Selection during crop diversification involves correlated evolution of the circadian clock and ecophysiological traits in Brassica rapa

Early human selection of crops' wild progenitors explains the acquisitive physiology of modern cultivars

Crops have resource-acquisitive leaf traits, which are usually attributed to the process of domestication. However, early choices of wild plants amenable for domestication may also have played a key role in the evolution of crops' physiological traits. Here we compiled data on 1,034 annual herbs to place the ecophysiological traits of 69 crops' wild progenitors in the context of global botanical variation, and we conducted a common-garden experiment to measure the effects of domestication on crop ecophysiology. Our study found that crops' wild progenitors already had high leaf nitrogen, photosynthesis, conductance and transpiration and soft leaves. After domestication, ecophysiological traits varied little and in idiosyncratic ways. Crops did not surpass the trait boundaries of wild species. Overall, the resource-acquisitive strategy of crops is largely due to the inheritance from their wild progenitors rather than to further breeding improvements. Our study concurs with recent literature highlighting constraints of crop breeding for faster ecophysiological traits.

Diurnal oscillations of epigenetic modifications are associated with variation in rhythmic expression of homoeologous genes in Brassica napus

BACKGROUND

Epigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression. Brassica napus is a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks.

RESULTS

In this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment in Brassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome in Brassica rapa, the An subgenome of Brassica napus displayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications.

CONCLUSIONS

Herein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes' rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes in Brassica napus.

Plant domestication: setting biological clocks

Through domestication of wild species, humans have induced large changes in the developmental and circadian clocks of plants. As a result of these changes, modern crops are more productive and adaptive to contrasting environments from the center of origin of their wild ancestors, albeit with low genetic variability and abiotic stress tolerance. Likewise, a complete restructuring of plant metabolic timekeeping probably occurred during crop domestication. Here, we highlight that contrasting timings among organs in wild relatives of crops allowed them to recognize environmental adversities faster. We further propose that connections among biological clocks, which were established during plant domestication, may represent a fundamental source of genetic variation to improve crop resilience and yield.

Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9

Circadian pace is modulated by light intensity, known as the Aschoff’s rule, with largely unrevealed mechanisms. Here we report that photoreceptor CRY2 mediates blue light input to the circadian clock by directly interacting with clock core component PRR9 in blue light dependent manner. This physical interaction dually blocks the accessibility of PRR9 protein to its co-repressor TPL/TPRs and the resulting kinase PPKs. Notably, phosphorylation of PRR9 by PPKs is critical for its DNA binding and repressive activity, hence to ensure proper circadian speed. Given the labile nature of CRY2 in strong blue light, our findings provide a mechanistic explanation for Aschoff’s rule in plants, i.e., blue light triggers CRY2 turnover in proportional to its intensity, which accordingly releasing PRR9 to fine tune circadian speed. Our findings not only reveal a network mediating light input into the circadian clock, but also unmask a mechanism by which the Arabidopsis circadian clock senses light intensity.

Circadian pace is modulated by light intensity. Here the authors show that CRY2 interacts with PRR9 to mediate blue light input to the circadian clock and is degraded at higher light intensity offering a mechanistic explanation as to how intensity can modify clock place.

Circadian regulation of the transcriptome in a complex polyploid crop

The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways

Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.

Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium

Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because-like many studies of organism-environment interaction-it is primarily informed by experiments considering performance at two discrete levels-wet and dry-rather than as a continuously varying environmental gradient. Here, we used experimental and statistical methods based on function-valued traits to explore genetic variation in responses to a continuous soil moisture gradient in physiological and morphological traits among 10 genotypes across two species of the model grass genus Brachypodium. We find that most traits exhibit significant genetic variation and nonlinear responses to soil moisture variability. We also observe differences in the shape of these nonlinear responses between traits and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. Our results point to the importance of considering diversity in nonlinear organism-environment relationships to understand plastic and evolutionary responses to changing climates.

Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F₂ progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.

Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication

Circadian clock rhythms are shown to be intertwined with crop adaptation. To realize the adaptive value of changes in these rhythms under crop domestication and improvement, there is a need to compare the genetics of clock and yield traits. We compared circadian clock rhythmicity based on Chl leaf fluorescence and transcriptomics among wild ancestors, landraces, and breeding lines of barley under optimal and high temperatures. We conducted a genome scan to identify pleiotropic loci regulating the clock and field phenotypes. We also compared the allelic diversity in wild and cultivated barley to test for selective sweeps. We found significant loss of thermal plasticity in circadian rhythms under domestication. However, transcriptome analysis indicated that this loss was only for output genes and that temperature compensation in the core clock machinery was maintained. Drivers of the circadian clock (DOC) loci were identified via genome-wide association study. Notably, these loci also modified growth and reproductive outputs in the field. Diversity analysis indicated selective sweep in these pleiotropic DOC loci. These results indicate a selection against thermal clock plasticity under barley domestication and improvement and highlight the importance of identifying genes underlying for understanding the biochemical basis of crop adaptation to changing environments.

Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three-quarters of the expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.

Next-generation sequencing-based bulked segregant analysis for QTL mapping in the heterozygous species Brassica rapa

An improved protocol of QTL-seq, an NGS-based method for bulked segregant analysis we previously developed in rice, allowed successful mapping of QTLs of interest in the highly heterozygous genome of B. rapa, demonstrating the power of this elegant method for genetic analyses in heterozygous species of economic importance. Recent advances in next-generation sequencing (NGS) and the various NGS-based methods developed for rapidly identifying candidate genes of interest have accelerated genetic analysis mainly in the model plants rice and Arabidopsis. Brassica rapa includes several economically important crops such as Chinese cabbage, turnip and various leafy vegetables. The application of NGS-based approaches for the analysis of B. rapa has been limited mainly due to its highly heterozygous genome and poor quality of the reference genome sequence currently available for this species. In this study, we have improved QTL-seq, a method for NGS-based bulked segregant analysis we previously developed in rice, extending its applicability for accelerating the genetic analysis and molecular breeding of B. rapa. Addition of new filters to the original QTL-seq pipeline allowed removal of spurious single-nucleotide polymorphisms caused by alignment/sequencing errors and variability between parents, significantly improving accuracy of the analysis. As proof of principle, we successfully applied the new approach to identify candidate genomic regions controlling flowering and trichome formation using segregating F2 progeny obtained from crosses made between cultivars of B. rapa showing contrasting phenotypes for these traits. We strongly believe that the improved QTL-seq method reported here will extend the applicability of NGS-based genetic analysis not only to B. rapa but also to other plant species of economic importance with heterozygous genomes.

The fitness benefits of genetic variation in circadian clock regulation

Functional circadian clocks are essential for fitness in diverse ecosystems, facilitating detection of predictable light-dark and temperature cycles. The molecular basis of endogenous clocks is variable across the tree of life, but it has one omnipresent attribute: natural genetic diversity that manifests as variation for instance in circadian period length around the hypothesised optimum of 24 hours. Latitudinal variation in photoperiod alone is unlikely to account for the vast diversity documented in varied organisms, but we have yet to achieve a solid understanding of the interplay between clock variability and natural selection. Recent circadian studies sampling populations have drawn attention to the hierarchical structure of genetic diversity in the wild, unveiling pronounced genetic variation even on a scale of metres.

New connections between circadian rhythms, photosynthesis, and environmental adaptation

This article comments on: Circadian rhythms are associated with variation in photosystem II function and photoprotective mechanisms.

Circadian rhythms are associated with variation in photosystem II function and photoprotective mechanisms

The circadian clock regulates many aspects of leaf gas supply and biochemical demand for CO₂ , and is hypothesized to improve plant performance. Yet the extent to which the clock may regulate the efficiency of photosystem II (PSII) and photoprotective mechanisms such as heat dissipation is less explored. Based on measurements of chlorophyll a fluorescence, we estimated the maximum efficiency of PSII in light (Fv'/Fm') and heat dissipation by nonphotochemical quenching (NPQ). We further dissected total NPQ into its main components, qE (pH-dependent quenching), qT (state-transition quenching), and qI (quenching related to photoinhibition), in clock mutant genotypes of Arabidopsis thaliana, the cognate wild-type genotypes, and a panel of recombinant inbred lines expressing quantitative variation in clock period. Compared with mutants with altered clock function, we observed that wild-type genotypes with clock period lengths of approximately 24 hr had both higher levels of Fv'/Fm', indicative of improved PSII function, and reduced NPQ, suggestive of lower stress on PSII light harvesting complexes. In the recombinant inbred lines, genetic variances were significant for Fv'/Fm' and all 3 components of NPQ, with qE explaining the greatest proportion of NPQ. Bivariate tests of association and structural equation models of hierarchical trait relationships showed that quantitative clock variation was empirically associated with Fv'/Fm' and NPQ, with qE mediating the relationship with gas exchange. The results demonstrate significant segregating variation for all photoprotective components, and suggest the adaptive significance of the clock may partly derive from its regulation of the light reactions of photosynthesis and of photoprotective mechanisms.

Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication

Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.

Circadian Rhythms and Redox State in Plants: Till Stress Do Us Part

A growing body of evidence demonstrates a significant relationship between cellular redox state and circadian rhythms. Each day these two vital components of plant biology influence one another, dictating the pace for metabolism and physiology. Diverse environmental stressors can disrupt this condition and, although plant scientists have made significant progress in re-constructing functional networks of plant stress responses, stress impacts on the clock-redox crosstalk is poorly understood. Inter-connected phenomena such as redox state and metabolism, internal and external environments, cellular homeostasis and rhythms can impede predictive understanding of coordinated regulation of plant stress response. The integration of circadian clock effects into predictive network models is likely to increase final yield and better predict plant responses to stress. To achieve such integrated understanding, it is necessary to consider the internal clock not only as a gatekeeper of environmental responses but also as a target of stress syndromes. Using chlorophyll fluorescence as a reliable and high-throughput probe of stress coupled to functional genomics and metabolomics will provide insights on the crosstalk across a wide range of stress severity and duration, including potential insights into oxidative stress response and signaling. We suggest the efficiency of photosystem II in light conditions (Fv'/Fm') to be the most dynamic of the fluorescence variables and therefore the most reliable parameter to follow the stress response from early sensing to mortality.

Phenotypic Trait Identification Using a Multimodel Bayesian Method: A Case Study Using Photosynthesis in Brassica rapa Genotypes

Agronomists have used statistical crop models to predict yield on a genotype-by-genotype basis. Mechanistic models, based on fundamental physiological processes common across plant taxa, will ultimately enable yield prediction applicable to diverse genotypes and crops. Here, genotypic information is combined with multiple mechanistically based models to characterize photosynthetic trait differentiation among genotypes of Brassica rapa. Infrared leaf gas exchange and chlorophyll fluorescence observations are analyzed using Bayesian methods. Three advantages of Bayesian approaches are employed: a hierarchical model structure, the testing of parameter estimates with posterior predictive checks and a multimodel complexity analysis. In all, eight models of photosynthesis are compared for fit to data and penalized for complexity using deviance information criteria (DIC) at the genotype scale. The multimodel evaluation improves the credibility of trait estimates using posterior distributions. Traits with important implications for yield in crops, including maximum rate of carboxylation (V_cmax ) and maximum rate of electron transport (J_max ) show genotypic differentiation. B. rapa shows phenotypic diversity in causal traits with the potential for genetic enhancement of photosynthesis. This multimodel screening represents a statistically rigorous method for characterizing genotypic differences in traits with clear biophysical consequences to growth and productivity within large crop breeding populations with application across plant processes.

The Importance of the Circadian Clock in Regulating Plant Metabolism

Carbohydrates are the primary energy source for plant development. Plants synthesize sucrose in source organs and transport them to sink organs during plant growth. This metabolism is sensitive to environmental changes in light quantity, quality, and photoperiod. In the daytime, the synthesis of sucrose and starch accumulates, and starch is degraded at nighttime. The circadian clock genes provide plants with information on the daily environmental changes and directly control many developmental processes, which are related to the path of primary metabolites throughout the life cycle. The circadian clock mechanism and processes of metabolism controlled by the circadian rhythm were studied in the model plant Arabidopsis and in the crops potato and rice. However, the translation of molecular mechanisms obtained from studies of model plants to crop plants is still difficult. Crop plants have specific organs such as edible seed and tuber that increase the size or accumulate valuable metabolites by harvestable metabolic components. Human consumers are interested in the regulation and promotion of these agriculturally significant crops. Circadian clock manipulation may suggest various strategies for the increased productivity of food crops through using environmental signal or overcoming environmental stress.

Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought.

Endogenous circadian rhythms in pigment composition induce changes in photochemical efficiency in plant canopies

There is increasing evidence that the circadian clock is a significant driver of photosynthesis that becomes apparent when environmental cues are experimentally held constant. We studied whether the composition of photosynthetic pigments is under circadian regulation, and whether pigment oscillations lead to rhythmic changes in photochemical efficiency. To address these questions, we maintained canopies of bean and cotton, after an entrainment phase, under constant (light or darkness) conditions for 30-48 h. Photosynthesis and quantum yield peaked at subjective noon, and non-photochemical quenching peaked at night. These oscillations were not associated with parallel changes in carbohydrate content or xanthophyll cycle activity. We observed robust oscillations of Chl a/b during constant light in both species, and also under constant darkness in bean, peaking when it would have been night during the entrainment (subjective nights). These oscillations could be attributed to the synthesis and/or degradation of trimeric light-harvesting complex II (reflected by the rhythmic changes in Chl a/b), with the antenna size minimal at night and maximal around subjective noon. Considering together the oscillations of pigments and photochemistry, the observed pattern of changes is counterintuitive if we assume that the plant strategy is to avoid photodamage, but consistent with a strategy where non-stressed plants maximize photosynthesis.

Polyploidy and the relationship between leaf structure and function: implications for correlated evolution of anatomy, morphology, and physiology in Brassica

BACKGROUND

Polyploidy is well studied from a genetic and genomic perspective, but the morphological, anatomical, and physiological consequences of polyploidy remain relatively uncharacterized. Whether these potential changes bear on functional integration or are idiosyncratic remains an open question. Repeated allotetraploid events and multiple genomic combinations as well as overlapping targets of artificial selection make the Brassica triangle an excellent system for exploring variation in the connection between plant structure (anatomy and morphology) and function (physiology). We examine phenotypic integration among structural aspects of leaves including external morphology and internal anatomy with leaf-level physiology among several species of Brassica. We compare diploid and allotetraploid species to ascertain patterns of phenotypic correlations among structural and functional traits and test the hypothesis that allotetraploidy results in trait disintegration allowing for transgressive phenotypes and additional evolutionary and crop improvement potential.

RESULTS

Among six Brassica species, we found significant effects of species and ploidy level for morphological, anatomical and physiological traits. We identified three suites of intercorrelated traits in both diploid parents and allotetraploids: Morphological traits (such as leaf area and perimeter) anatomic traits (including ab- and ad- axial epidermis) and aspects of physiology. In general, there were more correlations between structural and functional traits for allotetraploid hybrids than diploid parents. Parents and hybrids did not have any significant structure-function correlations in common. Of particular note, there were no significant correlations between morphological structure and physiological function in the diploid parents. Increased phenotypic integration in the allotetraploid hybrids may be due, in part, to increased trait ranges or simply different structure-function relationships.

CONCLUSIONS

Genomic and chromosomal instability in early generation allotetraploids may allow Brassica species to explore new trait space and potentially reach higher adaptive peaks than their progenitor species could, despite temporary fitness costs associated with unstable genomes. The trait correlations that disappear after hybridization as well as the novel trait correlations observed in allotetraploid hybrids may represent relatively evolutionarily labile associations and therefore could be ideal targets for artificial selection and crop improvement.