Quantitative trait loci mapping of phenotypic plasticity and genotype-environment interactions in plant and insect performance

Community genetic studies generally ignore the plasticity of the functional traits through which the effect is passed from individuals to the associated community. However, the ability of organisms to be phenotypically plastic allows them to rapidly adapt to changing environments and plasticity is commonly observed across all taxa. Owing to the fitness benefits of phenotypic plasticity, evolutionary biologists are interested in its genetic basis, which could explain how phenotypic plasticity is involved in the evolution of species interactions. Two current ideas exist: (i) phenotypic plasticity is caused by environmentally sensitive loci associated with a phenotype; (ii) phenotypic plasticity is caused by regulatory genes that simply influence the plasticity of a phenotype. Here, we designed a quantitative trait loci (QTL) mapping experiment to locate QTL on the barley genome associated with barley performance when the environment varies in the presence of aphids, and the composition of the rhizosphere. We simultaneously mapped aphid performance across variable rhizosphere environments. We mapped main effects, QTL × environment interaction (QTL×E), and phenotypic plasticity (measured as the difference in mean trait values) for barley and aphid performance onto the barley genome using an interval mapping procedure. We found that QTL associated with phenotypic plasticity were co-located with main effect QTL and QTL×E. We also located phenotypic plasticity QTL that were located separately from main effect QTL. These results support both of the current ideas of how phenotypic plasticity is genetically based and provide an initial insight into the functional genetic basis of how phenotypically plastic traits may still be important sources of community genetic effects.     

Plant genotype mediates the effects of nutrients on aphids

Soil nutrients, and factors which influence their concentrations and bioavailability, form a basic component of bottom–up control of ecosystem processes, including plant–herbivore interactions. Increased nutrient levels are linked, through plant defence theory, with increased levels of herbivore susceptibility. The focal point of many ecological experiments examining this link is at the species level, where the response of single species is the average of many different genotypes. Here, we focus on the genetic basis of indirect ecological interactions. We investigated the effects of nutrient concentration on the population growth of an aphid herbivore across multiple genotypes of barley in relation to plant growth rate. In general, both aphid population size and plant growth rate increased with nutrient concentration. However, they were both dependent on the interaction between nutrient concentration and barley genotype. Our data raise the testable possibility of differential defense responses between genotypes of barley, for example divergent, fixed and inducible defences against aphids. We provide evidence that the indirect effects of soil nutrients on aphid population size are mediated by the genetics of the host plant.     

Developing tools for investigating the multiple roles of ethylene: identification and mapping genes for ethylene biosynthesis and reception in barley

The plant hormone ethylene is important to many plant processes from germination through senescence, including responses to in vitro growth and plant regeneration. Knowledge of the number and function of genes that are involved in ethylene biosynthesis and reception is necessary to determine the role of specific genes within gene families known to influence ethylene biosynthesis and other aspects of ethylene function in plants. Our objective was built on previous studies that have established the critical role of ethylene in the in vitro response of barley (Hordeum vulgare L.), and that have identified ethylene-related QTL in the barley genome. In this study, we have identified the locations of genes in the barley 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), ACC oxidase (ACO), and ethylene receptor (ETR) gene families. Specific primers for PCR amplification of each gene were developed and used to map these genes in the Oregon Wolf Barley mapping population. Five ACS, 8 ACO, and 7 ETR genes were identified and mapped to six of the barley chromosomes. Gene locations were syntenous to the orthologs in rice except for two that mapped to chromosome 6H. Gene duplication was evident for ACO genes on chromosomes 5H and 6H. Gene-specific primers will be useful for determining expression of each gene under various environmental conditions, including in vitro environments, to better understand the role of ethylene. Of the six known QTL for green plant regeneration in barley, three were located near the genes mapped in this study.     

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)

MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.     

Mapping resistance to cereal aphids in barley

 A set of 150 doubled-haploid (DH) barley (Hordeum vulgare L.) lines derived from the cross of Harrington/TR306 was used to determine the number and chromosomal location of quantitative trait loci (QTLs) controlling resistance to cereal aphids. The experiments were conducted under natural infestation in the field during two growing seasons: 1994 and 1995. Aphid resistance was measured by counting the number of aphids per plot. Counts were made on a weekly basis. Each year at the time of maximum aphid density there was an obvious difference in reaction between the parental genotypes. The DH lines showed continuous variation for aphid density. Simple interval mapping and simplified composite interval mapping revealed that the principal QTL determining cereal aphid resistance is on the distal region of the short arm of chromosome 1. This aphid-resistance QTL is linked with a heading-date QTL. At the time of highest aphid infestation, this QTL accounted for 31% and 22% of the total variance of aphid density in 1994 and 1995, respectively. A QTL on chromosome 5 was also detected but only by simplified composite interval mapping. However, the largest consistent effect was due to the QTL on the short arm of chromosome 1. This QTL may be a useful target for marker-assisted selection for adult plant cereal aphid resistance in barley. Received: 10 September 1996/Accepted: 11 October 1996     

Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA

We used a well-characterized barley mapping population (BCD 47 × Baronesse) to determine if barley stripe rust (BSR) resistance quantitative trait loci (QTL) mapped in Mexico and the USA were effective against a reported new race in Peru. Essentially the same resistance QTL were detected using data from each of the three environments, indicating that these resistance alleles are effective against the spectrum of naturally occurring races at these sites. In addition to the mapping population, we evaluated a germplasm array consisting of lines with different numbers of mapped BSR resistance alleles. A higher BSR disease severity on CI10587, which has a single qualitative resistance gene, in Peru versus Mexico suggests there are differences in pathogen virulence between the two locations. Confirmation of a new race in Peru will require characterization using a standard set of differentials, an experiment that is underway. The highest levels of resistance in Peru were observed when the qualitative resistance gene was pyramided with quantitative resistance alleles. We also used the mapping population to locate QTL conferring resistance to barley leaf rust and barley powdery mildew. For mildew, we identified resistance QTL under field conditions in Peru that are distinct from the Mla resistance that we mapped using specific isolates under controlled conditions. These results demonstrate the long-term utility of a reference mapping population and a well-characterized germplasm array for locating and validating genes conferring quantitative and qualitative resistance to multiple pathogens.     

Identification of quantitative trait loci influencing foliar concentrations of terpenes and formylated phloroglucinol compounds in Eucalyptus nitens

Leaves of eucalypt species contain a variety of plant secondary metabolites, including terpenoids and formylated phloroglucinol compounds (FPCs). Both terpene and FPC concentrations are quantitative traits that can show large variation within a population and have been shown to be heritable. The molecular genetic basis of this variation is currently unknown. Progeny from a field trial of a three-generation mapping pedigree of Eucalyptus nitens were assayed for terpenes and FPCs. Quantitative trait loci (QTL) analyses were conducted using a map constructed from 296 markers to locate regions of the genome influencing foliar concentrations of these plant secondary compounds. A large number of significant QTL for 14 traits were located across nine linkage groups, with significant clustering of QTL on linkage groups 7, 8 and 9. As expected, QTL for biosynthetically related compounds commonly colocated, but QTL for unrelated monterpenes and FPCs also mapped closely together. Colocation of these QTL with mapped candidate genes from the various biosynthetic pathways, and subsequent use of these genes in association mapping, will assist in determining the causes of variation in plant secondary metabolites in eucalypts.     

A Novel and Major Quantitative Trait Locus for Fusarium Crown Rot Resistance in a Genotype of Wild Barley (Hordeum spontaneum L.)

Fusarium crown rot (FCR), caused by various Fusarium species, is a destructive disease of cereal crops in semiarid regions worldwide. As part of our contribution to the development of Fusarium resistant cultivars, we identified several novel sources of resistance by systematically assessing barley genotypes representing different geographical origins and plant types. One of these sources of resistance was investigated in this study by generating and analysing two populations of recombinant inbred lines. A major locus conferring FCR resistance, designated as Qcrs.cpi-4H, was detected in one of the populations (mapping population) and the effects of the QTL was confirmed in the other population. The QTL was mapped to the distal end of chromosome arm 4HL and it is effective against both of the Fusarium isolates tested, one F. pseudograminearum and the other F. graminearum. The QTL explains up to 45.3% of the phenotypic variance. As distinct from an earlier report which demonstrated co-locations of loci conferring FCR resistance and plant height in barley, a correlation between these two traits was not detected in the mapping population. However, as observed in a screen of random genotypes, an association between FCR resistance and plant growth rate was detected and a QTL controlling the latter was detected near the Qcrs.cpi-4H locus in the mapping population. Existing data indicate that, although growth rate may affect FCR resistance, different genes at this locus are likely involved in controlling these two traits.     

Does function follow form? Principal QTLs for Fusarium head blight (FHB) resistance are coincident with QTLs for inflorescence traits and plant height in a doubled-haploid population of barley

Fusarium head blight (FHB), an important disease of barley in many areas of the world, causes losses in grain yield and quality. Deoxynivalenol (DON) mycotoxin residues, produced by the primary pathogen Fusarium graminearum, pose potential health risks. Barley producers may not be able to profitably market FHB-infected barley, even though it has a low DON level. Three types of FHB resistance have been described in wheat: Type I (penetration), Type II (spread), and Type III (mycotoxin degradation). We describe putative measures of these three types of resistance in barley. In wheat, the three resistance mechanisms show quantitative inheritance. Accordingly, to study FHB resistance in barley, we used quantitative trait locus (QTL) mapping to determine the number, genome location, and effects of QTLs associated with Type-I and -II resistance and the concentration of DON in the grain. We also mapped QTLs for plant height, heading date, and morphological attributes of the inflorescence (seeds per inflorescence, inflorescence density, and lateral floret size). QTL analyses were based on a mapping population of F₁-derived doubled-haploid (DH) lines from the cross of the two-rowed genotypes Gobernadora and CMB643, a linkage map constructed with RFLP marker loci, and field evaluations of the three types of FHB resistance performed in China, Mexico, and two environments in North Dakota, USA. Resistance QTLs were detected in six of the seven linkage groups. Alternate favorable alleles were found at the same loci when different inoculation techniques were used to measure Type-I resistance. The largest-effect resistance QTL (for Type-II resistance) was mapped in the centromeric region of chromosome 2. All but two of the resistance QTLs coincided with QTLs determining morphological attributes of the inflorescence and/or plant height. Additional experiments are needed to determine if these coincident QTLs are due to linkage or pleiotropy and to more clearly define the biological basis of the FHB resistance QTLs. Plant architecture should be considered in FHB resistance breeding efforts, particularly those directed at resistance QTL introgression and/or pyramiding. Received: 22 November 1998 / Accepted: 2 June 1999     

Genomic regions determining resistance to leaf stripe (Pyrenophora graminea) in barley.

Leaf stripe is a seed-borne disease of barley (Hordeum vulgare) caused by Pyrenophora graminea. Little is known about the genetics of resistance to this pathogen. In the present work, QTL analysis was applied on two recombinant inbred line (RIL) populations derived from two- and six-rowed barley genotypes with different levels of partial resistance to barley leaf stripe. Quantitative trait loci for partial resistance were identified using the composite interval mapping (CIM) method of PLABQTL software, using the putative QTL markers as cofactors. In the L94 x 'Vada' mapping population, one QTL for resistance was detected on chromosome 2H; the same location as the leaf-stripe resistance gene Rdg1 mapped earlier in 'Alf', where it confers complete resistance to the pathogen. An additional minor-effect QTL was identified by further analyses in this segregating population on chromosome 7H. In L94 x C123, two QTLs for resistance were mapped, one each on chromosomes 7H and 2H.     

Co-localisation of host plant resistance QTLs affecting the performance and feeding behaviour of the aphid Myzus persicae in the peach tree

The architecture and action of quantitative trait loci (QTL) contributing to plant resistance mechanisms against aphids, the largest group of phloem-feeding insects, are not well understood. Comparative mapping of several components of resistance to the green peach aphid (Myzus persicae) was undertaken in Prunus davidiana, a wild species related to peach. An interspecific F(1) population of Prunus persica var. Summergrand × P. davidiana clone P1908 was scored for resistance (aphid colony development and foliar damage) and 17 aphid feeding behaviour traits monitored by means of the electrical penetration graph technique. Seven resistance QTLs were detected, individually explaining 6.1-43.1% of the phenotypic variation. Consistency was shown over several trials. Nine QTLs affecting aphid feeding behaviour were identified. All resistance QTLs except one co-located with QTLs underlying aphid feeding behaviour. A P. davidiana resistance allele at the major QTL was associated with drastic reductions in phloem sap ingestion by aphids, suggesting a phloem-based resistance mechanism. Resistance was also positively correlated with aphid salivation into sieve elements, suggesting an insect response to restore the appropriate conditions for ingestion after phloem occlusion. No significant QTL was found for traits characterising aphid mouthpart activity in plant tissues other than phloem vessels. Two QTLs with effects on aphid feeding behaviour but without effect on resistance were identified. SSR markers linked to the main QTLs involved in resistance are of potential use in marker-assisted selection for aphid resistance. Linking our results with the recent sequencing of the peach genome may help clarify the physiological resistance mechanisms.     

Genetic interactions influence host preference and performance in a plant-insect system

Phytophagous insects generally feed on a restricted range of host plants, using a number of different sensory and behavioural mechanisms to locate and recognize their host plants. Phloem-feeding aphids have been shown to exhibit genetic variation for host preference of different plant species and genetic variation within a plant species can also have an effect on aphid preference and acceptance. It is known that genotypic interactions between barley genotypes and Sitobion avenae aphid genotypes influence aphid fitness, but it is unknown if these different aphid genotypes exhibit active host choice (preference) for the different barley genotypes. Active host choice by aphid genotypes for particular plant genotypes would lead to assortative association (non-random association) between the different aphid and plant genotypes. The performance of each aphid genotype on the plant genotypes also has the ability to enhance these interactions, especially if the aphid genotypes choose the plant genotype that also infers the greatest fitness. In this study, we demonstrate that different aphid genotypes exhibit differential preference and performance for different barley genotypes. Three out of four aphid genotypes exhibited preference for (or against) particular barley genotypes that were not concordant with differences in their reproductive rate on the specific barley genotype. This suggests active host choice of aphids is the primary mechanism for the observed pattern of non-random associations between aphid and barley genotypes. In a community context, such genetic associations between the aphids and barley can lead to population-level changes within the aphid species. These interactions may also have evolutionary effects on the surrounding interacting community, especially in ecosystems of limited species and genetic diversity.     

Aphelinus albipodus(Hymenoptera: Aphelinidae) andDiaeretiella rapae(Hymenoptera: Braconidae) Parasitism onDiuraphis noxia(Homoptera: Aphididae) Infesting Barley Plants Differing in Plant Resistance to Aphids

Russian wheat aphid,Diuraphis noxia(Mordvilko), as a pest of small grains, has prompted research into biological control and host plant resistance. In the presence of Russian wheat aphid, leaves of a susceptible barley (Morex) are curled and chlorotic and sustain large densities of this aphid, while leaves of a resistant barley (STARS-9301B) remain flat and green and sustain fewer aphids. Might parasitism of Russian wheat aphid byAphelinus albipodusHayat & Fatima andDiaeretiella rapaeMcIntosh be affected differently by these plant types? When presented the plants separately and based on parasitism rate relative to aphid density, the largerD. rapaewas more effective in parasitizing relatively high densities of aphids within curled leaves of Morex than relatively low densities of aphids on uncurled leaves of STARS-9301B. Parasitism byA. albipodusdid not significantly differ among the plants. When given a choice of plants, approximately equal rates of parasitism occurred on the two plant lines for both parasitoid species, and parasitism byD. rapaewas greater thanA. albipodus.These data indicate that using parasitoid size as an indicator of success in a physically restricted environment may be misleading, when considered in a plant environment responsive in several manners to aphids (chlorosis, curling, and ability to sustain Russian wheat aphid). We expect that use of resistant barley will result in decreased parasitoid abundance as aphid densities decrease. However, parasitism rates are expected to be approximately equal on resistant and susceptible barley. In this system, plant resistance and biocontrol are compatible management strategies.     

Host‐plant genotypic diversity and community genetic interactions mediate aphid spatial distribution

Genetic variation in plants can influence the community structure of associated species, through both direct and indirect interactions. Herbivorous insects are known to feed on a restricted range of plants, and herbivore preference and performance can vary among host plants within a species due to genetically based traits of the plant (e.g., defensive compounds). In a natural system, we expect to find genetic variation within both plant and herbivore communities and we expect this variation to influence species interactions. Using a three‐species plant‐aphid model system, we investigated the effect of genetic diversity on genetic interactions among the community members. Our system involved a host plant (Hordeum vulgare) that was shared by an aphid (Sitobion avenae) and a hemi‐parasitic plant (Rhinanthus minor). We showed that aphids cluster more tightly in a genetically diverse host‐plant community than in a genetic monoculture, with host‐plant genetic diversity explaining up to 24% of the variation in aphid distribution. This is driven by differing preferences of the aphids to the different plant genotypes and their resulting performance on these plants. Within the two host‐plant diversity levels, aphid spatial distribution was influenced by an interaction among the aphid's own genotype, the genotype of a competing aphid, the origin of the parasitic plant population, and the host‐plant genotype. Thus, the overall outcome involves both direct (i.e., host plant to aphid) and indirect (i.e., parasitic plant to aphid) interactions across all these species. These results show that a complex genetic environment influences the distribution of herbivores among host plants. Thus, in genetically diverse systems, interspecific genetic interactions between the host plant and herbivore can influence the population dynamics of the system and could also structure local communities. We suggest that direct and indirect genotypic interactions among species can influence community structure and processes.     

Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population

In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTL affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.     

Effectiveness of selective genotyping for detection of quantitative trait loci: an analysis of grain and malt quality traits in three barley populations.

Marker genotype data and grain and malt quality phenotype data from three barley (Hordeum vulgare L.) mapping populations were used to investigate the feasibility of selective genotyping for detection of quantitative trait loci (QTLs). With selective genotyping, only individuals with high and low phenotypic values for the trait of interest are genotyped. Here, genotyping of 10 to 70% of each population (i.e., 5 to 35% in each tail of the phenotypic distribution) was considered. Genomic positions detected by selective genotyping were compared to QTL position estimates from interval mapping analysis using marker genotype data from the entire population. Selective genotyping reliably detected almost all of the mapped QTLs, often with only 10% of the population genotyped. Selective genotyping also detected spurious QTLs in regions of the genome where no significant QTL had been mapped. Even with additional genotyping to verify putative QTLs, the total genotyping effort for detection of QTLs for a single trait by selective genotyping was usually less than 30% of that required for conventional interval mapping. Simultaneous investigation of two or more traits by selective genotyping would require additional genotyping effort, but could still be worthwhile.     

Hordoindolines are associated with a major endosperm-texture QTL in barley (Hordeum vulgare).

Endosperm texture has a tremendous impact on the end-use quality of wheat (Triticum aestivum L.). Cultivars of barley (Hordeum vulgare L.), a close relative of wheat, also vary measurably in grain hardness. However, in contrast to wheat, little is known about the genetic control of barley grain hardness. Puroindolines are endosperm-specific proteins found in wheat and its relatives. In wheat, puroindoline sequence variation controls the majority of wheat grain texture variation. Hordoindolines, the puroindoline homologs of barley, have been identified and mapped. Recently, substantial allelic variation was found for hordoindolines among commercial barley cultivars. Our objective was to determine the influence of hordoindoline allelic variation upon grain hardness and dry matter digestibility in the 'Steptoe' x 'Morex' mapping population. This population is segregating for hordoindoline allele type, which was measured by a HinA/HinB/Gsp composite marker. One-hundred and fifty lines of the 'Steptoe' x 'Morex' population were grown in a replicated field trial. Grain hardness was estimated by near-infrared reflectance (NIR) and measured using the single kernel characterization system (SKCS). Variation attributable to the HinA/HinB/Gsp locus averaged 5.7 SKCS hardness units (SKCS U). QTL analysis revealed the presence of several areas of the genome associated with grain hardness. The largest QTL mapped to the HinA/HinB/Gsp region on the short arm of chomosome 7 (5H). This QTL explains 22% of the SKCS hardness difference observed in this study. The results indicate that the Hardness locus is present in barley and implicates the hordoindolines in endosperm texture control.     

Host preference of plant genotypes is altered by intraspecific competition in a phytophagous insect

Variation among aphid genotypes leads them to preferentially colonize different host-plant genotypes. In a natural community, different genotypes within a species are expected to coexist on a single host plant, and these aphids can interact, potentially, altering host-plant preferences. Using a model aphid (Sitobion avenae) and barley (Hordeum vulgare) system, we compared aphid preference and performance in one- or two-genotype colonies in pots with genetically diverse host plants (6 genotypes) or genetically uniform host plants (1 genotype per pot). Aphid host preference was shown to differ when a second aphid genotype was present, with one aphid genotype exhibiting a preference change due to the genotypic identity of the second aphid. The population growth rate of the aphids was not influenced by the competitor, and thus, we conclude that these effects are due to aphid distribution (preference) rather than effects through performance. Our work demonstrates that within a complex ecological community, an individual’s behavior can be influenced by interactions with other genotypes within the same species, as well as interactions with genotypes of other species.     

Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations

Linkage analysis and allelic association (also referred to as linkage disequilibrium) studies are two major approaches for mapping genes that control simple or complex traits in plants, animals, and humans. But these two approaches have limited utility when used alone, because they use only part of the information that is available for a mapping population. More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations. The new strategy makes use of a random sample from a panmictic population and the open-pollinated progeny of the sample. In this article, we extend the new strategy to map quantitative trait loci (QTL), using molecular markers within the EM-implemented maximum-likelihood framework. The most significant advantage of this extension is that both linkage and linkage disequilibrium between a marker and QTL can be estimated simultaneously, thus increasing the efficiency and effectiveness of genome mapping for recalcitrant outcrossing species. Simulation studies are performed to test the statistical properties of the MLEs of genetic and genomic parameters including QTL allele frequency, QTL effects, QTL position, and the linkage disequilibrium of the QTL and a marker. The potential utility of our mapping strategy is discussed.     

Genome-wide association mapping of agronomic traits in sugar beet

Recent results indicate that association mapping in populations from applied plant breeding is a powerful tool to detect QTL which are of direct relevance for breeding. The focus of this study was to unravel the genetic architecture of six agronomic traits in sugar beet. To this end, we employed an association mapping approach, based on a very large population of 924 elite sugar beet lines from applied plant breeding, fingerprinted with 677 single nucleotide polymorphism (SNP) markers covering the entire genome. We show that in this population linkage disequilibrium decays within a short genetic distance and is sufficient for the detection of QTL with a large effect size. To increase the QTL detection power and the mapping resolution a much higher number of SNPs is required. We found that for QTL detection, the mixed model including only the kinship matrix performed best, even in the presence of a considerable population structure. In genome-wide scans, main effect QTL and epistatic QTL were detected for all six traits. Our full two-dimensional epistasis scan revealed that for complex traits there appear to be epistatic master regulators, loci which are involved in a large number of epistatic interactions throughout the genome.