Heterosis in early seed development: a comparative study of F1 embryo and endosperm tissues 6 days after fertilization

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

KEY MESSAGE

Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F₁ hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.

Heterosis and Differential DNA Methylation in Soybean Hybrids and Their Parental Lines

Heterosis is an important biological phenomenon and is widely applied to increase agricultural productivity. However, the underlying molecular mechanisms of heterosis are still unclear. Here we constructed three combinations of reciprocal hybrids of soybean, and subsequently used MethylRAD-seq to detect CCGG and CCWGG (W = A or T) methylation in the whole genome of these hybrids and their parents at the middle development period of contemporary seed. We were able to prove that changes in DNA methylation patterns occurred in immature hybrid seeds and the parental variation was to some degree responsible for differential expression between the reciprocal hybrids. Non-additive differential methylation sites (DMSs) were also identified in large numbers in hybrids. Interestingly, most of these DMSs were hyper-methylated and were more concentrated in gene regions than the natural distribution of the methylated sites. Further analysis of the non-additive DMSs located in gene regions exhibited their participation in various biological processes, especially those related to transcriptional regulation and hormonal function. These results revealed DNA methylation reprogramming pattern in the hybrid soybean, which is associated with phenotypic variation and heterosis initiation.

Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development

To elucidate the mechanisms underlying seed development in maize, comprehensive RNA-seq analyses were conducted on Zhengdan1002 (ZD1002), Zhengdan958 (ZD958), and their parental lines during seven seed developmental stages. We found that gene expression levels were largely nonadditive in hybrids and that cis-only or trans × cis pattern played a large role in hybrid gene regulation during seed developmental stage. Weighted gene co-expression network (WGCNA) analysis showed that 36 modules were highly correlated (r = -0.90-0.92, p < 0.05) with kernel weight, length, and width during seed development. Forty-five transcription factors and 38 ribosomal protein genes were identified as major hub genes determining seed size/weight. We also described a network hub, Auxin Response Factor 12 of maize (ZmARF12), a member of a family of transcription factor that mediate gene expression in response to auxin, potentially links auxin signal pathways, cell division, and the size of the seeds. The ZmARF12 mutant exhibited larger seed size and higher grain weight. ZmARF12 transcription was negatively associated with cell division during seed development, which was confirmed by evaluating the yield of protoplasts that isolated from the kernels of the mutant and other inbred lines. Transient knock-down of ZmARF12 in maize plants facilitated cell expansion and division, whereas transient silencing of its potential interactor ZmIAA8 impaired cell division. ZmIAA8 expression was repressed in the ZmARF12 over-expressed protoplasts. The mutant phenotype and the genetics studies presented here illustrated evidence that ZmARF12 is a cell division repressor, and potentially determines the final seed size.

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.

Global transcriptional profiling between inbred parents and hybrids provides comprehensive insights into ear-length heterosis of maize (Zea mays)

BACKGROUND

Maize (Zea mays) ear length, which is an important yield component, exhibits strong heterosis. Understanding the potential molecular mechanisms of ear-length heterosis is critical for efficient yield-related breeding.

RESULTS

Here, a joint netted pattern, including six parent-hybrid triplets, was designed on the basis of two maize lines harboring long (T121 line) and short (T126 line) ears. Global transcriptional profiling of young ears (containing meristem) was performed. Multiple comparative analyses revealed that 874 differentially expressed genes are mainly responsible for the ear-length variation between T121 and T126 lines. Among them, four key genes, Zm00001d049958, Zm00001d027359, Zm00001d048502 and Zm00001d052138, were identified as being related to meristem development, which corroborated their roles in the superior additive genetic effects on ear length in T121 line. Non-additive expression patterns were used to identify candidate genes related to ear-length heterosis. A non-additively expressed gene (Zm00001d050649) was associated with the timing of meristematic phase transition and was determined to be the homolog of tomato SELF PRUNING, which assists SINGLE FLOWER TRUSS in driving yield-related heterosis, indicating that Zm00001d050649 is a potential contributor to drive heterotic effect on ear length.

CONCLUSION

Our results suggest that inbred parents provide genetic and heterotic effects on the ear lengths of their corresponding F₁ hybrids through two independent pathways. These findings provide comprehensive insights into the transcriptional regulation of ear length and improve the understanding of ear-length heterosis in maize.

Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively

BACKGROUND

Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.

RESULTS

Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value.

CONCLUSIONS

Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

Single-parent expression drives dynamic gene expression complementation in maize hybrids

Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.

Single-Parent Expression of Anti-sense RNA Contributes to Transcriptome Complementation in Maize Hybrid

Anti-sense transcription is increasingly being recognized as an important regulator of gene expression. But the transcriptome complementation of anti-sense RNA in hybrid relative to their inbred parents was largely unknown. In this study, we profiled strand-specific RNA sequencing (RNA-seq) in a maize hybrid and its inbred parents (B73 and Mo17) in two tissues. More anti-sense transcripts were present in the hybrid compared with the parental lines. We detected 293 and 242 single-parent expression of anti-sense (SPEA) transcripts in maize immature ear and leaf tissues, respectively. There was little overlap of the SPEA transcripts between the two maize tissues. These results suggested that SPEA is a general mechanism that drives extensive complementation in maize hybrids. More importantly, extremely high-level expression of anti-sense transcripts was associated with low-level expression of the cognate sense transcript by reducing the level of histone H3 lysine 36 methylation (H3K36me3). In summary, these SPEA transcripts increased our knowledge about the transcriptomic complementation in hybrid.

Temporal Regulation of the Metabolome and Proteome in Photosynthetic and Photorespiratory Pathways Contributes to Maize Heterosis

Heterosis or hybrid vigor is widespread in plants and animals. Although the molecular basis for heterosis has been extensively studied, metabolic and proteomic contributions to heterosis remain elusive. Here we report an integrative analysis of time-series metabolome and proteome data in maize (Zea mays) hybrids and their inbred parents. Many maize metabolites and proteins are diurnally regulated, and many of these show nonadditive abundance in the hybrids, including key enzymes and metabolites involved in carbon assimilation. Compared with robust trait heterosis, metabolic heterosis is relatively mild. Interestingly, most amino acids display negative mid-parent heterosis (MPH), i.e., having lower values than the average of the parents, while sugars, alcohols, and nucleoside metabolites show positive MPH. From the network perspective, metabolites in the photosynthetic pathway show positive MPH, whereas metabolites in the photorespiratory pathway show negative MPH, which corresponds to nonadditive protein abundance and enzyme activities of key enzymes in the respective pathways in the hybrids. Moreover, diurnally expressed proteins that are upregulated in the hybrids are enriched in photosynthesis-related gene-ontology terms. Hybrids may more effectively remove toxic metabolites generated during photorespiration, and thus maintain higher photosynthetic efficiency. These metabolic and proteomic resources provide unique insight into heterosis and its utilization for high yielding maize and other crop plants.

Exploitation of Heterosis in Pearl Millet: A Review

The phenomenon of heterosis has fascinated plant breeders ever since it was first described by Charles Darwin in 1876 in the vegetable kingdom and later elaborated by George H Shull and Edward M East in maize during 1908. Heterosis is the phenotypic and functional superiority manifested in the F1 crosses over the parents. Various classical complementation mechanisms gave way to the study of the underlying potential cellular and molecular mechanisms responsible for heterosis. In cereals, such as maize, heterosis has been exploited very well, with the development of many single-cross hybrids that revolutionized the yield and productivity enhancements. Pearl millet (Pennisetum glaucum (L.) R. Br.) is one of the important cereal crops with nutritious grains and lower water and energy footprints in addition to the capability of growing in some of the harshest and most marginal environments of the world. In this highly cross-pollinating crop, heterosis was exploited by the development of a commercially viable cytoplasmic male-sterility (CMS) system involving a three-lines breeding system (A-, B- and R-lines). The first set of male-sterile lines, i.e., Tift 23A and Tift18A, were developed in the early 1960s in Tifton, Georgia, USA. These provided a breakthrough in the development of hybrids worldwide, e.g., Tift 23A was extensively used by Punjab Agricultural University (PAU), Ludhiana, India, for the development of the first single-cross pearl millet hybrid, named Hybrid Bajra 1 (HB 1), in 1965. Over the past five decades, the pearl millet community has shown tremendous improvement in terms of cytoplasmic and nuclear diversification of the hybrid parental lines, which led to a progressive increase in the yield and adaptability of the hybrids that were developed, resulting in significant genetic gains. Lately, the whole genome sequencing of Tift 23D2B1 and re-sequencing of circa 1000 genomes by a consortium led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been a significant milestone in the development of cutting-edge genetic and genomic resources in pearl millet. Recently, the application of genomics and molecular technologies has provided better insights into genetic architecture and patterns of heterotic gene pools. Development of whole-genome prediction models incorporating heterotic gene pool models, mapped traits and markers have the potential to take heterosis breeding to a new level in pearl millet. This review discusses advances and prospects in various fronts of heterosis for pearl millet.

Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants

Heterosis, or hybrid vigour, is said to occur when F1 individuals exhibit increased performance for a number of traits compared to their parental lines. Improved traits can include increased size, better yield, faster development and a higher tolerance to pathogens or adverse conditions. The molecular basis for the phenomenon remains disputed, despite many decades of theorising and experimentation. In this study, we add a genetics layer to a constraint-based model of plant (Arabidopsis) primary metabolism and show that we can realistically reproduce and quantify heterosis in a highly complex trait (the rate of biomass production). The results demonstrate that additive effects coupled to the complex patterns of epistasis generated by a large metabolic network are sufficient to explain most or all the heterosis seen in typical F1 hybrids. Such models provide a simple approach to exploring and understanding heterosis and should assist in designing breeding strategies to exploit this phenomenon in the future.

Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype-by-environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F₁ hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele-specific expression (ASE) in the F₁ hybrid to the allelic expression in both parental lines, respectively, 3005 genes in leaf and 2857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types of factors. A total of 328 genes in leaf and 113 in fruit exhibited significant ASE-by-watering regime interaction, among which ~80% presented trans-by-watering regime interaction, suggesting a response to water deficit mediated through a majority of trans-acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 recombinant inbred lines (RILs) and identified 163 expression quantitative trait loci (eQTLs) mostly confirming the divergences identified by ASE. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.

Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems

Heterosis or hybrid vigor is a phenomenon where hybrid progeny have superior performance compared to their parental inbred lines. This is important in the use of F₁ hybrid cultivars in many crops and vegetables. However, the molecular mechanism of heterosis is not clearly understood. Gene interactions between the two genomes such as dominance, overdominance, and epistasis have been suggested to explain the increased biomass and yield. Genetic analyses of F₁ hybrids in maize, rice, and canola have defined a large number of quantitative trait loci, which may contribute to heterosis. Recent molecular analyses of transcriptomes together with reference to the epigenome of the parents and hybrids have begun to uncover new facts about the generation of heterosis. These include the identification of gene expression changes in hybrids, which may be important for heterosis, the role of epigenetic processes in heterosis, and the development of stable high yielding lines.

Accumulation Profiles of Embryonic Salt-Soluble Proteins in Maize Hybrids and Parental Lines Indicate Matroclinous Inheritance: A Proteomic Analysis

Maize is one of the most widely cultivated crops. It accumulates a large quantity of seed storage proteins, which are important for seed development and germination, and contribute to the nutritional quality of seeds. Based on solubility, the storage proteins are divided into albumins (water-soluble), globulins (salt-soluble), prolamins (alcohol-soluble), and glutelins (acid- or alkali-soluble). Maize hybrids are cultivated due to the superior performance of F₁ hybrids than that of their parents, a phenomenon known as heterosis. However, the accumulation patterns of seed storage proteins in maize embryos between the hybrids and their parental inbred lines have not been compared. In the present study, two elite inbred lines of China, Zheng 58 and Chang 7-2, and their reciprocal hybrids (Zheng 58 × Chang 7-2 and Chang 7-2 × Zheng 58) were used to explore parental influences on the accumulation patterns of seed storage proteins in maize embryos. For this purpose, we focused on seed salt-soluble proteins (SSPs) in our experiments. The SSPs were selectively extracted from maize mature embryos after extensive removal of water-soluble albumin and separated using two-dimensional gel electrophoresis (2-DE), followed by mass spectrometry analysis. Our results indicated that the 2-DE SSP profiles of hybrids closely resembled those of their maternal parent rather than the paternal parent. In other words, 2-DE SSP profiles of Zheng 58 × Chang 7-2 were more similar those of Zheng 58 whereas such profiles of Chang 7-2 × Zheng 58 were more similar to those of Chang 7-2 although the 2-DE profiles of all four maize types were quite similar. In total, 12 relatively abundant SSPs spots representing five kinds of proteins were identified, of which nine protein spots displayed non-additive accumulation in at least one hybrid. This study provided additional data on dominance and partial dominance effects on maize hybrids embryos. Besides, earlier studies on accumulation profiles of globulin-1 (also known as vicilin), which is one of the most abundant globulins in maize embryos, also support the above results. This study would be helpful in revealing the mechanisms underlying SSPs accumulation patterns in the hybrids.

Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field

Heterosis has been extensively exploited for yield gain in maize (Zea mays L.). Here we conducted a comparative metabolomics-based analysis of young roots from in vitro germinating seedlings and from leaves of field-grown plants in a panel of inbred lines from the Dent and Flint heterotic patterns as well as selected F₁ hybrids. We found that metabolite levels in hybrids were more robust than in inbred lines. Using state-of-the-art modeling techniques, the most robust metabolites from roots and leaves explained up to 37 and 44% of the variance in the biomass from plants grown in two distinct field trials. In addition, a correlation-based analysis highlighted the trade-off between defense-related metabolites and hybrid performance. Therefore, our findings demonstrated the potential of metabolic profiles from young maize roots grown under tightly controlled conditions to predict hybrid performance in multiple field trials, thus bridging the greenhouse-field gap.

Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour

Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non-additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non-additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.

Comparative Study on the Transcriptome of Maize Mature Embryos from Two China Elite Hybrids Zhengdan958 and Anyu5

Zhengdan958 and Anyu5 are two elite maize hybrids of China, which manifest similar paternal lines (Chang7-2) but different maternal lines (Zheng58 and Ye478). Zhengdan958 has a 10–15% yield advantage over Anyu5. In this study, we applied digital gene expression technology to analyze transcriptomes of mature embryos from the two hybrids and their parents, aimed to investigate molecular mechanism of heterosis and genetic effects of maternal lines. Results showed that 71.66% and 49.70% of differentially expressed genes exhibited non-additive expression in Zhengdan958 and Anyu5, respectively. The number of non-additive genes involved in abiotic and biotic stress responses in Zhengdan958 was higher than that in Anyu5, which was in agreement with their phenotypic performance. Furthermore, common over-dominance and under-dominance genes (137 and 162, respectively) between the two hybrids focused on plant development and abiotic stress response. Zhengdan958 contained 97 maternal expression-level dominance (maternal-ELD) genes, and the number was higher than that of Anyu5 (45). Common up-regulated maternal-ELD genes were significantly enriched in meristem and shoot development while common down-regulated maternal-ELD genes were involved in pyruvate metabolic process, negative regulation of catalytic activity and response to stress. Therefore, non-additive genes mainly contribute to heterosis in Zhengdan958, including many genes for plant development, abiotic and biotic stress responses. Maternal effects may play important roles in maize heterosis.

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

BACKGROUND

Heterosis 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.

RESULTS

We 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.

CONCLUSIONS

In 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.

Ectopic expression of a maize hybrid up-regulated gene, ErbB-3 binding Protein 1 (ZmEBP1), increases organ size by promoting cell proliferation in Arabidopsis

The alteration of gene expression in hybrids may be an important factor promoting phenotypic variation and plasticity. To provide insight into the underlying molecular basis of maize heterosis in terms of the kernel number per ear, we established DGE profiles for the immature ears of maize hybrid Zong3/87-1 and its parental lines at the floral organ differentiation stage. Among 4,337 identified differentially expressed genes, 4,021 (92%) exhibited nonadditive expression patterns in the hybrid. Notably, the maize homolog of Arabidopsis EBP1, designated ZmEBP1, displayed an overdominant expression pattern in the Zong3/87-1 hybrid. Moreover, the results of qRT-PCR revealed that the ZmEBP1 gene was upregulated in the immature ears of the reciprocal hybrids Zong3/87-1 and 87-1/Zong3 at different developmental stages. Additionally, ectopic expression of ZmEBP1 in Arabidopsis increased organ size, which was mainly attributed to an increase in cell numbers, rather than cell size. Considering all of these findings together, we speculate that upregulation of ZmEBP1 in maize hybrids may accelerate cell proliferation and promote ear development.

Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana

Heterosis is the phenomenon whereby hybrid offspring of genetically divergent parents display superior characteristics compared with their parents. Although hybridity and polyploidy can influence heterosis in hybrid plants, the differential contributions of hybridity vs polyploidy to heterosis effects remain unknown. To address this question, we investigated heterosis effects on rosette size and growth rate of 88 distinct F1 lines of Arabidopsis thaliana consisting of diploids, reciprocal triploids and tetraploids in isogenic and hybrid genetic contexts. 'Heterosis without hybridity' effects on plant size can be generated in genetically isogenic F1 triploid plants. Paternal genome excess F1 triploids display positive heterosis, whereas maternal genome excess F1 s display negative heterosis effects. Paternal genome dosage increases plant size in F1 hybrid triploid plants by, on average, 57% (in contrast with 35% increase displayed by F1 diploid hybrids). Such effects probably derive from differential seed size, as the growth rate of triploids was similar to diploids. Tetraploid plants display a lower growth rate compared with other ploidies, whereas hybrids display increased early stage growth rate. By disaggregating heterosis effects caused by hybridity vs genome dosage, we advance our understanding of heterosis in plants and facilitate novel paternal genome dosage-based strategies to enhance heterosis effects in crop plants.

Hierarchical additive effects on heterosis in rice (Oryza sativa L.)

Exploitation of heterosis in crops has contributed greatly to improvement in global food and energy production. In spite of the pervasive importance of heterosis, a complete understanding of its mechanisms has remained elusive. In this study, a small test-crossed rice population was constructed to investigate the formation mechanism of heterosis for 13 traits. The results of the relative mid-parent heterosis and modes of inheritance of all investigated traits demonstrated that additive effects were the foundation of heterosis for complex traits in a hierarchical structure, and multiplicative interactions among the component traits were the framework of heterosis in complex traits. Furthermore, new balances between unit traits and related component traits provided hybrids with the opportunity to achieve an optimal degree of heterosis for complex traits. This study dissected heterosis of both reproductive and vegetative traits from the perspective of hierarchical structure for the first time. Additive multiplicative interactions of component traits were proven to be the origin of heterosis in complex traits. Meanwhile, more attention should be paid to component traits, rather than complex traits, in the process of revealing the mechanism of heterosis.

Intraspecific Arabidopsis hybrids show different patterns of heterosis despite the close relatedness of the parental genomes

Heterosis is important for agriculture; however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development.

Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid

Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosis. To determine the parental contributions and their regulation during maize ear-development-genesis, we analyzed genome-wide digital gene expression profiles in two maize elite inbred lines (B73 and Mo17) and their F₁ hybrid using deep sequencing technology. Our analysis revealed 17,128 genes expressed in these three genotypes and 22,789 genes expressed collectively in the present study. Approximately 38% of the genes were differentially expressed in early maize ear inflorescences from heterotic cross, including many transcription factor genes and some presence/absence variations (PAVs) genes, and exhibited multiple modes of gene action. These different genes showing differential expression patterns were mainly enriched in five cellular component categories (organelle, cell, cell part, organelle part and macromolecular complex), five molecular function categories (structural molecule activity, binding, transporter activity, nucleic acid binding transcription factor activity and catalytic activity), and eight biological process categories (cellular process, metabolic process, biological regulation, regulation of biological process, establishment of localization, cellular component organization or biogenesis, response to stimulus and localization). Additionally, a significant number of genes were expressed in only one inbred line or absent in both inbred lines. Comparison of the differences of modes of gene action between previous studies and the present study revealed only a small number of different genes had the same modes of gene action in both maize seedlings and ear inflorescences. This might be an indication that in different tissues or developmental stages, different global expression patterns prevail, which might nevertheless be related to heterosis. Our results support the hypotheses that multiple molecular mechanisms (dominance and overdominance modes) contribute to heterosis.

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

Background

Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.

Results

Here, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.

Conclusions

These results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.

Progress toward understanding heterosis in crop plants

Although heterosis, or hybrid vigor, is widely exploited in agriculture, a complete description of its molecular underpinnings has remained elusive despite extensive investigation. It appears that there is not a single, simple explanation for heterosis. Instead, it is likely that heterosis arises in crosses between genetically distinct individuals as a result of a diversity of mechanisms. Heterosis generally results from the action of multiple loci, and different loci affect heterosis for different traits and in different hybrids. Hence, multigene models are likely to prove most informative for understanding heterosis. Complementation of allelic variation, as well as complementation of variation in gene content and gene expression patterns, is likely to be an important contributor to heterosis. Epigenetic variation has the potential to interact in hybrid genotypes via novel mechanisms. Several other intriguing hypotheses are also under investigation. In crops, heterosis must be considered within the context of the genomic impacts of prior selection for agronomic traits.

Heterosis: emerging ideas about hybrid vigour

Perceived by Charles Darwin in many vegetable plants and rediscovered by George H Shull and Edward M East in maize, heterosis or hybrid vigour is one of the most widely utilized phenomena, not only in agriculture but also in animal breeding. Although, numerous studies have been carried out to understand its genetic and/or molecular basis in the past 100 years, our knowledge of the underlying molecular processes that results in hybrid vigour can best be defined as superficial. Even after century long deliberations, there is no consensus on the relative/individual contribution of the genetic/epigenetic factors in the manifestation of heterosis. However, with the recent advancements in functional genomics, transcriptomics, proteomics, and metabolomics-related technologies, the riddle of heterosis is being reinvestigated by adopting systems-level approaches to understand the underlying molecular mechanisms. A number of intriguing hypotheses are converging towards the idea of a cumulative positive effect of the differential expression of a variety of genes, on one or several yield-affecting metabolic pathways or overall energy-use efficiency, as the underlying mechanism for the manifestation of heterosis. Presented here is a brief account of clues gathered from various investigative approaches targeted towards better scientific understanding of this process.

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Typically, F₁-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ∼10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome.

Specific changes in total and mitochondrial proteomes are associated with higher levels of heterosis in maize hybrids

The phenomenon of hybrid vigor (heterosis) has long been harnessed by plant breeders to improve world food production. However, the changes that are essential for heterotic responses and the mechanisms responsible for heterosis remain undefined. Large increases in biomass and yield in high-heterosis hybrids suggest that alterations in bioenergetic processes may contribute to heterosis. Progeny from crosses between various inbred lines vary in the extent of vigor observed. Field-grown maize F₁ hybrids that consistently exhibited either low or high heterosis across a variety of environments were examined for changes in proteins that may be correlated with increased plant vigor and yield. Unpollinated ears at the time of flowering (ear shoots) were selected for the studies because they are metabolically active, rich in mitochondria, and the sizes of the ears are diagnostic of yield heterosis. Total protein and mitochondrial proteomes were compared among low- and higher-heterosis hybrids. Two-dimensional difference gel electrophoresis was used to identify allelic and/or isoform differences linked to heterosis. Identification of differentially regulated spots by mass spectrometry revealed proteins involved in stress responses as well as primary carbon and protein metabolism. Many of these proteins were identified in multiple spots, but analysis of their abundances by label-free mass spectrometry suggested that most of the expression differences were due to isoform variation rather than overall protein amount. Thus, our proteomics studies suggest that expression of specific alleles and/or post-translational modification of specific proteins correlate with higher levels of heterosis.

Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids

Heterosis-associated cellular and molecular processes were analyzed in seeds and seedlings of Arabidopsis thaliana accessions Col-0 and C24 and their heterotic hybrids. Microscopic examination revealed no advantages in terms of hybrid mature embryo organ sizes or cell numbers. Increased cotyledon sizes were detectable 4 days after sowing. Growth heterosis results from elevated cell sizes and numbers, and is well established at 10 days after sowing. The relative growth rates of hybrid seedlings were most enhanced between 3 and 4 days after sowing. Global metabolite profiling and targeted fatty acid analysis revealed maternal inheritance patterns for a large proportion of metabolites in the very early stages. During developmental progression, the distribution shifts to dominant, intermediate and heterotic patterns, with most changes occurring between 4 and 6 days after sowing. The highest incidence of heterotic patterns coincides with establishment of size differences at 4 days after sowing. In contrast, overall transcript patterns at 4, 6 and 10 days after sowing are characterized by intermediate to dominant patterns, with parental transcript levels showing the largest differences. Overall, the results suggest that, during early developmental stages, intermediate gene expression and higher metabolic activity in the hybrids compared to the parents lead to better resource efficiency, and therefore enhanced performance in the hybrids.

MicroRNA transcriptomic analysis of heterosis during maize seed germination

Heterosis has been utilized widely in the breeding of maize and other crops, and plays an important role in increasing yield, improving quality and enhancing stresses resistance, but the molecular mechanism responsible for heterosis is far from clear. To illustrate whether miRNA-dependent gene regulation is responsible for heterosis during maize germination, a deep-sequencing technique was applied to germinating embryos of a maize hybrid, Yuyu22, which is cultivated widely in China and its parental inbred lines, Yu87-1 and Zong3. The target genes of several miRNAs showing significant expression in the hybrid and parental lines were predicted and tested using real-time PCR. A total of 107 conserved maize miRNAs were co-detected in the hybrid and parental lines. Most of these miRNAs were expressed non-additively in the hybrid compared to its parental lines. These results indicated that miRNAs might participate in heterosis during maize germination and exert an influence via the decay of their target genes. Novel miRNAs were predicted follow a rigorous criterion and only the miRNAs detected in all three samples were treated as a novel maize miRNA. In total, 34 miRNAs belonged to 20 miRNA families were predicted in germinating maize seeds. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid showed higher embryo germination vigor compared to its parental lines.

Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis

Defining the contributions and interactions of paternal and maternal genomes during embryo development is critical to understand the fundamental processes involved in hybrid vigor, hybrid sterility, and reproductive isolation. To determine the parental contributions and their regulation during Arabidopsis embryogenesis, we combined deep-sequencing-based RNA profiling and genetic analyses. At the 2-4 cell stage there is a strong, genome-wide dominance of maternal transcripts, although transcripts are contributed by both parental genomes. At the globular stage the relative paternal contribution is higher, largely due to a gradual activation of the paternal genome. We identified two antagonistic maternal pathways that control these parental contributions. Paternal alleles are initially downregulated by the chromatin siRNA pathway, linked to DNA and histone methylation, whereas transcriptional activation requires maternal activity of the histone chaperone complex CAF1. Our results define maternal epigenetic pathways controlling the parental contributions in plant embryos, which are distinct from those regulating genomic imprinting.

A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding

Hybrids between genetically diverse varieties display enhanced growth, and increased total biomass, stress resistance and grain yield. Gene expression and metabolic studies in maize, rice and other species suggest that protein metabolism plays a role in the growth differences between hybrids and inbreds. Single trait heterosis can be explained by the existing theories of dominance, overdominance and epistasis. General multigenic heterosis is observed in a wide variety of different species and is likely to share a common underlying biological mechanism. This review presents a model to explain differences in growth and yield caused by general multigenic heterosis. The model describes multigenic heterosis in terms of energy-use efficiency and faster cell cycle progression where hybrids have more efficient growth than inbreds because of differences in protein metabolism. The proposed model is consistent with the observed variation of gene expression in different pairs of inbred lines and hybrid offspring as well as growth differences in polyploids and aneuploids. It also suggests an approach to enhance yield gains in both hybrid and inbred crops via the creation of an appropriate computational analysis pipeline coupled to an efficient molecular breeding program.

Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development

Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.

Heterotic patterns of sugar and amino acid components in developing maize kernels

Heterosis is the superior performance of hybrids over their inbred parents. Despite its importance, little is known about the genetic and molecular basis of this phenomenon. Heterosis has been extensively exploited in plant breeding, particularly in maize (Zea mays, L.), and is well documented in the B73 and Mo17 maize inbred lines and their F1 hybrids. In this study, we determined the dry matter, the levels of starch and protein components and a total of 24 low-molecular weight metabolites including sugars, sugar-phosphates, and free amino acids, in developing maize kernels between 8 and 30 days post-pollination (DPP) of the hybrid B73 x Mo17 and its parental lines. The tissue specificity of amino acid and protein content was investigated between 16 and 30 DPP. Key observations include: (1) most of the significant differences in the investigated tissue types occurred between Mo17 and the other two genotypes; (2) heterosis of dry matter and metabolite content was detectable from the early phase of kernel development onwards; (3) the majority of metabolites exhibited an additive pattern. Nearly 10% of the metabolites exhibited nonadditive effects such as overdominance, underdominance, and high-parent and low-parent dominance; (4) The metabolite composition was remarkably dependent on kernel age, and this large developmental effect could possibly mask genotypic differences; (5) the metabolite profiles and the heterotic patterns are specific for endosperm and embryo. Our findings illustrate the power of metabolomics to characterize heterotic maize lines and suggest that the metabolite composition is a potential marker in the context of heterosis research.

Background correction of two-colour cDNA microarray data using spatial smoothing methods

The analysis of two-colour cDNA microarray data usually involves subtracting background values from foreground values prior to normalization and further analysis. This approach has the advantage of reducing bias and the disadvantage of blowing up the variance of lower abundant spots. Whenever background subtraction is considered, it implicitly assumes locally constant background values. In practice, this assumption is often not met, which casts doubts on the usefulness of simple background subtraction. In order to improve background correction, we propose local background smoothing within the pre-processing pipeline of cDNA microarray data prior to background correction. For this purpose, we employ a geostatistical framework with ordinary kriging using both isotropic and anisotropic models of spatial correlation and 2-D locally weighted regression. We show that application of local background smoothing prior to background correction is beneficial in comparison to using raw background estimates. This is done using data of a self-versus-self experiment in Arabidopsis where subsets of differentially expressed genes were simulated. Using locally smoothed background values in conjunction with existing background correction methods increases the power, increases the accuracy and decreases the number of false positive results.