Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

An allometry perspective on crops

Understanding trait-trait coordination is essential for successful plant breeding and crop modeling. Notably, plant size drives variation in morphological, physiological, and performance-related traits, as described by allometric laws in ecology. Yet, as allometric relationships have been limitedly studied in crops, how they influence and possibly limit crop performance remains unknown. Here, we review how an allometry perspective on crops gains insights into the phenotypic evolution during crop domestication, the breeding of varieties adapted to novel conditions, and the prediction of crop yields. As allometry is an active field of research, modeling and manipulating crop allometric relationships can help to develop more resilient and productive agricultural systems to face future challenges.

Synergy of gut microbiota and host genome in driving heterosis expression of chickens

Heterosis has been widely utilized in agricultural production. Despite over a century of extensive research, the underlying mechanisms of heterosis remain elusive. Most hypotheses and research have focused on the genetic basis of heterosis. However, the potential role of gut microbiota in heterosis has been largely ignored. Here, we carefully design a crossbreeding experiment with two distinct broiler breeds and conduct 16S rRNA amplicon and transcriptome sequencing to investigate the synergistic role of gut microbiota and host genes in driving heterosis. We find that the breast muscle weight of hybrids exhibits a high heterosis, 6.28% higher than the mid-parent value. A notable difference is observed in the composition and potential function of cecal microbiota between hybrids and their parents. Over 90% of differentially colonized microbiota and differentially expressed genes exhibit nonadditive patterns. Integrative analyses uncover associations between nonadditive genes and nonadditive microbiota, including a connection between the expression of cellular signaling pathways and metabolism-related genes and the abundance of Odoribacter, Oscillibacter, and Alistipes in hybrids. Moreover, higher abundances of these microbiota are related to better meat yield. In summary, these findings highlight the importance of gut microbiota in heterosis, serving as crucial factors that modulate heterosis expression in chickens.

Detecting directional epistasis and dominance from cross-line analyses in alpine populations of Arabidopsis thaliana

The contribution of non-additive genetic effects to the genetic architecture of fitness and to the evolutionary potential of populations has been a topic of theoretical and empirical interest for a long time. Yet, the empirical study of these effects in natural populations remains scarce, perhaps because measuring dominance and epistasis relies heavily on experimental line crosses. In this study, we explored the contribution of dominance and epistasis in natural alpine populations of Arabidopsis thaliana for 2 fitness traits, the dry biomass and the estimated number of siliques, measured in a greenhouse. We found that, on average, crosses between inbred lines of A. thaliana led to mid-parent heterosis for dry biomass but outbreeding depression for an estimated number of siliques. While heterosis for dry biomass was due to dominance, we found that outbreeding depression for an estimated number of siliques could be attributed to the breakdown of beneficial epistatic interactions. We simulated and discussed the implication of these results for the adaptive potential of the studied populations, as well as the use of line-cross analyses to detect non-additive genetic effects.

Small proteins modulate ion-channel-like ACD6 to regulate immunity in Arabidopsis thaliana

The multi-pass transmembrane protein ACCELERATED CELL DEATH 6 (ACD6) is an immune regulator in Arabidopsis thaliana with an unclear biochemical mode of action. We have identified two loci, MODULATOR OF HYPERACTIVE ACD6 1 (MHA1) and its paralog MHA1-LIKE (MHA1L), that code for ∼7 kDa proteins, which differentially interact with specific ACD6 variants. MHA1L enhances the accumulation of an ACD6 complex, thereby increasing the activity of the ACD6 standard allele for regulating plant growth and defenses. The intracellular ankyrin repeats of ACD6 are structurally similar to those found in mammalian ion channels. Several lines of evidence link increased ACD6 activity to enhanced calcium influx, with MHA1L as a direct regulator of ACD6, indicating that peptide-regulated ion channels are not restricted to animals.

Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids

BACKGROUND

Complex traits, such as growth and fitness, are typically controlled by a very large number of variants, which can interact in both additive and non-additive fashion. In an attempt to gauge the relative importance of both types of genetic interactions, we turn to hybrids, which provide a facile means for creating many novel allele combinations.

RESULTS

We focus on the interaction between alleles of the same locus, i.e., dominance, and perform a transcriptomic study involving 141 random crosses between different accessions of the plant model species Arabidopsis thaliana. Additivity is rare, consistently observed for only about 300 genes enriched for roles in stress response and cell death. Regulatory rare-allele burden affects the expression level of these genes but does not correlate with F1 rosette size. Non-additive, dominant gene expression in F1 hybrids is much more common, with the vast majority of genes (over 90%) being expressed below the parental average. Unlike in the additive genes, regulatory rare-allele burden in the dominant gene set is strongly correlated with F1 rosette size, even though it only mildly covaries with the expression level of these genes.

CONCLUSIONS

Our study underscores under-dominance as the predominant gene action associated with emergence of rosette growth trajectories in the A. thaliana hybrid model. Our work lays the foundation for understanding molecular mechanisms and evolutionary forces that lead to dominance complementation of rare regulatory alleles.

Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit

Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.

Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice

Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection

Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley (Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

Intrinsic emergence and modulation of sex-specific dominance reversals in threshold traits

Sex-specific dominance reversals (SSDRs) in fitness-related traits, where heterozygotes' phenotypes resemble those of alternative homozygotes in females versus males, can simultaneously maintain genetic variation in fitness and resolve sexual conflict and thereby shape key evolutionary outcomes. However, the full implications of SSDRs will depend on how they arise and the resulting potential for evolutionary, ecological and environmental modulation. Recent field and laboratory studies have demonstrated SSDRs in threshold(-like) traits with dichotomous or competitive phenotypic outcomes, implying that such traits could promote the emergence of SSDRs. However, such possibilities have not been explicitly examined. I show how phenotypic SSDRs can readily emerge in threshold traits given genetic architectures involving large-effect loci alongside sexual dimorphism in the mean and variance in polygenic liability. I also show how multilocus SSDRs can arise in line-cross experiments, especially given competitive reproductive systems that generate nonlinear fitness outcomes. SSDRs can consequently emerge in threshold(-like) traits as functions of sexual antagonism, sexual dimorphism and reproductive systems, even with purely additive underlying genetic effects. Accordingly, I identify theoretical and empirical advances that are now required to discern the basis and occurrence of SSDRs in nature, probe forms of (co-)evolutionary, ecological and environmental modulation, and evaluate net impacts on sexual conflict.

Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection

In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis in limnetic crosses and breakdown in benthic crosses, which is suggestive of process- and ecotype-specific environment-dependence. In ponds, heterosis and breakdown were three times greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, the observation of qualitatively similar patterns of heterosis and hybrid breakdown for both ecotypes when averaging the lake pairs indicates that the outcome of hybridization is repeatable in a general sense.

Environment dependence of the expression of mutational load and species' range limits

Theoretical and empirical research on the causes of species' range limits suggest the contribution of several intrinsic and extrinsic factors, with potentially complex interactions among them. An intrinsic factor proposed by recent theory is mutational load increasing towards range edges because of genetic drift. Furthermore, environmental quality may decline towards range edges and enhance the expression of load. Here, we tested whether the expression of mutational load associated with range limits in the North American plant Arabidopsis lyrata was enhanced under stressful environmental conditions by comparing the performance of within- versus between-population crosses at common garden sites across the species' distribution and beyond. Heterosis, reflecting the expression of load, increased with heightened estimates of genomic load and with environmental stress caused by warming, but the interaction was not significant. We conclude that range-edge populations suffer from a twofold genetic Allee effect caused by increased mutational load and stress-dependent load linked to general heterozygote deficiency, but there is no synergistic effect between them.

Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.

Advances in lentil production through heterosis: Evaluating generations and breeding systems

Heterosis is defined as increased performance of the F1 hybrid relative to its parents. In the current study, a cohort of populations and parents were created to evaluate and understand heterosis across generations (i.e., F1 to F3) in lentil, a self-pollinated annual diploid (2n = 2× = 14) crop species. Lentil plants were evaluated for heterotic traits in terms of plant height, biomass fresh weight, seed number, yield per plant and 100 grain weight. A total of 47 selected lentil genotypes were cross hybridized to generate 72 F1 hybrids. The F1 hybrids from the top five crosses exhibited between 31%-62% heterosis for seed number with reference to the better parent. The five best performing heterotic crosses were selected with a negative control for evaluation at the subsequent F2 generation and only the tails of the distribution taken forward to be assessed in the F3 generation as a sub selection. Overall, heterosis decreases across the subsequent generations for all traits studied. However, some individual genotypes were identified at the F2 and sub-selected F3 generations with higher levels of heterosis than the best F1 mean value (hybrid mimics). The phenotypic data for the selected F2 and sub selected F3 hybrids were analysed, and the study suggested that 100 grain weight was the biggest driver of yield followed by seed number. A genetic diversity analysis of all the F1 parents failed to correlate genetic distance and divergence among parents with heterotic F1's. Therefore, genetic distance was not a key factor to determine heterosis in lentil. The study highlights the challenges associated with different breeding systems for heterosis (i.e., F1 hybrid-based breeding systems and/or via hybrid mimics) but demonstrates the potential significant gains that could be achieved in lentil productivity.

Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts

Genetic admixture, resulting from the recombination between structural groups, is frequently encountered in breeding populations. In hybrid breeding, crossing admixed lines can generate substantial nonadditive genetic variance and contrasted levels of inbreeding which can impact trait variation. This study aimed at testing recent methodological developments for the modeling of inbreeding and nonadditive effects in order to increase prediction accuracy in admixed populations. Using two maize (Zea mays L.) populations of hybrids admixed between dent and flint heterotic groups, we compared a suite of five genomic prediction models incorporating (or not) parameters accounting for inbreeding and nonadditive effects with the natural and orthogonal interaction approach in single and multienvironment contexts. In both populations, variance decompositions showed the strong impact of inbreeding on plant yield, height, and flowering time which was supported by the superiority of prediction models incorporating this effect (+0.038 in predictive ability for mean yield). In most cases dominance variance was reduced when inbreeding was accounted for. The model including additivity, dominance, epistasis, and inbreeding effects appeared to be the most robust for prediction across traits and populations (+0.054 in predictive ability for mean yield). In a multienvironment context, we found that the inclusion of nonadditive and inbreeding effects was advantageous when predicting hybrids not yet observed in any environment. Overall, comparing variance decompositions was helpful to guide model selection for genomic prediction. Finally, we recommend the use of models including inbreeding and nonadditive parameters following the natural and orthogonal interaction approach to increase prediction accuracy in admixed populations.

Additive genetic variation in Pinus radiata bark chemistry and the chemical traits associated with variation in mammalian bark stripping

Secondary metabolites are suggested as a major mechanism explaining genetic variation in herbivory levels in Pinus radiata. The potential to incorporate these chemical traits into breeding/deployment programmes partly depends on the presence of additive genetic variation for the relevant chemical traits. In this study, near-infrared spectroscopy was used to quantify the constitutive and induced levels of 54 compounds in the bark of trees from 74 P. radiata full-sib families. The trees sampled for chemistry were protected from browsing and induced levels were obtained by subjecting half of the trees to artificial bark stripping. The treatment effect on bark chemistry was assessed along with narrow-sense heritability, the significance of non-additive genetic effects and the additive genetic correlations of compounds with bark stripping by mammalian herbivores that was observed in unprotected replicates of the field trial. The results indicated: (i) significant additive genetic variation, with low-moderate narrow-sense heritability estimates for most compounds; (ii) while significant induced effects were detected for some chemicals, no significant genetic variation in inducibility was detected; and (iii) sugars, fatty acids and a diterpenoid positively genetically correlated while a sesquiterpenoid negatively genetically correlated with bark stripping by the mammalian herbivore, the Bennett's wallaby (Macropus rufogriseus). At the onset of browsing, a trade-off with height was detected for selecting higher amounts of this sesquiterpenoid. However, overall, results showed potential to incorporate chemical traits into breeding/deployment programmes. The quantitative genetic analyses of the near infrared predicted chemical traits produced associations with mammalian bark stripping that mostly conform with those obtained using standard wet chemistry.

Revisiting Plant Heterosis-From Field Scale to Molecules

Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future.

High Phenotypic Plasticity in a Prominent Plant Invader along Altitudinal and Temperature Gradients

Studies on plant growth and trait variation along environmental gradients can provide important information for identifying drivers of plant invasions and for deriving management strategies. We used seeds of the annual plant invader Ambrosia artemisiifolia L. (common ragweed) collected from an agricultural site in Northern Italy (226 m. a.s.l; Mean Annual Air Temperature: 12.9 °C; precipitations: 930 mm) to determine variation in growth trajectories and plant traits when grown along a 1000-m altitudinal gradient in Northern Italy, and under different temperature conditions in the growth chamber (from 14/18 °C to 26/30 °C, night/day), using a non-liner modeling approach. Under field conditions, traits related to plant height (maximum height, stem height, number of internodes) followed a three-parameter logistic curve. In contrast, leaf traits (lateral spread, number of leaves, leaf length and width) followed non-monotonic double-Richards curves that captured the decline patterns evident in the data. Plants grew faster, reaching a higher maximum plant height, and produced more biomass when grown at intermediate elevations. Under laboratory conditions, plants exhibited the same general growth trajectory of field conditions. However, leaf width did not show the recession after the maximum value shown by plants grown in the field, although the growth trajectories of some individuals, particularly those grown at 18 °C, showed a decline at late times. In addition, the plants grown at lower temperatures exhibited the highest value of biomass and preserved reproductive performances (e.g., amount of male inflorescence, pollen weight). From our findings, common ragweed exhibits a high phenotypic plasticity of vegetative and reproductive traits in response to different altitudes and temperature conditions. Under climate warming, this plasticity may facilitate the shift of the species towards higher elevation, but also the in situ resistance and (pre)adaptation of populations currently abundant at low elevations in the invasive European range. Such results may be also relevant for projecting the species management such as the impact by possible biocontrol agents.

Fitness consequences of hybridization in a predominantly selfing species: insights into the role of dominance and epistatic incompatibilities

Studying the consequences of hybridization on plant performance is insightful to understand the adaptive potential of populations, notably at local scales. Due to reduced effective recombination, predominantly selfing species are organized in highly homozygous multi-locus-genotypes (or lines) that accumulate genetic differentiation both among- and within-populations. This high level of homozygosity facilitates the dissection of the genetic basis of hybrid performance in highly selfing species, which gives insights into the mechanisms of reproductive isolation between lines. Here, we explored the fitness consequences of hybridization events between natural inbred lines of the predominantly selfing species Medicago truncatula, at both within- and among-populations scales. We found that hybridization has opposite effects pending on studied fitness proxies, with dry mass showing heterosis, and seed production showing outbreeding depression. Although we found significant patterns of heterosis and outbreeding depression, they did not differ significantly for within- compared to among-population crosses. Family-based analyses allowed us to determine that hybrid differentiation was mostly due to dominance and epistasis. Dominance and/or dominant epistatic interactions increased dry mass, while decreasing seed production, and recessive epistatic interactions mostly had a positive effect on both fitness proxies. Our results illustrate how genetic incompatibilities can accumulate at a very local scale among multi-locus-genotypes, and how non-additive genetic effects contribute to heterosis and outbreeding depression.

Back to the future: Implications of genetic complexity for the structure of hybrid breeding programs

Commercial hybrid breeding operations can be described as decentralized networks of smaller, more or less isolated breeding programs. There is further a tendency for the disproportionate use of successful inbred lines for generating the next generation of recombinants, which has led to a series of significant bottlenecks, particularly in the history of the North American and European maize germplasm. Both the decentralization and the disproportionate contribution of inbred lines reduce effective population size and constrain the accessible genetic space. Under these conditions, long-term response to selection is not expected to be optimal under the classical infinitesimal model of quantitative genetics. In this study, we therefore aim to propose a rationale for the success of large breeding operations in the context of genetic complexity arising from the structure and properties of interactive genetic networks. For this, we use simulations based on the NK model of genetic architecture. We indeed found that constraining genetic space through program decentralization and disproportionate contribution of parental inbred lines, is required to expose additive genetic variation and thus facilitate heritable genetic gains under high levels of genetic complexity. These results introduce new insights into why the historically grown structure of hybrid breeding programs was successful in improving the yield potential of hybrid crops over the last century. We also hope that a renewed appreciation for “why things worked” in the past can guide the adoption of novel technologies and the design of future breeding strategies for navigating biological complexity.

Integrated transcript and metabolite profiling reveals coordination between biomass size and nitrogen metabolism in Arabidopsis F1 hybrids

Heterosis refers to the improved agronomic performance of F₁ hybrids relative to their parents. Although this phenomenon is widely employed to increase biomass, yield, and stress tolerance of plants, the underlying molecular mechanisms remain unclear. To dissect the metabolic fluctuations derived from genomic and/or environmental differences contributing to the improved biomass of F₁ hybrids relative to their parents, we optimized the growth condition for Arabidopsis thaliana F₁ hybrids and their parents. Modest but statistically significant increase in the biomass of F₁ hybrids was observed. Plant samples grown under the optimized condition were also utilized for integrated omics analysis to capture specific changes in the F₁ hybrids. Metabolite profiling of F₁ hybrids and parent plants was performed using gas chromatography-mass spectrometry. Among the detected 237 metabolites, 2-oxoglutarate (2-OG) and malate levels were lower and the level of aspartate was higher in the F₁ hybrids than in each parent. In addition, microarray analysis revealed that there were 44 up-regulated and 12 down-regulated genes with more than 1.5-fold changes in expression levels in the F₁ hybrid compared to each parent. Gene ontology (GO) analyses indicated that genes up-regulated in the F₁ hybrids were largely related to organic nitrogen (N) process. Quantitative PCR verified that glutamine synthetase 2 (AtGLN2) was upregulated in the F₁ hybrids, while other genes encoding enzymes in the GS-GOGAT cycle showed no significant differences between the hybrid and parent lines. These results suggested the existence of metabolic regulation that coordinates biomass and N metabolism involving AtGLN2 in F₁ hybrids.

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature

Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.

Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding

Transgressive segregation and heterosis are the reasons that plant breeding works. Molecular explanations for both phenomena have been suggested and play a contributing role. However, it is often overlooked by molecular genetic researchers that transgressive segregation and heterosis are most simply explained by dispersion of favorable alleles. Therefore, advances in molecular biology will deliver the most impact on plant breeding when integrated with sources of heritable trait variation - and this will be best achieved within a quantitative genetics framework. An example of the power of quantitative approaches is the implementation of genomic selection, which has recently revolutionized animal breeding. Genomic selection is now being applied to both hybrid and inbred crops and is likely to be the major source of improvement in plant breeding practice over the next decade. Breeders' ability to efficiently apply genomic selection methodologies is due to recent technology advances in genotyping and sequencing. Furthermore, targeted integration of additional molecular data (such as gene expression, gene copy number and methylation status) into genomic prediction models may increase their performance. In this review, we discuss and contextualize a suite of established quantitative genetics themes relating to hybrid vigour, transgressive segregation and their central relevance to plant breeding, with the aim of informing crop researchers outside of the quantitative genetics discipline of their relevance and importance to crop improvement. Better understanding between molecular and quantitative disciplines will increase the potential for further improvements in plant breeding methodologies and so help underpin future food security.

Genomic instability in an interspecific hybrid of the genus Saccharomyces: a matter of adaptability

Ancient events of polyploidy have been linked to huge evolutionary leaps in the tree of life, while increasing evidence shows that newly established polyploids have adaptive advantages in certain stress conditions compared to their relatives with a lower ploidy. The genus Saccharomyces is a good model for studying such events, as it contains an ancient whole-genome duplication event and many sequenced Saccharomyces cerevisiae are, evolutionary speaking, newly formed polyploids. Many polyploids have unstable genomes and go through large genome erosions; however, it is still unknown what mechanisms govern this reduction. Here, we sequenced and studied the natural S. cerevisiae × Saccharomyces kudriavzevii hybrid strain, VIN7, which was selected for its commercial use in the wine industry. The most singular observation is that its nuclear genome is highly unstable and drastic genomic alterations were observed in only a few generations, leading to a widening of its phenotypic landscape. To better understand what leads to the loss of certain chromosomes in the VIN7 cell population, we looked for genetic features of the genes, such as physical interactions, complex formation, epistatic interactions and stress responding genes, which could have beneficial or detrimental effects on the cell if their dosage is altered by a chromosomal copy number variation. The three chromosomes lost in our VIN7 population showed different patterns, indicating that multiple factors could explain the mechanisms behind the chromosomal loss. However, one common feature for two out of the three chromosomes is that they are among the smallest ones. We hypothesize that small chromosomes alter their copy numbers more frequently as a low number of genes is affected, meaning that it is a by-product of genome instability, which might be the chief driving force of the adaptability and genome architecture of this hybrid.

The Pitfalls of Heterosis Coefficients

Heterosis (hybrid vigour) is a universal phenomenon of crucial agro-economic and evolutionary importance. We show that the most common heterosis coefficients do not properly measure deviation from additivity because they include both a component accounting for "real" heterosis and a term that is not related to heterosis, since it is derived solely from parental values. Therefore, these coefficients are inadequate whenever the aim of the study is to compare heterosis levels between different traits, environments, genetic backgrounds, or developmental stages, as these factors may affect not only the level of non-additivity, but also parental values. The only relevant coefficient for such comparisons is the so-called "potence ratio". Because most heterosis studies consider several traits/stages/environmental conditions, our observations support the use of the potence ratio, at least in non-agronomic contexts, because it is the only non-ambiguous heterosis coefficient.

In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F1 Hybrid Population

Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F₁ hybrid cultivars in many crops. A similar level of heterosis in all F₁ individuals is expected as they are genetically identical. However, we found variation in rosette size in individual F₁ plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big-sized F₁ plants had 26.1% larger leaf area in the first and second leaves than medium-sized F₁ plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big- and medium-sized F₁ plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, and some lines had increased plant size at 14 or 21 days after sowing but not at all time points during development. Change of expression levels in stress-responsive genes among individual F₁ plants could generate the variation in plant size of individual F₁ plants in A. thaliana.

Transgressivity in Key Functional Traits Rather Than Phenotypic Plasticity Promotes Stress Tolerance in A Hybrid Cordgrass

Hybridization might promote offspring fitness via a greater tolerance to environmental stressors due to heterosis and higher levels of phenotypic plasticity. Thus, analyzing the phenotypic expression of hybrids provides an opportunity to elucidate further plant responses to environmental stress. In the case of coastal salt marshes, sea level rise subjects hybrids, and their parents, to longer tidal submergence and higher salinity. We analyzed the phenotypic expression patterns in the hybrid Spartina densiflora x foliosa relative to its parental species, native S. foliosa, and invasive S. densiflora, from the San Francisco Estuary when exposed to contrasting salinities and inundations in a mesocosm experiment. 37% of the recorded traits displayed no variability among parents and hybrids, 3% showed an additive inheritance, 37% showed mid-parent heterosis, 18% showed best-parent heterosis, and 5% presented worst-parent heterosis. Transgressivity, rather than phenotypic plasticity, in key functional traits of the hybrid, such as tiller height, conveyed greater stress tolerance to the hybrid when compared to the tolerance of its parents. As parental trait variability increased, phenotypic transgressivity of the hybrid increased and it was more important in response to inundation than salinity. Increases in salinity and inundation associated with sea level rise will amplify the superiority of the hybrid over its parental species. These results provide evidence of transgressive traits as an underlying source of adaptive variation that can facilitate plant invasions. The adaptive evolutionary process of hybridization is thought to support an increased invasiveness of plant species and their rapid evolution.

An elucidation of over a century old enigma in genetics-Heterosis

Recognition and exploitation of hybrid vigor or heterosis among individual crosses of plants and animals has a long and distinguished history. Its manifestation is influenced by a combination of genetic, epigenetic, phenotypic, and environmental factors. Although heterosis is known to be governed by both dominant and epistatic gene action, its expression is greatly influenced by nonlinear interaction among epigenetic and phenotypic (phenomic) components. The magnitude of heterosis is generally inferred post hoc by the phenotypic performance of hybrids among laboriously made individual crosses. The expression of dominance, however, is nonlinear at the cellular level and obeys the principles underlying metabolic flux. Then, is it possible to exploit these relationships to predict heterosis? Vasseur and colleagues have indeed demonstrated the feasibility of such an approach in a series of experiments taking integrated biochemical and computational approaches, as well as testing these results on large samples of model organisms. The results offer promise toward phenomic prediction of heterosis across a wide array of organisms.

A recent study applies allometric models to test Sewall Wright’s 85 year-old conjecture on the expression of dominance among traits that contribute to productivity and Darwinian fitness in Arabidopsis thaliana. This Primer explores the wide-ranging implications for agriculture and human health.

Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.