Floral genetic architecture: an examination of QTL architecture underlying floral (co)variation across environments

An integrated QTL and RNA-seq analysis revealed new petal morphology loci in Brassica napus L

BACKGROUND

Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding.

RESULTS

In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals.

CONCLUSIONS

The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals.

Does the definition of a novel environment affect the ability to detect cryptic genetic variation?

Anthropogenic change exposes populations to environments that have been rare or entirely absent from their evolutionary past. Such novel environments are hypothesized to release cryptic genetic variation, a hidden store of variance that can fuel evolution. However, support for this hypothesis is mixed. One possible reason is a lack of clarity in what is meant by 'novel environment', an umbrella term encompassing conditions with potentially contrasting effects on the exposure or concealment of cryptic variation. Here, we use a meta-analysis approach to investigate changes in the total genetic variance of multivariate traits in ancestral versus novel environments. To determine whether the definition of a novel environment could explain the mixed support for a release of cryptic genetic variation, we compared absolute novel environments, those not represented in a population's evolutionary past, to extreme novel environments, those involving frequency or magnitude changes to environments present in a population's ancestry. Despite sufficient statistical power, we detected no broad-scale pattern of increased genetic variance in novel environments, and finding the type of novel environment did not explain any significant variation in effect sizes. When effect sizes were partitioned by experimental design, we found increased genetic variation in studies based on broad-sense measures of variance, and decreased variation in narrow-sense studies, in support of previous research. Therefore, the source of genetic variance, not the definition of a novel environment, was key to understanding environment-dependant genetic variation, highlighting non-additive genetic variance as an important component of cryptic genetic variation and avenue for future research.

Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed

Petal size determines the value of ornamental plants, and thus their economic value. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes controlling petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 16 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with contrasting differences in petal size identified 52 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, the rapeseed gene BnaA05.RAP2.2, homologous to Arabidopsis RAP2.2, may be critical to the negative control of petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two contrasting accessions were determined mainly by differences in cell number. Finally, we propose a model for the control of petal size in rapeseed through ethylene and cytokinin signaling pathways. Our results provide insights into the genetic mechanisms regulating petal size in flowering plants.

Plastic responses to novel environments are biased towards phenotype dimensions with high additive genetic variation

Environmentally induced phenotypes have been proposed to initiate and bias adaptive evolutionary change toward particular directions. The potential for this to happen depends in part on how well plastic responses are aligned with the additive genetic variance and covariance in traits. Using meta-analysis, we demonstrate that plastic responses to novel environments tend to occur along phenotype dimensions that harbor substantial amounts of additive genetic variation. This suggests that selection for or against environmentally induced phenotypes typically will be effective. One interpretation of the alignment between the direction of plasticity and the main axis of additive genetic variation is that developmental systems tend to respond to environmental novelty as they do to genetic mutation. This makes it challenging to distinguish if the direction of evolution is biased by plasticity or genetic "constraint." Our results therefore highlight a need for new theoretical and empirical approaches to address the role of plasticity in evolution.

Allocation to male vs female floral function varies by currency and responds differentially to density and moisture stress

Allocation of finite resources to separate reproductive functions is predicted to vary across environments and affect fitness. Biomass is the most commonly measured allocation currency; however, in comparison with nutrients it may be less limited and express different environmental and evolutionary responses. Here, we measured carbon, nitrogen, phosphorus, and biomass allocation among floral whorls in recombinant inbred lines of Brassica rapa in multiple environments to characterize the genetic architecture of floral allocation, including its sensitivity to environmental heterogeneity and to choice of currency. Mass, carbon, and nitrogen allocation to female whorls (pistils and sepals) decreased under high density, whereas nitrogen allocation to male organs (stamens) decreased under drought. Phosphorus allocation decreased by half in pistils under drought, while stamen phosphorus was unaffected by environment. While the contents of each currency were positively correlated among whorls, selection to improve fitness through female (or male) function typically favored increased allocation to pistils (or stamens) but decreased allocation to other whorls. Finally, genomic regions underlying correlations among allocation metrics were mapped, and loci related to nitrogen uptake and floral organ development were located within mapped quantitative trait loci. Our candidate gene identification suggests that nutrient uptake may be a limiting step in maintaining male allocation. Taken together, allocation to male vs female function is sensitive to distinct environmental stresses, and the choice of currency affects the interpretation of floral allocation responses to the environment. Further, genetic correlations may counter the evolution of allocation patterns that optimize fitness through female or male function.

Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.

Genotypic variation in biomass allocation in response to field drought has a greater affect on yield than gas exchange or phenology

BACKGROUND

Plant performance in agricultural and natural settings varies with moisture availability, and understanding the range of potential drought responses and the underlying genetic architecture is important for understanding how plants will respond to both natural and artificial selection in various water regimes. Here, we raised genotypes of Brassica rapa under well-watered and drought treatments in the field. Our primary goal was to understand the genetic architecture and yield effects of different drought-escape and dehydration-avoidance strategies.

RESULTS

Drought treatments reduced soil moisture by 62 % of field capacity. Drought decreased biomass accumulation and fruit production by as much as 48 %, whereas instantaneous water-use efficiency and root:shoot ratio increased. Genotypes differed in the mean value of all traits and in the sensitivity of biomass accumulation, root:shoot ratio, and fruit production to drought. Bivariate correlations involving gas-exchange and phenology were largely constant across environments, whereas those involving root:shoot varied across treatments. Although root:shoot was typically unrelated to gas-exchange or yield under well-watered conditions, genotypes with low to moderate increases in root:shoot allocation in response to drought survived the growing season, maintained maximum photosynthesis levels, and produced more fruit than genotypes with the greatest root allocation under drought. QTL for gas-exchange and yield components (total biomass or fruit production) had common effects across environments while those for root:shoot were often environment-specific.

CONCLUSIONS

Increases in root allocation beyond those needed to survive and maintain favorable water relations came at the cost of fruit production. The environment-specific effects of root:shoot ratio on yield and the differential expression of QTL for this trait across water regimes have important implications for efforts to improve crops for drought resistance.

Accessibility, constraint, and repetition in adaptive floral evolution

Adaptive phenotypic evolution is shaped by natural selection on multiple organismal traits as well as by genetic correlations among traits. Genetic correlations can arise through pleiotropy and can bias the production of phenotypic variation to certain combinations of traits. This phenomenon is referred to as developmental bias or constraint. Developmental bias may accelerate or constrain phenotypic evolution, depending on whether selection acts parallel or in opposition to genetic correlations among traits. We discuss examples from floral evolution where genetic correlations among floral traits contribute to rapid, coordinated evolution in multiple floral organ phenotypes and suggest future research directions that will explore the relationship between the genetic basis of adaptation and the pre-existing structure of genetic correlations. On the other hand, natural selection may act perpendicular to a strong genetic correlation, for example when two traits are encoded by a subset of the same genes and natural selection favors change in one trait and stability in the second trait. In such cases, adaptation is constrained by the availability of genetic variation that can influence the focal trait with minimal pleiotropic effects. Examples from plant diversification suggest that the origin of certain adaptations depends on the prior evolution of a gene copy with reduced pleiotropic effects, generated through the process of gene duplication followed by subfunctionalization or neofunctionalization. A history of gene duplication in some developmental pathways appears to have allowed particular flowering plant linages to have repeatedly evolved adaptations that might otherwise have been developmentally constrained.

Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning

Floral attraction traits can significantly affect pollinator visitation patterns, but adaptive evolution of these traits may be constrained by correlations with other traits. In some cases, molecular pathways contributing to floral attraction are well characterized, offering the opportunity to explore loci potentially underlying variation among individuals. Here, we quantify the range of variation in floral UV patterning (i.e. UV 'bulls-eye nectar guides) among crop and wild accessions of Brassica rapa. We then use experimental crosses to examine the genetic architecture, candidate loci and biochemical underpinnings of this patterning as well as phenotypic manipulations to test the ecological impact. We find qualitative variation in UV patterning between wild (commonly lacking UV patterns) and crop (commonly exhibiting UV patterns) accessions. Similar to the majority of crops, recombinant inbred lines (RILs) derived from an oilseed crop × WI fast-plant® cross exhibit UV patterns, the size of which varies extensively among genotypes. In RILs, we further observe strong statistical-genetic and QTL correlations within petal morphological traits and within measurements of petal UV patterning; however, correlations between morphology and UV patterning are weak or nonsignificant, suggesting that UV patterning is regulated and may evolve independently of overall petal size. HPLC analyses reveal a high concentration of sinapoyl glucose in UV-absorbing petal regions, which, in concert with physical locations of UV-trait QTLs, suggest a regulatory and structural gene as candidates underlying observed quantitative variation. Finally, insects prefer flowers with UV bulls-eye patterns over those that lack patterns, validating the importance of UV patterning in pollen-limited populations of B. rapa.

Evolutionary constraints or opportunities?

Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection).

Evolutionary constraints or opportunities?

Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection).

QTL architecture of reproductive fitness characters in Brassica rapa

BACKGROUND

Reproductive output is critical to both agronomists seeking to increase seed yield and to evolutionary biologists interested in understanding natural selection. We examine the genetic architecture of diverse reproductive fitness traits in recombinant inbred lines (RILs) developed from a crop (seed oil) × wild-like (rapid cycling) genotype of Brassica rapa in field and greenhouse environments.

RESULTS

Several fitness traits showed strong correlations and QTL-colocalization across environments (days to bolting, fruit length and seed color). Total fruit number was uncorrelated across environments and most QTL affecting this trait were correspondingly environment-specific. Most fitness components were positively correlated, consistent with life-history theory that genotypic variation in resource acquisition masks tradeoffs. Finally, we detected evidence of transgenerational pleiotropy, that is, maternal days to bolting was negatively correlated with days to offspring germination. A QTL for this transgenerational correlation was mapped to a genomic region harboring one copy of FLOWERING LOCUS C, a genetic locus known to affect both days to flowering as well as germination phenotypes.

CONCLUSIONS

This study characterizes the genetic structure of important fitness/yield traits within and between generations in B. rapa. Several identified QTL are suitable candidates for fine-mapping for the improvement of yield in crop Brassicas. Specifically, brFLC1, warrants further investigation as a potential regulator of phenology between generations.

Quantitative trait loci × environment interactions for plant morphology vary over ontogeny in Brassica rapa

Growth in plants occurs via the addition of repeating modules, suggesting that the genetic architecture of similar subunits may vary between earlier- and later-developing modules. These complex environment × ontogeny interactions are not well elucidated, as studies examining quantitative trait loci (QTLs) expression over ontogeny have not included multiple environments. Here, we characterized the genetic architecture of vegetative traits and onset of reproduction over ontogeny in recombinant inbred lines of Brassica rapa in the field and glasshouse. The magnitude of genetic variation in plasticity of seedling internodes was greater than in those produced later in ontogeny. We correspondingly detected that QTLs for seedling internode length were environment-specific, whereas later in ontogeny the majority of QTLs affected internode lengths in all treatments. The relationship between internode traits and onset of reproduction varied with environment and ontogenetic stage. This relationship was observed only in the glasshouse environment and was largely attributable to one environment-specific QTL. Our results provide the first evidence of a QTL × environment × ontogeny interaction, and provide QTL resolution for differences between early- and later-stage plasticity for stem elongation. These results also suggest potential constraints on morphological evolution in early vs later modules as a result of associations with reproductive timing.

Indirect effects of domestic and wild herbivores on butterflies in an African savanna

Indirect interactions driven by livestock and wild herbivores are increasingly recognized as important aspects of community dynamics in savannas and rangelands. Large ungulate herbivores can both directly and indirectly impact the reproductive structures of plants, which in turn can affect the pollinators of those plants. We examined how wild herbivores and cattle each indirectly affect the abundance of a common pollinator butterfly taxon, Colotis spp., at a set of long-term, large herbivore exclosure plots in a semiarid savanna in central Kenya. We also examined effects of herbivore exclusion on the main food plant of Colotis spp., which was also the most common flowering species in our plots: the shrub Cadaba farinosa. The study was conducted in four types of experimental plots: cattle-only, wildlife-only, cattle and wildlife (all large herbivores), and no large herbivores. Across all plots, Colotis spp. abundances were positively correlated with both Cadaba flower numbers (adult food resources) and total Cadaba canopy area (larval food resources). Structural equation modeling (SEM) revealed that floral resources drove the abundance of Colotis butterflies. Excluding browsing wildlife increased the abundances of both Cadaba flowers and Colotis butterflies. However, flower numbers and Colotis spp. abundances were greater in plots with cattle herbivory than in plots that excluded all large herbivores. Our results suggest that wild browsing herbivores can suppress pollinator species whereas well-managed cattle use may benefit important pollinators and the plants that depend on them. This study documents a novel set of ecological interactions that demonstrate how both conservation and livelihood goals can be met in a working landscape with abundant wildlife and livestock.

A genetic linkage map of Brassica carinata constructed with a doubled haploid population

Brassica carinata is an important oilseed crop with unique favourable traits that are desirable for other Brassica crops. However, given the limited research into genetic resources in B. carinata, knowledge of the genetic structure of this species is relatively poor. Nine homozygous, genetically distinct accessions of B. carinata were obtained via microspore culture, from which two divergent doubled haploid (DH) lines were used to develop a DH mapping population that consisted of 183 lines. The mapping population showed segregation of multiple traits of interest. A genetic map was constructed with PCR-based markers, and a total of 212 loci, which covered 1,703 cM, were assigned to eight linkage groups in the B genome and nine linkage groups in the C genome, which allowed comparison with genetic maps of other important Brassica species that contain the B/C genome(s). Loci for two Mendelian-inherited traits related to pigmentation (petal and anther tip colour) and one quantitative trait (seed coat colour) were identified using the linkage map. The significance of the mapping population in the context of genetic improvement of Brassica crops is discussed.

Natural variation in GA1 associates with floral morphology in Arabidopsis thaliana

• The genetic architecture of floral traits is evolutionarily important due to the fitness consequences of quantitative variation in floral morphology. Yet, little is known about the genes underlying these traits in natural populations. Using Arabidopsis thaliana, we examine molecular variation at GIBBERELLIC ACID REQUIRING 1 (GA1) and test for associations with floral morphology. • We examined full-length sequence in 32 accessions and describe two haplotypes (comprising four nonsynonymous polymorphisms) in GA1 that segregate at intermediate frequencies. In 133 A. thaliana accessions, we test for genotype-phenotype associations and corroborate these findings in segregating progenies. • The two common GA1 haplotypes were associated with the length of petals, stamens, and to a lesser extent style-stigma length. Associations were confirmed in a segregating progeny developed from 19 accessions. We find analogous results in recombinant inbred lines of the Bayreuth × Shahdara cross, which differ only at one of 4 SNPs, suggesting that this SNP may contribute to the observed association. • Assuming GA1 causally affects floral organ size, it is interesting that adjacent petal and stamen whorls are most strongly affected. This pattern suggests that GA1 could contribute to the greater strength of petal-stamen correlations relative to other floral-length correlations observed in some Brassicaceous species.

Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus

Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation-selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency-dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated for Mendelian traits, but there is little comparable data for loci affecting quantitative characters. Here, we report a 3-year field study of selection on intrapopulation quantitative trait loci (QTL) of flower size, a highly polygenic trait in Mimulus guttatus. The QTL exhibit antagonistic pleiotropy: alleles that increase flower size, reduce viability, but increase fecundity. The magnitude and direction of selection fluctuates yearly and on a spatial scale of metres. This study provides direct evidence of balancing selection mechanisms on QTL of an ecologically relevant trait.

Quantitative variation in water-use efficiency across water regimes and its relationship with circadian, vegetative, reproductive, and leaf gas-exchange traits

Drought limits light harvesting, resulting in lower plant growth and reproduction. One trait important for plant drought response is water-use efficiency (WUE). We investigated (1) how the joint genetic architecture of WUE, reproductive characters, and vegetative traits changed across drought and well-watered conditions, (2) whether traits with distinct developmental bases (e.g. leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture, and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa. Overall, WUE increased in drought, primarily because stomatal conductance, and thus water loss, declined more than carbon fixation. Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions, and had the largest vegetative and floral organs in both treatments. Thus, large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments. The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions, but not for floral traits. Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments, indicating that circadian period affects physiological function regardless of water availability. These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE.

Interactions among flower-size QTL of Mimulus guttatus are abundant but highly variable in nature

The frequency and character of interactions among genes influencing complex traits remain unknown. Our ignorance is most acute for segregating variation within natural populations, the epistasis most relevant for quantitative trait evolution. Here, we report a comprehensive survey of interactions among a defined set of flower-size QTL: loci polymorphic within a single natural population of yellow monkeyflower (Mimulus guttatus). We find that epistasis is typical. Observed phenotypes routinely differ from those predicted on the basis of direct allelic affects in the isogenic background, although the direction of deviations is highly variable. Across QTL pairs, there are significantly positive and negative interactions for every trait. Across traits, specific locus pairs routinely exhibit both positive and negative interactions. There was a tendency for negative epistasis to accompany positive direct effects and vice versa for the trait of corolla width, which may be due, at least in part, to the fact that QTL were identified from their direct effects on this trait.

The genetic architecture of ecophysiological and circadian traits in Brassica rapa

Developmental mechanisms that enable perception of and response to the environment may enhance fitness. Ecophysiological traits typically vary depending on local conditions and contribute to resource acquisition and allocation, yet correlations may limit adaptive trait expression. Notably, photosynthesis and stomatal conductance vary diurnally, and the circadian clock, which is an internal estimate of time that anticipates diurnal light/dark cycles, may synchronize physiological behaviors with environmental conditions. Using recombinant inbred lines of Brassica rapa, we examined the quantitative-genetic architecture of ecophysiological and phenological traits and tested their association with the circadian clock. We also investigated how trait expression differed across treatments that simulated seasonal settings encountered by crops and naturalized populations. Many ecophysiological traits were correlated, and some correlations were consistent with expected biophysical constraints; for example, stomata jointly regulate photosynthesis and transpiration by affecting carbon dioxide and water vapor diffusion across leaf surfaces, and these traits were correlated. Interestingly, some genotypes had unusual combinations of ecophysiological traits, such as high photosynthesis in combination with low stomatal conductance or leaf nitrogen, and selection on these genotypes could provide a mechanism for crop improvement. At the genotypic and QTL level, circadian period was correlated with leaf nitrogen, instantaneous measures of photosynthesis, and stomatal conductance as well as with a long-term proxy (carbon isotope discrimination) for gas exchange, suggesting that gas exchange is partly regulated by the clock and thus synchronized with daily light cycles. The association between circadian rhythms and ecophysiological traits is relevant to crop improvement and adaptive evolution.

The quantitative-genetic and QTL architecture of trait integration and modularity in Brassica rapa across simulated seasonal settings

Within organisms, groups of traits with different functions are frequently modular, such that variation among modules is independent and variation within modules is tightly integrated, or correlated. Here, we investigated patterns of trait integration and modularity in Brassica rapa in response to three simulated seasonal temperature/photoperiod conditions. The goals of this research were to use trait correlations to understand patterns of trait integration and modularity within and among floral, vegetative and phenological traits of B. rapa in each of three treatments, to examine the QTL architecture underlying patterns of trait integration and modularity, and to quantify how variation in temperature and photoperiod affects the correlation structure and QTL architecture of traits. All floral organs of B. rapa were strongly correlated, and contrary to expectations, floral and vegetative traits were also correlated. Extensive QTL co-localization suggests that covariation of these traits is likely due to pleiotropy, although physically linked loci that independently affect individual traits cannot be ruled out. Across treatments, the structure of genotypic and QTL correlations was generally conserved. Any observed variation in genetic architecture arose from genotype × environment interactions (GEIs) and attendant QTL × E in response to temperature but not photoperiod.