soon know what genes do, particularly genes involved in human diseases and those of importance to agriculture. We now have the full genomic sequence of human, chimpanzee, mouse, chicken, dog, worm, fly, rice, and cress, as well as those for a wide variety of other species, and yet we still have a lot of trouble figuring out what genes do. Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered.

Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations

Plant growth and development are tightly linked to primary metabolism and are subject to natural variation. In order to obtain an insight into the genetic factors controlling biomass and primary metabolism and to determine their relationships, two Arabidopsis thaliana populations [429 recombinant inbred lines (RIL) and 97 introgression lines (IL), derived from accessions Col-0 and C24] were analyzed with respect to biomass and metabolic composition using a mass spectrometry-based metabolic profiling approach. Six and 157 quantitative trait loci (QTL) were identified for biomass and metabolic content, respectively. Two biomass QTL coincide with significantly more metabolic QTL (mQTL) than statistically expected, supporting the notion that the metabolic profile and biomass accumulation of a plant are linked. On the same basis, three out the six biomass QTL can be simulated purely on the basis of metabolic composition. QTL based on analysis of the introgression lines were in substantial agreement with the RIL-based results: five of six biomass QTL and 55% of the mQTL found in the RIL population were also found in the IL population at a significance level of P < or = 0.05, with >80% agreement on the allele effects. Some of the differences could be attributed to epistatic interactions. Depending on the search conditions, metabolic pathway-derived candidate genes were found for 24-67% of all tested mQTL in the database AraCyc 3.5. This dataset thus provides a comprehensive basis for the detection of functionally relevant variation in known genes with metabolic function and for identification of genes with hitherto unknown roles in the control of metabolism.

The role of epistasis in the manifestation of heterosis: a systems-oriented approach

Heterosis is widely used in breeding, but the genetic basis of this biological phenomenon has not been elucidated. We postulate that additive and dominance genetic effects as well as two-locus interactions estimated in classical QTL analyses are not sufficient for quantifying the contributions of QTL to heterosis. A general theoretical framework for determining the contributions of different types of genetic effects to heterosis was developed. Additive x additive epistatic interactions of individual loci with the entire genetic background were identified as a major component of midparent heterosis. On the basis of these findings we defined a new type of heterotic effect denoted as augmented dominance effect di* that comprises the dominance effect at each QTL minus half the sum of additive x additive interactions with all other QTL. We demonstrate that genotypic expectations of QTL effects obtained from analyses with the design III using testcrosses of recombinant inbred lines and composite-interval mapping precisely equal genotypic expectations of midparent heterosis, thus identifying genomic regions relevant for expression of heterosis. The theory for QTL mapping of multiple traits is extended to the simultaneous mapping of newly defined genetic effects to improve the power of QTL detection and distinguish between dominance and overdominance.

Genetic basis of heterosis for growth-related traits in Arabidopsis investigated by testcross progenies of near-isogenic lines reveals a significant role of epistasis

Epistasis seems to play a significant role in the manifestation of heterosis. However, the power of detecting epistatic interactions among quantitative trait loci (QTL) in segregating populations is low. We studied heterosis in Arabidopsis thaliana hybrid C24 x Col-0 by testing near-isogenic lines (NILs) and their triple testcross (TTC) progenies. Our objectives were to (i) provide the theoretical basis for estimating different types of genetic effects with this experimental design, (ii) determine the extent of heterosis for seven growth-related traits, (iii) map the underlying QTL, and (iv) determine their gene action. Two substitution libraries, each consisting of 28 NILs and covering approximately 61 and 39% of the Arabidopsis genome, were assayed by 110 single-nucleotide polymorphism (SNP) markers. With our novel generation means approach 38 QTL were detected, many of which confirmed heterotic QTL detected previously in the same cross with TTC progenies of recombinant inbred lines. Furthermore, many of the QTL were common for different traits and in common with the 58 QTL detected by a method that compares triplets consisting of a NIL, its recurrent parent, and their F(1) cross. While the latter approach revealed mostly (75%) overdominant QTL, the former approach allowed separation of dominance and epistasis by analyzing all materials simultaneously and yielded substantial positive additive x additive effects besides directional dominance. Positive epistatic effects reduced heterosis for growth-related traits in our materials.