Heterotic Phenotype Research Articles

One Hundred Years of Progress and Pitfalls: Maximising Heterosis through Increasing Multi-Locus Nuclear Heterozygosity.

The improvement in quantitative traits (e.g., yield, size) in F1 offspring over parent lines is described as hybrid vigour, or heterosis. There exists a fascinating relationship between parental genetic distance and genome dosage (polyploidy), and heterosis effects. The contribution of nuclear heterozygosity to heterosis is not uniform across diploid and polyploid crops, even within same species, thus demonstrating that polyploid crops should be part of any discussion on the mechanisms of heterosis. This review examines the records of correlating heterosis with parental genetic distance and the influence of adding supplementary genomes in wide crosses. Increasing nuclear heterozygosity through parental genetic distance has been shown to be an imperfect predictor for heterosis in a variety of commercial crops such as maize, rice, and pepper. However, increasing the ploidy level raises the maximum number of alleles that can be harboured at any one locus, and studies on crops such as oilseed rape, potato, alfalfa, maize, and rice have demonstrated that heterosis may be maximised upon increasing multi-locus nuclear heterozygosity. The novel heterotic phenotypes observed above the diploid level will contribute to our understanding on the mechanisms of heterosis and aid plant breeders in achieving the righteous goal of producing more food with fewer inputs.

Genetic and molecular regulation of increased photosynthetic cell number contributes to leaf size heterosis in Arabidopsis

Heterosis is an important genetic phenomenon that has been observed and widely utilized in agriculture. However, the genetic and molecular bases of heterosis are unclear. Through transcriptome-wide association studies (TWAS) and expression quantitative trait locus (eQTL) analysis to integrate genome, transcriptome, and heterotic phenotype of a half-sibling Arabidopsis hybrid population, we report that the genetic and molecular bases of variations in leaf growth heterosis can be explained by the varied expression levels of growth-regulating genes resulting from distinct sets of heterozygous eQTLs carried by the half-sibling hybrids. In F1 versus parent, the degree of up-regulated gene expression in the cell cycle pathway in the shoot apex and the photosynthesis pathway in true leaf positively correlates with true leaf area heterosis level, and this is affected by the accumulation of superior heterozygous eQTLs. This was further corroborated by the major contribution of increased photosynthetic cell number to leaf area heterosis.

Synthetic apomixis with normal hybrid rice seed production

Synthetic apomixis with normal hybrid rice seed production

Synthetic apomixis enables stable transgenerational transmission of heterotic phenotypes in hybrid rice

In hybrid plants, heterosis often produces large, vigorous plants with high yields; however, hybrid seeds are generated by costly and laborious crosses of inbred parents. Apomixis, in which a plant produces a clone of itself via asexual reproduction through seeds, may produce another revolution in plant biology. Recently, synthetic apomixis enabled clonal reproduction of F1 hybrids through seeds in rice (Oryza sativa), but the inheritance of the synthetic apomixis trait and superior heterotic phenotypes across generations remained unclear. Here, we propagated clonal plants to the T4 generation and investigated their genetic and molecular stability at each generation. By analyzing agronomic traits, as well as the genome, methylome, transcriptome, and allele-specific transcriptome, we showed that the descendant clonal plants remained stable. Unexpectedly, in addition to normal clonal seeds, the plants also produced a few aneuploids that had eliminated large genomic segments in each generation. Despite the identification of rare aneuploids, the observation that the synthetic apomixis trait is stably transmitted through multiple generations helps confirm the feasibility of using apomixis in the future.

Heterosis for capsacinoids accumulation in chili pepper hybrids is dependent on parent-of-origin effect

Heterosis for agronomic traits is a widespread phenomenon that underpins hybrid crop breeding. However, heterosis at the level of cellular metabolites has not yet been fully explored. Some metabolites are highly sought after, like capsaicinoids found in peppers of the Capsicum genus, which confer the characteristic pungent (‘hot’) flavour of the fruits. We analysed the metabolic profile of the fruit placenta and pericarp of inter- and intra-specific hybrids of two species of Capsicum peppers, C. chinense (cv. Habanero and cv. Biquinho) and C. annuum var. annuum (cv. Jalapeño and cv. Cascadura Ikeda) in complete diallel crosses with reciprocals. The parents and hybrids were grown in a glasshouse and the profile of primary metabolites (sugars, amino acids and organic acids) and capsaicinoids was generated via gas chromatography–time of flight-mass spectrometry (GC–TOF-MS) and ultra-performance liquid chromatography coupled to a mass spectrometer (UPLC-MS), respectively. We found considerable heterotic effects specifically for capsaicinoids accumulation in the fruit placenta of the hybrids, including those derived from non-pungent parents. Furthermore, a large fraction of fruit primary metabolism was influenced by the specific cross combination, with marked parent-of-origin effects, i.e. whether a specific genotype was used as the pistillate or pollen parent. The differences in metabolite levels between the hybrids and their parents provide a snapshot of heterosis for primary and secondary metabolites and may contribute to explain the manifestation of whole-plant heterotic phenotypes.

Hybridization of Saccharomyces cerevisiae Sourdough Strains with Cryotolerant Saccharomyces bayanus NBRC1948 as a Strategy to Increase Diversity of Strains Available for Lager Beer Fermentation.

The search for novel brewing strains from non-brewing environments represents an emerging trend to increase genetic and phenotypic diversities in brewing yeast culture collections. Another valuable tool is hybridization, where beneficial traits of individual strains are combined in a single organism. This has been used successfully to create de novo hybrids from parental brewing strains by mimicking natural Saccharomyces cerevisiae ale × Saccharomyces eubayanus lager yeast hybrids. Here, we integrated both these approaches to create synthetic hybrids for lager fermentation using parental strains from niches other than beer. Using a phenotype-centered strategy, S. cerevisiae sourdough strains and the S. eubayanus × Saccharomyces uvarum strain NBRC1948 (also referred to as Saccharomyces bayanus) were chosen for their brewing aptitudes. We demonstrated that, in contrast to S. cerevisiae × S. uvarum crosses, hybridization yield was positively affected by time of exposure to starvation, but not by staggered mating. In laboratory-scale fermentation trials at 20 °C, one triple S. cerevisiae × S. eubayanus × S. uvarum hybrid showed a heterotic phenotype compared with the parents. In 2 L wort fermentation trials at 12 °C, this hybrid inherited the ability to consume efficiently maltotriose from NBRC1948 and, like the sourdough S. cerevisiae parent, produced appreciable levels of the positive aroma compounds 3-methylbutyl acetate (banana/pear), ethyl acetate (general fruit aroma) and ethyl hexanoate (green apple, aniseed, and cherry aroma). Based on these evidences, the phenotype-centered approach appears promising for designing de novo lager beer hybrids and may help to diversify aroma profiles in lager beer.

Cotyledons contribute to plant growth and hybrid vigor in Arabidopsis.

In hybrids of Arabidopsis, cotyledons influence the amount and proportion of hybrid vigor in total plant growth. We found Arabidopsis cotyledons are essential for plant growth and in some hybrids for hybrid vigor. In hybrids between C24 and Landsberg erecta (Ler), biomass vigor (heterosis) occurs in the first few days after sowing (DAS), with hybrid cotyledons being larger than those of their parents. C24xLer hybrids are ahead of their parents in activating photosynthesis and auxin pathway genes in cotyledons at 3-4 DAS. "Earliness" is also present in newly emerged C24xLer hybrid leaves. We showed cotyledon removal at 4 DAS caused significant biomass reduction in later growth in hybrids and parental lines. The biomass decrease caused by cotyledon removal can be partially rescued by exogenous sucrose or auxin with different genotypes responding to sucrose and/or auxin differently. Cotyledon removal has different effects on heterosis in different hybrids. After cotyledon removal, in C24xLer hybrids, both growth and heterosis were reduced in similar proportions, but the level of hybrid vigor was reduced as a proportion of growth in C24xColumbia (Col) and ColxLer hybrids. The removal of cotyledons at 4 DAS markedly decreased the level of growth and eliminated the heterotic phenotype of Wassilewskija (Ws)/Ler hybrids. In mutant Ws/Ler hybrids which had a reduced level of photosynthesis in the cotyledons, there was a reduction in plant growth and loss of heterosis. The variation in contribution of cotyledons to heterosis in different hybrids indicates there are multiple pathways to achieve heterotic phenotypes.

Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids.

Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance; however, it remains unclear whether epigenetic changes are a cause or a consequence of heterosis. Here, we analyze a large panel of over 500 Arabidopsis (Arabidopsis thaliana) epigenetic hybrid plants (epiHybrids), which we derived from near-isogenic but epigenetically divergent parents. This proof-of-principle experimental system allowed us to quantify the contribution of parental methylation differences to heterosis. We measured traits such as leaf area, growth rate, flowering time, main stem branching, rosette branching, and final plant height and observed several strong positive and negative heterotic phenotypes among the epiHybrids. Using an epigenetic quantitative trait locus mapping approach, we were able to identify specific differentially methylated regions in the parental genomes that are associated with hybrid performance. Sequencing of methylomes, transcriptomes, and genomes of selected parent-epiHybrid combinations further showed that these parental differentially methylated regions most likely mediate the remodeling of methylation and transcriptional states at specific loci in the hybrids. Taken together, our data suggest that locus-specific epigenetic divergence between the parental lines can directly or indirectly trigger heterosis in Arabidopsis hybrids independent of genetic changes. These results add to a growing body of evidence that points to epigenetic factors as one of the key determinants of hybrid performance.

Theoretical aspects of heterosis

The phenomenon of heterosis, known as the superior performance of hybrid organisms over their parents, has been exploited by agricultural practices in the production of various crops since the beginning of the last century; however, its genetic basis has remained obscure. With the experimental data obtained from the study of maize hybrids and mathematical calculations, some genetic models have been proposed to explain heterosis in terms of various types of gene interaction, such as dominance, overdominance, and epistasis. However, each of the proposed concepts has weak points, which impose limitations on the possibility of the overall interpretation of the heterotic response in F1. This review provides a critical assessment of the theoretical concepts of heterosis from the perspective of the currently accumulated data of genetics and molecular biology, which are focused on specific mechanisms acting for specific traits. In particular, the role of lethal and semi-lethal mutations in the formation of a heterotic phenotype in plants is shown. The issues of the interpretation of genetic effects in case of gene linkage, which are referred to as pseudo-overdominance, are considered. Particular attention is paid to nonallelic interactions of genes, which add new nuances when discussing the effects of dominance and overdominance. Information on combining ability and its practical use in the context of the concept of heterotic groups is presented. Some aspects of the genotype–environment interaction are shown. The analysis of the theoretical concepts of heterosis from the perspective of modern genetic data testifies to the important role of various types of gene action in the formation of an outstanding phenotype and confirms the need for a systematic approach to this complex and unique phenomenon.

Patterns of gene expression in developing embryos of Arabidopsis hybrids.

Hybrids between the Arabidopsis ecotypes C24 and Ler have high levels of hybrid vigour, or heterosis, in both biomass and seed yield. Heterosis can be detected throughout the development of the plant and in different tissues. We examined developing embryos and seeds of C24/Ler reciprocal hybrids with the aim of detecting the earliest time at which heterotic gene activity occurs. In the transcriptomes of 4-dap (days after pollination; dermatogen to globular) and 6-dap (heart) embryos from both parents and hybrids, 95% of expressed genes were at the mid parent value (MPV) and 95% of the genes with single nucleotide polymorphisms between C24 and Ler retained the same relative allelic expression levels in the hybrids as existed in the parents. This included loci that had equivalent levels of transcription in the two parents, together with loci which had different levels of expression in the parents. Amongst the genes which did not have MPV expression levels in the hybrids (non-additively expressed genes), approximately 40 in the globular embryo stage and 89 in the heart embryo stage had altered levels of transcription in both reciprocal hybrids; these genes could contribute to the heterotic phenotype of the hybrid embryo. Many of the non-additively expressed genes had expression levels that were shifted towards maternal levels of transcription, and these differed in the reciprocal hybrids. Allelic expression analysis indicated that most genes with altered allelic contributions in the hybrids had an increase in the expression level of the hybrid's maternal allele. Consistent with the maternal pattern of gene expression, embryo and seed also show maternally influenced phenotypes.

Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage.

BackgroundHeterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior performance compared to their parental inbred lines. Most commercial Chinese cabbage cultivars are F1 hybrids and their level of hybrid vigour is of critical importance and is a key selection criterion in the breeding system.ResultsWe have characterized the heterotic phenotype of one F1 hybrid cultivar of Chinese cabbage and its parental lines from early- to late-developmental stages of the plants. Hybrid cotyledons are larger than those of the parents at 4 days after sowing and biomass in the hybrid, determined by the fresh weight of leaves, is greater than that of the larger parent line by approximately 20 % at 14 days after sowing. The final yield of the hybrid harvested at 63 days after sowing is 25 % greater than the yield of the better parent. The larger leaves of the hybrid are a consequence of increased cell size and number of the photosynthetic palisade mesophyll cells and other leaf cells. The accumulation of plant hormones in the F1 was within the range of the parental levels at both 2 and 10 days after sowing. Two days after sowing, the expression levels of chloroplast-targeted genes in the cotyledon cells were upregulated in the F1 hybrid relative to their mid parent values. Shutdown of chlorophyll biosynthesis in the cotyledon by norflurazon prevented the increased leaf area in the F1 hybrid.ConclusionsIn the cotyledons of F1 hybrids, chloroplast-targeted genes were upregulated at 2 days after sowing. The increased activity levels of this group of genes suggested that their differential transcription levels could be important for establishing early heterosis but the increased transcription levels were transient. Inhibition of the photosynthetic process in the cotyledon reduced heterosis in later seedling stages. These observations suggest early developmental events in the germinating seedling of the hybrid may be important for later developmental vigour and yield advantage.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0734-3) contains supplementary material, which is available to authorized users.

Theoretical aspects of heterosis

The phenomenon of heterosis, known as superior performance of hybrid organism compared with either of their parents, has been exploited by agricultural practices in the production of various crops since the beginning of the last century; however, its genetic basis has remained obscure. With experimental data obtained from the study of maize hybrids, and mathematical calculations, some genetic models have been proposed to explain heterosis from various types of gene interaction, such as dominance, over-dominance and epistasis. However, any of the proposed concepts has weak points, which place limitations on the possibility of overall interpretation of heterotic response in F1. In this review we gather a brief account of findings from various studies for critical evaluation of the main theoretical concepts based on the information accumulated to date by genetics and molecular biology and focused on particular mechanisms acting for specific traits. We discussed some aspects concerning the role of mutation loads in the formation of heterotic phenotype. Also, we gathered a brief account of findings for interpretation of genetic effects due to linkage and non-allelic genes’ interactions that make nuances to analysis of dominance and over-dominance. We have provided information about combining ability, its practical application in the context of the concept of heterotic groups. Here we also discussed some aspects of “genotype–environment” interaction. Recent advancements in genetics and molecular biology indicate the importance of various types of gene action for heterosis and confirm the necessity of systemlevel approaches to understanding this unique phenomenon.

Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids

Plant hybrids are extensively used in agriculture to deliver increases in yields, yet the molecular basis of their superior performance (heterosis) is not well understood. Our transcriptome analysis of a number of Arabidopsis F1 hybrids identified changes to defense and stress response gene expression consistent with a reduction in basal defense levels. Given the reported antagonism between plant immunity and growth, we suggest that these altered patterns of expression contribute to the greater growth of the hybrids. The altered patterns of expression in the hybrids indicate decreases to the salicylic acid (SA) biosynthesis pathway and increases in the auxin [indole-3-acetic acid (IAA)] biosynthesis pathway. SA and IAA are hormones known to control stress and defense responses as well as plant growth. We found that IAA-targeted gene activity is frequently increased in hybrids, correlating with a common heterotic phenotype of greater leaf cell numbers. Reduced SA concentration and target gene responses occur in the larger hybrids and promote increased leaf cell size. We demonstrated the importance of SA action to the hybrid phenotype by manipulating endogenous SA concentrations. Increasing SA diminished heterosis in SA-reduced hybrids, whereas decreasing SA promoted growth in some hybrids and phenocopied aspects of hybrid vigor in parental lines. Pseudomonas syringae infection of hybrids demonstrated that the reductions in basal defense gene activity in these hybrids does not necessarily compromise their ability to mount a defense response comparable to the parents.

Hybrid mimics and hybrid vigor in Arabidopsis.

F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.

Small RNAs as important regulators for the hybrid vigour of super-hybrid rice.

Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.

Heterosis, stress, and the environment: a possible road map towards the general improvement of crop yield

Contemporary plant breeding is under pressure to improve crop productivity at a rate surpassing past achievements. Different research groups dealing with this issue reached similar conclusions that the solution lies in improved biomass production by way of enhanced light capture and use efficiency, modified photosystem biochemistry, and improved partitioning of assimilates to the economic part of the plant. There seems to be a consensus of sorts. This 'opinion paper' calls attention to the phenomenon of heterosis, as expressed in maize, sorghum, and other crops where, depending on the case and the trait, larger biomass and greater yield have been achieved without a change in growth duration, photosystem biochemistry, or harvest index. This discussion maintains that there is no consensus about the genetics or the genomics of heterosis in regulating yield under diverse environments. Therefore, in a search for the basis of heterosis in yield and adaptation, the discussion bypasses the genetics and searches for answers in the phenomics of heterosis. The heterotic phenotype in itself provides challenging and important hints towards improving the yield of open-pollinated crops in general. These hints are linked to the homeostasis of photosynthesis with respect to temperature, the photobiology of the plant as mediated by phytochrome, the architectural foundations of the formation of a large sink, and the associated hormones and signals in controlling sink differentiation and source-sink communication. This discussion does not lay out plans and protocols but provides clues to explore within and beyond the current thinking about breeding for high yield.

Heterosis: Many Genes, Many Mechanisms—End the Search for an Undiscovered Unifying Theory

Heterosis is the increase in vigor that is observed in progenies of matings of diverse individuals from different species, isolated populations, or selected strains within species or populations. Heterosis has been of immense economic value in agriculture and has important implications regarding the fitness and fecundity of individuals in natural populations. Genetic models based on complementation of deleterious alleles, especially in the context of linkage and epistasis, are consistent with many observed manifestations of heterosis. The search for the genes and alleles that underlie heterosis, as well as for broader allele-independent, genomewide mechanisms, has encompassed many species and systems. Common themes across these studies indicate that sequence diversity is necessary but not sufficient to produce heterotic phenotypes, and that the molecular pathways that produce heterosis involve chromatin modification, transcriptional control, translation and protein processing, and interactions between and within developmental and biochemical pathways. Taken together, there are many and diverse molecular mechanisms that translate DNA into phenotype, and it is the combination of all these mechanisms across many genes that produce heterosis in complex traits.

Predicting Arabidopsis Freezing Tolerance and Heterosis in Freezing Tolerance from Metabolite Composition

Heterosis, or hybrid vigor, is one of the most important tools in plant breeding and has previously been demonstrated for plant freezing tolerance. Freezing tolerance is an important trait because it can limit the geographical distribution of plants and their agricultural yield. Plants from temperate climates increase in freezing tolerance during exposure to low, non-freezing temperatures in a process termed ‘cold acclimation’. Metabolite profiling has indicated a major reprogramming of plant metabolism in the cold, but it has remained unclear in previous studies which of these changes are related to freezing tolerance. In the present study, we have used metabolic profiling to discover combinations of metabolites that predict freezing tolerance and its heterosis in Arabidopsis thaliana. We identified compatible solutes and, in particular, the pathway leading to raffinose as crucial statistical predictors for freezing tolerance and its heterosis, while some TCA cycle intermediates contribute only to predicting the heterotic phenotype. This indicates coordinate links between heterosis and metabolic pathways, suggesting that a limited number of regulatory genes may determine the extent of heterosis in this complex trait. In addition, several unidentified metabolites strongly contributed to the prediction of both freezing tolerance and its heterosis and we present an exemplary analysis of one of these, identifying it as a hexose conjugate.

Allelic variation and heterosis in maize: How do two halves make more than a whole?

In this review, we discuss the recent research on allelic variation in maize and possible implications of this work toward our understanding of heterosis. Heterosis, or hybrid vigor, is the increased performance of a hybrid relative to the parents, and is a result of the variation that is present within a species. Intraspecific comparisons of sequence and expression levels in maize have documented a surprisingly high level of allelic variation, which includes variation for the content of genic fragments, variation in repetitive elements surrounding genes, and variation in gene expression levels. There is evidence that transposons and repetitive DNA play a major role in the generation of this allelic diversity. The combination of allelic variants provides a more comprehensive suite of alleles in the hybrid that may be involved in novel allelic interactions. A major unresolved question is how the combined allelic variation and interactions in a hybrid give rise to heterotic phenotypes. An understanding of allelic variation present in maize provides an opportunity to speculate on mechanisms that might lead to heterosis. Variation for the presence of genes, the presence of novel beneficial alleles, and modified levels of gene expression in hybrids may all contribute to the heterotic phenotypes.