Molecular Mechanism Of Heterosis Research Articles

Integrating Dynamic 3D Chromatin Architecture and Gene Expression Alterations Reveal Heterosis in Brassica rapa.

Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F1) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F1. Further study revealed that the DEGs detected in the F1 and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F1 plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F1 had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F1. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa.

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean.

Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.

Genetic variation between a hybrid abalone and its parents (Haliotis discus hannai ♀ and H. fulgens ♂) based on 5S rDNA gene and genomic resequencing

Abalones are a group of economically important species of mollusks that represent a source of high-quality protein. China accounts for 90% of the world's abalone production, and make a significant contribution to the aquaculture industry's economic value. With the increasing scale of abalone farming, problems such as the degradation of germplasm resources and a reduced ability to resist environmental changes and stresses have become increasingly prominent. The hybrid breeding technique has significantly ameliorated this situation. The distant hybrid species H. discus hannai ♀ × H. fulgens ♂ (the Lvpan abalone) shows significant heterosis in terms of growth and stress resistance. However, our knowledge of the cytogenetics and molecular mechanisms of heterosis in the hybrid abalone remains limited. In this study, we found significant non-transcribed spacer (NTS) variation of 5S rDNA gene among H. discus hannai, H. fulgens, and the Lvpan abalone, with five, two, and four types of NTSs identified, respectively. These NTSs exhibited genomic polymorphisms within and between species, making them reliable markers for species identification. Furthermore, the sequence alignment of NTSs and genomic resequencing analysis indicated that the hybrid abalone was biased toward H. discus hannai, suggesting a maternal effect. Moreover, numerous mutation sites that were identified only in the hybrid abalone potentially contributed to heterosis. This study provides a valuable molecular data reference for future research on distant hybridization and contributes to a better understanding of the molecular mechanisms underlying heterosis in mollusks.

Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel

Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.

Molecular Genetic Mechanisms of Heterosis in Sugarcane Cultivars Using a Comparative Transcriptome Analysis of Hybrids and Ancestral Parents

Modern sugarcane cultivars (Saccharum spp. hybrids) are the major contributors to sucrose and bioenergy in the world. The global changes in gene expression and the molecular mechanism of heterosis between modern sugarcane hybrids and their parents remain to be elucidated. In this study, we performed a comparative transcriptome analysis between hybrids and their parents using the Illumina RNA-Seq method to understand the differences in transcript expression after hybridization. The results show that (1) introduction of the S. spontaneum lineage resulted in significant upregulation of biotic and abiotic stress resistance genes in S. hybrids, including hexokinase (HXK) genes, pathogenesis-related protein (PR1) genes, coronatine-insensitive protein (COI-1), jasmonate ZIM domain-containing protein (JAZ) genes, and serine/threonine protein kinase 2 (SnRK2) genes. (2) Transgressive genes in hybrids were mainly concentrated in the synthesis pathways of biotin and vitamin B6, helping establish advantages in terms of stress resistance, antioxidant activity, and growth. (3) Glutathione-S-transferase (GST) was likely to enhance stress resistance in hybrids, and corresponding genes were key positive selection genes in processes, including round-robin selection and other adaptations. In this study, we propose explanations for heterosis in sugarcane hybrids from a transcriptomic perspective, in addition to identifying candidate genes to aid in the improvement of sugarcane cultivars.

Changes in Alternative Splicing Revealed Special Metabolic Pathways Related to Heterosis of Heading Chinese Cabbage

As an important genetic improvement technique in current production practice, heterosis is widely used to enhance the productive traits of hybrid progeny from their parents. Alternative splicing (AS) analysis can be used as a method for exploring the molecular manifestations of heterosis. In our research, 16 hybrids and their parents were utilized to analyze the heterosis performance and AS events. Statistics of plant gross weight (PGW) showed that these hybrids had prominent heterosis, with the mid-parent heterosis values (MPV) ranging from 15.69% to 233.98%. Through pairwise comparison among the female parent, male parent, and hybrid, there were 2980–3205 AS events in each combination, with intron retention being the most common type followed by alternate 3’ splice site, alternative 5’ splice site, skipped exon, and mutually exclusive exon.There were 263–409 differential AS genes (DASGs) between the female parent and the hybrid, and 234–425 DASGs between the male parent and the hybrid in cross combinations. The DASGs were significantly enriched in 33 metabolic pathways in 16 cross combinations, and DASGs of different cross combinations were enriched in different metabolic pathways. Moreover, 76 DASGs in the strong heterosis combinations were identified and significantly enriched in the metabolic pathways related to amino acid metabolism. Further analysis revealed that most of these DASGs in amino acid metabolism were expressed differently in strong heterosis combinations. In addition, the expression levels of BraA06g014310.3C and BraA03g041700.3C in amino acid metabolism significantly correlated with PGW. These results could provide an index for future studies of the genetic and molecular mechanism of heterosis in hybrids.

Dominant complementation of biological pathways in maize hybrid lines is associated with heterosis.

Allele-specific expressed genes (ASEGs) are widespread in maize hybrid lines and play important roles of complementation of biological pathways in heterosis. Heterosis (hybrid vigor) is an important phenomenon with both theoretical and practical value. However, our understanding of the genetic and molecular mechanisms behind heterosis is still limited. Here, we analyzed a comprehensive dataset of maize (Zea mays L.), including RNA-seq data from three hybrid-parent triplets (HPTs) and acetylated protein data from one HPT. The gene expression patterns exhibited extensive variation between the hybrids and their parents, and a substantial number of allele-specific expressed genes (ASEGs) were identified in the hybrids. Notably, ASEGs from different HPTs were significantly enriched in various conserved pathways. The parental alleles of ASEGs with fewer deleterious single-nucleotide polymorphisms were more likely to be expressed in hybrid lines than other parental alleles. ASEGs were mainly enriched in the functional gene ontology terms protein biosynthesis, photosynthesis, and metabolism. In addition, the ASEGs across the three HPTs were involved in key photosynthetic pathways and might enhance the photosynthetic efficiency of the hybrids. These findings suggest that ASEGs involved in complementary biological pathways in maize hybrids contribute to heterosis, shedding new light on the molecular mechanism of heterosis.

Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage

BackgroundHeterosis is widely used in many crops and is important for global food safety, and maize is one of the most successful crops to take advantage of heterosis. Gene expression patterns control the development of the maize ear, but the mechanisms by which heterosis affects transcriptional-level control are not fully understood.ResultsIn this study, we sampled ear inflorescence meristems (IMs) from the single-segment substitution maize (Zea mays) line lx9801hlEW2b, which contains the heterotic locus hlEW2b associated with ear width, as well as the receptor parent lx9801, the test parent Zheng58, and their corresponding hybrids Zheng58 × lx9801hlEW2b (HY) and Zheng58 × lx9801 (CK). After RNA sequencing and transcriptomic analysis, 2531 unique differentially expressed genes (DEGs) were identified between the two hybrids (HY vs. CK). Our results showed that approximately 64% and 48% of DEGs exhibited additive expression in HY and CK, whereas the other genes displayed a non-additive expression pattern. The DEGs were significantly enriched in GO functional categories of multiple metabolic processes, plant organ morphogenesis, and hormone regulation. These essential processes are potentially associated with heterosis performance during the maize ear developmental stage. In particular, 125 and 100 DEGs from hybrids with allele-specific expression (ASE) were specifically identified in HY and CK, respectively. Comparison between the two hybrids suggested that ASE genes were involved in different development-related processes that may lead to the hybrid vigor phenotype during maize ear development. In addition, several critical genes involved in auxin metabolism and IM development were differentially expressed between the hybrids and showed various expression patterns (additive, non-additive, and ASE). Changes in the expression levels of these genes may lead to differences in auxin homeostasis in the IM, affecting the transcription of core genes such as WUS that control IM development.ConclusionsOur research suggests that additive, non-additive, and allele-specific expression patterns may fine-tune the expression of crucial DEGs that modulate carbohydrate and protein metabolic processes, nitrogen assimilation, and auxin metabolism to optimal levels, and these transcriptional changes may play important roles in maize ear heterosis. The results provide new information that increases our understanding of the relationship between transcriptional variation and heterosis during maize ear development, which may be helpful for clarifying the genetic and molecular mechanisms of heterosis.

Comparative Transcriptomic Analysis of Gene Expression Inheritance Patterns Associated with Cabbage Head Heterosis

The molecular mechanism of heterosis or hybrid vigor, where F1 hybrids of genetically diverse parents show superior traits compared to their parents, is not well understood. Here, we studied the molecular regulation of heterosis in four F1 cabbage hybrids that showed heterosis for several horticultural traits, including head size and weight. To examine the molecular mechanisms, we performed a global transcriptome profiling in the hybrids and their parents by RNA sequencing. The proportion of genetic variations detected as single nucleotide polymorphisms and small insertion–deletions as well as the numbers of differentially expressed genes indicated a larger role of the female parent than the male parent in the genetic divergence of the hybrids. More than 86% of hybrid gene expressions were non-additive. More than 81% of the genes showing divergent expressions showed dominant inheritance, and more than 56% of these exhibited maternal expression dominance. Gene expression regulation by cis-regulatory mechanisms appears to mediate most of the gene expression divergence in the hybrids; however, trans-regulatory factors appear to have a higher effect compared to cis-regulatory factors on parental expression divergence. These observations bring new insights into the molecular mechanisms of heterosis during the cabbage head development.

Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules.

Simple SummaryMules have better and greater muscle endurance than hinnies and their parents. However, the molecular mechanisms underlying heterosis in their muscles are still much less understood. In this study, we conducted comparative transcriptome and alternative splicing analysis on the heterosis mechanism of muscular endurance in mules. Our results showed that 8 genes were significantly enriched in the “muscle contraction” pathway. In addition, 68% of the genes with alternative splicing events from the mule muscle tissue were validated by the long transcript reads generated from PacBio sequencing platform. Our findings provide a research foundation for studying the genetic basis of heterosis in mules.Heterosis has been widely exploited in animal and plant breeding programs to enhance the productive traits of hybrid progeny from two breeds or species. However, its underlying genetic mechanisms remain enigmatic. Transcriptome profiling analysis can be used as a method for exploring the mechanism of heterosis. Here, we performed genome-wide gene expression and alternative splicing (AS) analyses in different tissues (muscle, brain, and skin) from crosses between donkeys and horses. Our results indicated that 86.1% of the differentially expressed genes (DEGs) and 87.2% of the differential alternative splicing (DAS) genes showed over-dominance and dominance in muscle. Further analysis showed that the “muscle contraction” pathway was significantly enriched for both the DEGs and DAS genes in mule muscle tissue. Taken together, these DEGs and DAS genes could provide an index for future studies of the genetic and molecular mechanism of heterosis in the hybrids of donkey and horse.

Proteomic profiling of foxtail millet hybrid Zhangzagu10 and its parent lines using iTRAQ-based technique

Heterosis had been increasingly applied in crop production for nearly a century, but the molecular basis of it was poorly understood especially in foxtail millet (Setaria italica). Zhangzagu10 which derived from two-line hybrid breeding system has the characters of ultra-high yield, good stability and extensive disease and lodging resistance. To gain a better understanding of the molecular basis of S.italica heterosis, the isobaric tags for relative and absolute quantification based quantitative proteomic analyses was performed between S.italica hybrid Zhangzagu10 and it parents (male parent Zhangzagu10fu and female parent A2). A total of 4015 proteins were detected, among which 610/276 differentially expressed proteins (DEPs) between Zhangzagu10 and the female/male parent, respectively. The cluster analysis showed that the DEPs expression profiles of Zhangzagu10 were closer to those of the male parent. GO functional classification divided the DEPs into three functional categories (Cellular component, Biological process and Molecular function) and 26 subfamilies, among which three subfamilies had 100% difference between Zhangzagu10 and its parents. KEGG metabolic pathway exhibited significant enrichment of DEPs in Metabolic pathways, Carbon fixation in photosynthetic organisms and Photosynthesis. qRT-PCR verification confirmed the differential expression data and revealed that the expression level of 3 selected genes (such as peroxidase 5-like,G-type lectin S-receptor-like serine/threonine-protein kinase SD2-5,two-on-two hemoglobin-3, etc.) was higher in Zhangzagu10 than that in its male parent. The expression level of 7 selected genes (such as peroxidase 64-like, cysteine-rich receptor-like protein kinase 45, indole-3-acetaldehyde oxidase, etc.) was higher in Zhangzagu10 than that in its male parent, but significantly lower than that in A2. Thus, A2 can potentially optimise the agricultural qualities of Zhangzagu10. Taken together, we hope that this study provides valuable information for the further utilisation and study on the molecular mechanisms of heterosis in hybrid millet.

Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis

Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.

Exploring the molecular basis of heterosis for plant breeding.

Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

Proteomic analysis of Zhangzagu3 (Setaria italica) and its parents based on iTRAQ technique

Zhangzagu3, derived from Zhangzagu3fu and A2 (photoperiod- and thermo-sensitive genic male-sterile line) is well-known for its strong adaptability, good stability, disease, and lodging resistance. To evaluate the parental contributions to its elite traits, isobaric tags for relative and absolute quantitation (iTRAQ) and mass spectrometry (MS) were used to analyze the protein expression profile of these three lines. Enrichment analysis of differentially expressed proteins (DEPs) was performed through GO term and KEGG pathway. A total of 4015 proteins were detected, among which 504/390 DEPs between Zhangzagu3 and the female/male parent, respectively. The cluster analysis using Cluster 3.0 showed that the DEP expression profiles of Zhangzagu3 were closer to those of the male parent. GO functional classification divided the DEPs into three functional categories (cellular component, biological process and molecular function) and 71 subfamilies, among which three subfamilies had 100% difference between Zhangzagu3 and its parents. KEGG metabolic pathway exhibited significant enrichment of differentially expressed genes (DEGs) in Carbon metabolism (mainly Carbon fixation, Glycolysis and Gluconeogenesis), Photosynthesis and Oxidative phosphorylation. qRT-PCR verification confirmed the differential expression data and revealed that the expression level of 17 selected genes (such as putative receptor-like protein kinase, copper chaperone for superoxide dismutase etc.) was higher in Zhangzagu3 than that in its male parent, but significantly lower than that in A2. Thus, A2 can potentially optimize the agricultural qualities of Zhangzagu3. Taken together, we hope that this study provides valuable information for the further utilization and study on the molecular mechanisms of heterosis in hybrid millet.AbbreviationsiTRAQisobaric tags for relative and absolute quantitationDEPsdifferentially expressed proteinsDEGsdifferentially expressed genesPMSFphenylmethanesulfonyl fluorideHEPES4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acidDTTdithiothreitolEDTAethylene diamine tetraacetic acidGOgene ontologyIAMiodoacetamideMSmass spectrometryKEGGKyoto Encyclopedia of Genes and GenomesPVPPpolyvinylpolypyrrolidoneHPLChigh performance liquid chromatographyTCAtrichloroacetic acidTEABtetraethylammonium bicarbonateACNacetonitrileHCDhigher collision energy dissociationFDRfalse discovery rateSDSsodium dodecyl sulphateqRT-PCRquantitative real-time polymerase chain reaction

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.

Role of DNA methylation in hybrid vigor in Arabidopsis thaliana

Hybrid vigor or heterosis refers to the superior performance of F1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.

Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement.

The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (AnAnCC genome), B. rapa (ArAr genome), and its hybrid F1 (AnArC genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.

Molecular mechanisms of heterosis in Arabidopsis intraspecific hybrids

Molecular mechanisms of heterosis in Arabidopsis intraspecific hybrids

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.