Enriched partial correlations in genome-wide gene expression profiles of hybrids (A. thaliana): a systems biological approach towards the molecular basis of heterosis

GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize

Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding. We analyzed plant height (PH), ear height (EH), and transcriptomic data from a maize hybrid population. Genome-wide association studies (GWASs) revealed that dominance effects of quantitative trait loci (QTLs) play a significant role in hybrid traits and mid-parent heterosis. By integrating GWAS, expression GWAS (eGWAS), and module eGWAS analysis, we prioritized six candidate heterotic genes underlying six QTLs, including one QTL that spans the bZIP29 gene. In the hybrid population, bZIP29 exhibits additive expression and dominance effects for both hybrid traits and mid-parent heterosis, with its favorable allele correlating positively with PH and EH. bZIP29 demonstrates dominance or over-dominance patterns in hybrids derived from crosses between transgenic and wild-type lines, contingent upon its expression. A tsCUT&Tag assay revealed that bZIP29 protein binds directly to a gene regulated by its associated expression QTL (eQTL) and six genes within expression modules governed by its associated module-eQTLs (meQTLs). Regulatory networks involving bZIP29 are more extensive in hybrid subpopulations than in the parental population. This study offers insights into key heterotic genes and networks that underpin the robust growth of hybrid maize.

GeneTrail: A Framework for the Analysis of High-Throughput Profiles

Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms. GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de.

Tomato fruit quality traits and metabolite content are affected by reciprocal crosses and heterosis

Heterosis occurs when the F1s outperform their parental lines for a trait. Reciprocal hybrids are obtained by changing the cross direction of parental genotypes. Both biological phenomena could affect the external and internal attributes of fleshy fruits. This work aimed to detect reciprocal effects and heterosis in tomato (Solanum lycopersicum) fruit quality traits and metabolite content. Twelve agronomic traits and 28 metabolites identified and estimated by 1H-NMR were evaluated in five cultivars grown in two environments. Given that the genotype component was more important than the phenotype, the traits were evaluated following a full diallel mating design among those cultivars, in a greenhouse. Hybrids showed a higher phenotypic diversity than parental lines. Interestingly, the metabolites, mainly amino acids, displayed more reciprocal effects and heterosis. Agronomic traits were more influenced by general combining ability (GCA) and metabolites by specific combining ability (SCA). Furthermore, the genetic distance between parental lines was not causally related to the occurrence of reciprocal effects or heterosis. Hybrids with heterosis and a high content of metabolites linked to tomato flavour and nutritious components were obtained. Our results highlight the impact of selecting a cultivar as male or female in a cross to enhance the variability of fruit attributes through hybrids as well as the possibility to exploit heterosis for fruit composition.

Transcriptome and Metabolite Profiling Reveal Novel Insights into Volatile Heterosis in the Tea Plant (Camellia Sinensis)

Tea aroma is a key indicator for evaluating tea quality. Although notable success in tea aroma improvement has been achieved with heterosis breeding technology, the molecular basis underlying heterosis remains largely unexplored. Thus, the present report studies the tea plant volatile heterosis using a high-throughput next-generation RNA-seq strategy and gas chromatography-mass spectrometry. Phenotypically, we found higher terpenoid volatile and green leaf volatile contents by gas chromatography-mass spectrometry in the F1 hybrids than in their parental lines. Volatile heterosis was obvious in both F1 hybrids. At the molecular level, the comparative transcriptomics analysis revealed that approximately 41% (9027 of 21,995) of the genes showed non-additive expression, whereas only 7.83% (1723 of 21,995) showed additive expression. Among the non-additive genes, 42.1% showed high parental dominance and 17.6% showed over-dominance. Among different expression genes with high parental dominance and over-dominance expression patterns, KEGG and GO analyses found that plant hormone signal transduction, tea plant physiological process related pathways and most pathways associated with tea tree volatiles were enriched. In addition, we identified multiple genes (CsDXS, CsAATC2, CsSPLA2, etc.) and transcription factors (CsMYB1, CsbHLH79, CsWRKY40, etc.) that played important roles in tea volatile heterosis. Based on transcriptome and metabolite profiling, we conclude that non-additive action plays a major role in tea volatile heterosis. Genes and transcription factors involved in tea volatiles showing over-dominance expression patterns can be considered candidate genes and provide novel clues for breeding high-volatile tea varieties.

A novel discovery of a long terminal repeat retrotransposon-induced hybrid weakness in rice

Hybrid weakness is a post-zygotic hybridization barrier frequently observed in plants, including rice. In this study, we describe the genomic variation among three temperate japonica rice (Oryza sativa ssp. japonica) varieties 'Aranghyangchalbyeo' ('CH7'), 'Sanghaehyangheolua' ('CH8') and 'Shinseonchalbyeo' ('CH9'), carrying different hybrid weakness genes. The reciprocal progeny obtained from crossing any two varieties displayed characteristic hybrid weakness traits. We mapped and cloned a new locus, Hwc3 (hybrid weakness 3), on chromosome 4. Sequence analysis identified that a long terminal repeat (LTR) retrotransposon was inserted into the promoter region of the Hwc3 gene in 'CH7'. A 4-kb DNA fragment from 'CH7' containing the Hwc3 gene with the inserted LTR retrotransposon was able to induce hybrid weakness in hybrids with 'CH8' plants carrying the Hwc1 gene by genetic complementation. We investigated the differential gene expression profile of F1 plants exhibiting hybrid weakness and detected that the genes associated with energy metabolism were significantly down-regulated compared with the parents. Based on our results, we propose that LTR retrotransposons could be a potential cause of hybrid weakness in intrasubspecific hybrids in japonica rice. Understanding the molecular mechanisms underlying intrasubspecific hybrid weakness is important for increasing our knowledge on reproductive isolation and could have significant implications for rice improvement and hybrid breeding.

Gibberellins Promote Brassinosteroids Action and Both Increase Heterosis for Plant Height in Maize (Zea mays L.)

Brassinosteroids (BRs) and Gibberellins (GAs) are two classes of plant hormones affecting plant height (PHT). Thus, manipulation of BR and GA levels or signaling enables optimization of crop grain and biomass yields. We established backcross (BC) families, selected for increased PHT, in two elite maize inbred backgrounds. Various exotic accessions used in the germplasm enhancement in maize project served as donors. BC1-derived doubled haploid lines in the same two elite maize inbred backgrounds established without selection for plant height were included for comparison. We conducted genome-wide association studies to explore the genetic control of PHT by BR and GA. In addition, we used BR and GA inhibitors to compare the relationship between PHT, BR, and GA in inbred lines and heterozygotes from a physiological and biological perspective. A total of 73 genomic loci were discovered to be associated with PHT, with seven co-localized with GA, and two co-localized with BR candidate genes. PHT determined in field trials was significantly correlated with seedling stage BR and GA inhibitor responses. However, this observation was only true for maize heterozygotes, not for inbred lines. Path analysis results suggest that heterozygosity increases GA levels, which in turn promote BR levels. Thus, at least part of heterosis for PHT in maize can be explained by increased GA and BR levels, and seedling stage hormone inhibitor response is promising to predict heterosis for PHT.

Bacterial metabolism in immediate response to nutritional perturbation with temporal and network view of metabolites

In this study, the initial propagation of metabolic perturbation in Escherichia coli was visualized to understand the dynamic characteristics of the metabolic pathways without the association of transcription alterations. E. coli cells were exposed to the sudden relief of glucose starvation, and time-dependent variances in metabolite balances were traced in the second scale. The acquired time-course data were represented by structural variations of the metabolite-metabolite correlation network. The initial correlation structure was altered immediately by the glucose pulse, followed by further structural variations within a few minutes. It was demonstrated that one metabolite temporally correlated with distinct metabolites with different timings, and such a behavior could imply a regulatory role for the metabolite in the metabolic network. Centrality analysis of the networks and partial correlation analysis indicated that preparation for growth and oxidative stress could be coupled as a structural property of the metabolic pathways.

A Boolean gene regulatory model of heterosis and speciation

BACKGROUND

Modelling genetic phenomena affecting biological traits is important for the development of agriculture as it allows breeders to predict the potential of breeding for certain traits. One such phenomenon is heterosis or hybrid vigor: crossing individuals from genetically distinct populations often results in improvements in quantitative traits, such as growth rate, biomass production and stress resistance. Heterosis has become a very useful tool in global agriculture, but its genetic basis remains controversial and its effects hard to predict. We have taken a computational approach to studying heterosis, developing a simulation of evolution, independent reassortment of alleles and hybridization of Gene Regulatory Networks (GRNs) in a Boolean framework. These artificial regulatory networks exhibit topological properties that reflect those observed in biology, and fitness is measured as the ability of a network to respond to external inputs in a pre-defined way.

RESULTS

Our model reproduced common experimental observations on heterosis using only biologically justified parameters, such as mutation rates. Hybrid vigor was observed and its extent was seen to increase as parental populations diverged, up until a point of sudden collapse of hybrid fitness. Thus, the model also describes a process akin to speciation due to genetic incompatibility of the separated populations. We also reproduce, for the first time in a model, the fact that hybrid vigor cannot easily be fixed by within a breeding line, currently an important limitation of the use of hybrid crops. The simulation allowed us to study the effects of three standard models for the genetic basis of heterosis: dominance, over-dominance, and epistasis.

CONCLUSION

This study describes the most detailed simulation of heterosis using gene regulatory networks to date and reproduces several phenomena associated with heterosis for the first time in a model. The level of detail in our model allows us to suggest possible warning signs of the impending collapse of hybrid vigor in breeding. In addition, the simulation provides a framework that can be extended to study other aspects of heterosis and alternative evolutionary scenarios.

Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides

Background

Plants with heterosis/hybrid vigor perform better than their parents in many traits. However, the biological mechanisms underlying heterosis remain unclear. To investigate the significance of DNA methylation to heterosis, a comprehensive analysis of whole-genome DNA methylome profiles of Populus deltoides cl.'55/65' and '10/17' parental lines and their intraspecific F1 hybrids lines was performed using methylated DNA immunoprecipitation (MeDIP) and high-throughput sequencing.

Results

Here, a total of 486.27 million reads were mapped to the reference genome of Populus trichocarpa, with an average unique mapping rate of 57.8%. The parents with similar genetic background had distinct DNA methylation levels. F1 hybrids with hybrid vigor possessed non-additive DNA methylation level (their levels were higher than mid-parent values). The DNA methylation levels in promoter and repetitive sequences and transposable element of better-parent F1 hybrids and parents and lower-parent F1 hybrids were different. Compared with the maternal parent, better-parent F1 hybrids had fewer hypermethylated genes and more hypomethylated ones. Compared with the paternal parent and lower-parent L1, better-parent F1 hybrids had more hypermethylated genes and fewer hypomethylated ones. The differentially methylated genes between better-parent F1 hybrids, the parents and lower-parent F1 hybrids were enriched in the categories metabolic processes, response to stress, binding, and catalytic activity, development, and involved in hormone biosynthesis, signaling pathway.

Conclusions

The methylation patterns of the parents both partially and dynamically passed onto their hybrids, and F1 hybrids has a non-additive mathylation level. A multidimensional process is involved in the formation of heterosis.

Genomic and epigenetic insights into the molecular bases of heterosis

Heterosis, also known as hybrid vigour, is widespread in plants and animals, but the molecular bases for this phenomenon remain elusive. Recent studies in hybrids and allopolyploids using transcriptomic, proteomic, metabolomic, epigenomic and systems biology approaches have provided new insights. Emerging genomic and epigenetic perspectives suggest that heterosis arises from allelic interactions between parental genomes, leading to altered programming of genes that promote the growth, stress tolerance and fitness of hybrids. For example, epigenetic modifications of key regulatory genes in hybrids and allopolyploids can alter complex regulatory networks of physiology and metabolism, thus modulating biomass and leading to heterosis. The conceptual advances could help to improve plant and animal productivity through the manipulation of heterosis.

Comparative proteomic analysis of embryos between a maize hybrid and its parental lines during early stages of seed germination

In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. It was observed that maize hybrid Zong3/87-1 exhibited an earlier onset or heterosis in radicle emergence. To get insights into the underlying mechanism of heterosis in radicle emergence, differential proteomic analysis between hybrid and its parental lines was performed. In total, the number of differentially expressed protein spots between hybrid and its parental lines in dry and 24 h imbibed seed embryos were 134 and 191, respectively, among which 47.01% (63/134) and 34.55% (66/191) protein spots displayed nonadditively expressed pattern. Remarkably, 54.55% of nonadditively accumulated proteins in 24 h imbibed seed embryos displayed above or equal to the level of the higher parent patterns. Moreover, 155 differentially expressed protein spots were identified, which were grouped into eight functional classes, including transcription & translation, energy & metabolism, signal transduction, disease & defense, storage protein, transposable element, cell growth & division and unclassified proteins. In addition, one of the upregulated proteins in F₁ hybrids was ZmACT2, a homolog of Arabidopsis thaliana ACT7 (AtACT7). Expressing ZmACT2 driven by the AtACT7 promoter partially complemented the low germination phenotype in the Atact7 mutant. These results indicated that hybridization between two parental lines can cause changes in the expression of a variety of proteins, and it is concluded that the altered pattern of gene expression at translational level in the hybrid may be responsible for the observed heterosis.

Pollen transcriptome analysis of Solanum tuberosum (2n = 4x = 48), S. demissum (2n = 6x = 72), and their reciprocal F1 hybrids

Pollen mRNAs were different in reciprocal F 1 hybrids, which were probably caused by a cytoplasm-nuclear chromosomal genes interaction. We have found reciprocal differences in crossability between F1 hybrids of Solanum tuberosum (T) and a Mexican wild potato species S. demissum (D). When the reciprocal hybrids were crossed as pollen parents with S. demissum, a significantly higher berry-setting rate was obtained in TD compared with DT. In this study, we performed a whole-genome transcript analysis of the pollen mRNA using a high-throughput sequencer. We obtained 12.6 billion bases that were aligned into 13,020 transcripts with 9,366 loci. All possible genetic modes were observed between the parents and their progeny, where over-dominance and under-recessive types were relatively frequent (15.7 and 15.3 %, respectively). We found that 59.1 % of transcripts were more abundant in TD and over fourfold higher transcription levels were found in 66 TD transcripts and three DT transcripts. A higher proportion of over-dominance and a lower proportion of under-recessive transcription types were also observed in TD. The percentage contributions of multiple transcripts at the same locus varied greatly and were transcribed differently between species. In the new allelic combinations created by hybridization, approximately three-fourth of the transcripts had intermediate percentage contributions between the parents but no differential transcription patterns were apparent between the reciprocal hybrids. A broad spectrum of functionally different nuclear genes was over-represented in TD pollen, some of which were directly related to pollen behavior. Since TD and DT pollen had the same composition of nuclear genes, a cytoplasm-nuclear chromosomal genes interaction is suggested for the cause of transcriptional and phenotypic differences between reciprocal hybrids.

Integration of a systems biological network analysis and QTL results for biomass heterosis in Arabidopsis thaliana

To contribute to a further insight into heterosis we applied an integrative analysis to a systems biological network approach and a quantitative genetics analysis towards biomass heterosis in early Arabidopsis thaliana development. The study was performed on the parental accessions C24 and Col-0 and the reciprocal crosses. In an over-representation analysis it was tested if the overlap between the resulting gene lists of the two approaches is significantly larger than expected by chance. Top ranked genes in the results list of the systems biological analysis were significantly over-represented in the heterotic QTL candidate regions for either hybrid as well as regarding mid-parent and best-parent heterosis. This suggests that not only a few but rather several genes that influence biomass heterosis are located within each heterotic QTL region. Furthermore, the overlapping resulting genes of the two integrated approaches were particularly enriched in biomass related pathways. A chromosome-wise over-representation analysis gave rise to the hypothesis that chromosomes number 2 and 4 probably carry a majority of the genes involved in biomass heterosis in the early development of Arabidopsis thaliana.

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.

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.

Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize

Grouping of germplasm and prediction of hybrid performance and heterosis are important applications in hybrid breeding programs. Gene expression analysis is a promising tool to achieve both tasks efficiently. Our objectives were to (1) investigate distance measures based on transcription profiles, (2) compare these with genetic distances based on AFLP markers, and (3) assess the suitability of transcriptome-based distances for grouping of germplasm and prediction of hybrid performance and heterosis in maize. We analyzed transcription profiles from seedlings of the 21 parental maize lines of a 7 x 14 factorial with a 46-k oligonucleotide array. The hybrid performance and heterosis of the 98 hybrids were assessed in field trials. In cluster and principal coordinate analyses for germplasm grouping, the transcriptome-based distances were as powerful as the genetic distances for separating flint from dent inbreds. Cross validation showed that prediction of hybrid performance with transcriptome-based distances using selected markers was more precise than earlier prediction models using DNA markers or general combining ability estimates using field data. Our results suggest that transcriptome-based prediction of hybrid performance and heterosis has a great potential to improve the efficiency of maize hybrid breeding programs.