Non-additive Expression Research Articles

Comparative transcriptomics analysis at the key stage of maize ear development dissect heterosis.

Important traits related to maize (Zea mays L.) grain yield, such as kernel row number, ear length, kernel number per row, are determined during the development of female inflorescence. There is a significant positive correlation between yield component and the activity of inflorescence meristem (IM). To find the key stage of heterosis in the development of the ear, immature ears (from the IM stage until the end of the floral meristem [FM] stage) of Yudan888 and its parent lines were sampled to assay phenotype and for comparative transcriptomics analysis. The immature ear length of Yudan888 at the IM stage fitted an additive (mid-parental) model, but it showed high parental dominance at the spikelet-pair meristem (SPM) stage. Comparative analysis of transcriptomes suggested significant differences between additive and nonadditive expression patterns for different developmental stages. The number of distinct maternal or paternal genes (DMP) (genes expressed only in one parental line and their hybrid but silenced in another line) was greater than ABF1 (genes expressed in both parental lines but silenced in hybrid) at each stage. Gene Ontology (GO) enrichment suggested that the cell redox homeostasis genes with overdominance expression patterns in hybrids have an important contribution to heterosis. According to our research, anear lengthheterosis networkwas established. The discovery of the inflection point for ear length heterosis allows us for inferring that the transition state of IM to SPM may be the starting point of ear length heterosis. These findings improved the understanding of maize ear lengthheterosis.

MicroRNAs with non-additive expression in the ovary of hybrid hens target genes enriched in key reproductive pathways that may influence heterosis for egg laying traits.

Heterosis has been extensively exploited in chicken breeding to improve laying traits in commercial hybrid stock. However, the molecular mechanisms underlying it remains elusive. This study characterizes the miRNAome in the pre-hierarchical follicles of purebred and hybrid laying hens, and investigate the functions of miRNAs with non-additive expression in the pre-hierarchical follicles as they modulate heterosis for egg number and clutch size. To achieve that aim, White Leghorn and Rhode Island Red chicken lines were reciprocally crossed to generate hybrids. The crossbreds demonstrated heterosis for egg number and clutch size, and pre-hierarchical follicles from 4 birds of each genotype were collected at 53 weeks of age. Mode of miRNA expression was characterized after miRNA sequencing. A total of 50 miRNAs including 30 novel ones, were found to exhibit non-additive expression. Dominance was the predominant mode of expression exhibited by majority of the miRNAs. Functional analysis of target genes of the known miRNAs with non-additive expression revealed Gene Ontology terms related to regulation of transcription, metabolic processes and gene expression. KEGG and REACTOME pathways including hedgehog, cellular senescence, wnt, TGF-β, progesterone-mediated oocyte maturation, oocyte meiosis, GnRH signaling, signal transduction and generic transcription, which can be linked to primordial follicle activation, growth and ovulation, were significantly enriched by target genes of miRNAs with non-additive expression. Majority of the genes enriched in these biological pathways were targeted by gga-miR-19a, gga-miR-19b, gga-miR-375, gga-miR-135a, and gga-miR-7 and 7b, thus, revealing their synergistic roles in enhancing processes that could influence heterosis for egg number and clutch size in hybrid hens.

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice.

Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.

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.

Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone

BackgroundHeterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively improve the genetic characteristics of organisms through heterosis. Abalone has become an increasingly economically important aquaculture resource with high commercial value. However, due to changing climate, abalone is now facing serious threats of high temperature in summer. Interspecific hybrid abalone (Haliotis gigantea ♀ × H. discus hannai ♂, SD) has been cultured at large scale in southern China and has been shown high survival rates under heat stress in summer. Therefore, SD has become a good model material for heterosis research, but the molecular basis of heterosis remains elusive.ResultsHeterosis in thermal tolerance of SD was verified through Arrhenius break temperatures (ABT) of cardiac performance in this study. Then RNA-Sequencing was conducted to obtain gene expression patterns and alternative splicing events at control temperature (20 °C) and heat stress temperature (30 °C). A total of 356 (317 genes), 476 (435genes), and 876 (726 genes) significantly diverged alternative splicing events were identified in H. discus hannai (DD), H. gigantea (SS), and SD in response to heat stress, respectively. In the heat stress groups, 93.37% (20,512 of 21,969) of the expressed genes showed non-additive expression patterns, and over-dominance expression patterns of genes account for the highest proportion (40.15%). KEGG pathway enrichment analysis showed that the overlapping genes among common DEGs and NAGs were significantly enriched in protein processing in the endoplasmic reticulum, mitophagy, and NF-κB signaling pathway. In addition, we found that among these overlap genes, 39 genes had undergone alternative splicing events in SD. These pathways and genes may play an important role in the thermal resistance of hybrid abalone.ConclusionMore alternative splicing events and non-additive expressed genes were detected in hybrid under heat stress and this may contribute to its thermal heterosis. These results might provide clues as to how hybrid abalone has a better physiological regulation ability than its parents under heat stress, to increase our understanding of heterosis in abalone.

Formation of awns in wheat lines with introgressions from Aegilops spp. caused by novel regulatory genes

Awns play a significant role in the plant physiology and are a well-known morphological marker in wheat. Awnedness in wheat is regulated by three inhibitors – Hd, B1, and B2, but awn promoters are still largely unknown. The present study is aimed at analysis of the expression level of awn development regulatory genes orthologs, TaDL, TaTOB1, TaETT2, and TaKNOX3, in Triticum aestivum, genome substitution amphidiploids AABBSshSsh and AABBUU, and derived lines with introgressions from Aegilops sharonensis and Ae. umbellulata.Expression of four mentioned genes was detected in the lemma of all strains studied, and the role of these genes in awn development was assumed. In awned introgression lines, expression of all studied genes differed from mid-parent value: it was present in parent genotypes and absent in derived lines. Non-additive expression of four studied genes in introgression lines is considered to be the possible reason that caused development of nonparental awned phenotype. The presence of two products resulting from TaTOB1 cDNA amplification, one of which contained fourth intron and another lacking it, is considered to be the result of two mRNA presence due to different TaTOB1 homoeoalleles expression.

Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins.

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.

Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids.

The remodeling of transcriptome, epigenome, proteome, and metabolome in hybrids plays an important role in heterosis. N(6)-methyladenosine (m6A) methylation is the most abundant type of post-transcriptional modification for mRNAs, but the pattern of inheritance from parents to hybrids and potential impact on heterosis are largely unknown. We constructed transcriptome-wide mRNA m6A methylation maps of Arabidopsis thaliana Col-0 and Landsberg erecta (Ler) and their reciprocal F1 hybrids. Generally, the transcriptome-wide pattern of m6A methylation tends to be conserved between accessions. Approximately 74% of m6A methylation peaks are consistent between the parents and hybrids, indicating that a majority of the m6A methylation is maintained after hybridization. We found a significant association between differential expression and differential m6A modification, and between non-additive expression and non-additive methylation on the same gene. The overall RNA m6A level between Col-0 and Ler is clearly different but tended to disappear at the allelic sites in the hybrids. Interestingly, many enriched biological functions of genes with differential m6A modification between parents and hybrids are also conserved, including many heterosis-related genes involved in biosynthetic processes of starch. Collectively, our study revealed the overall pattern of inheritance of mRNA m6A modifications from parents to hybrids and a potential new layer of regulatory mechanisms related to heterosis formation.

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

BackgroundMaize (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.ResultsHere, 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.ConclusionOur 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.

Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize.

Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.

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 PAVSPE. 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 PAVSPE and non-PAVSPE 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 PAVSPE and non-PAVSPE genes. PAVSPE genes were more frequently expressed in hybrids than non-PAVSPE genes. The expression of parentally silent alleles in hybrids of non-PAVSPE genes was relatively rare but occurred in most hybrids. Non-PAVSPE 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-PAVSPE and PAVSPE genes and their roles in gene expression complementation in maize hybrids.

Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid.

Polyploidization is a universal phenomenon in plants and plays a crucial role in evolution. In this study, the transcriptomes of developing seeds of a synthetic Brassica hexaploid and its parents (B. rapa and B. carinata) were analyzed to find the gene expression changes in hexaploid seeds. There were 3166 and 3893 DEGs between the Brassica hexaploid and its parents at the full-size stage and mature stage, respectively, most of which were upregulated in hexaploid seeds compared to its parents. At the mature stage, the hexaploid seeds showed a greater difference from its parents. These DEGs had a wide range of functions, which may account for the physiological and morphological differences between the Brassica hexaploid and its parents. The KEGG pathway analysis revealed that hexaploid seeds had higher levels of expression of genes involved in metabolic pathways, RNA transport and biosynthesis of secondary metabolites, and the expression levels in the photosynthesis-related pathways were significantly higher than those in B. rapa. Transgressive expression was the main non-additive expression pattern of the Brassica hexaploid. The gene expression difference between the Brassica hexaploid and its paternal parent was more significant than that with its maternal parent, which may be due in part to the cytoplasmic and maternal effects. Moreover, transcription factor genes, such as G2-like, MYB and mTERF, were highly expressed in hexaploid seeds, possibly promoting their resistance to stress. Our results may provide valuable insights into the adaptation mechanisms of polyploid plants.

Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae).

Polyploidy is an important evolutionary mechanism and is prevalent among land plants. Most polyploid species examined have multiple origins, which provide genetic diversity and may enhance the success of polyploids. In some polyploids, recurrent origins can result from reciprocal crosses between the same diploid progenitors. Although great progress has been made in understanding the genetic consequences of polyploidy, the genetic implications of reciprocal polyploidization remain poorly understood, especially in natural polyploids. Tragopogon (Asteraceae) has become an evolutionary model system for studies of recent and recurrent polyploidy. Allotetraploid T. miscellus has formed reciprocally in nature with resultant distinctive floral and inflorescence morphologies (i.e., short- vs. long-liguled forms). In this study, we performed comparative inflorescence transcriptome analyses of reciprocally formed T. miscellus and its diploid parents, T. dubius and T. pratensis. In both forms of T. miscellus, homeolog expression of ∼70% of the loci showed vertical transmission of the parental expression patterns (i.e., parental legacy), and ∼20% of the loci showed biased homeolog expression, which was unbalanced toward T. pratensis. However, 17.9% of orthologous pairs showed different homeolog expression patterns between the two forms of T. miscellus. No clear effect of cytonuclear interaction on biased expression of the maternal homeolog was found. In terms of the total expression level of the homeologs studied, 22.6% and 16.2% of the loci displayed non-additive expression in short- and long-liguled T. miscellus, respectively. Unbalanced expression level dominance toward T. pratensis was observed in both forms of T. miscellus. Significantly, genes annotated as being involved in pectin catabolic processes were highly expressed in long-liguled T. miscellus relative to the short-liguled form, and the majority of these differentially expressed genes were transgressively down-regulated in short-liguled T. miscellus. Given the known role of these genes in cell expansion, they may play a role in the differing floral and inflorescence morphologies of the two forms. In summary, the overall inflorescence transcriptome profiles are highly similar between reciprocal origins of T. miscellus. However, the dynamic homeolog-specific expression and non-additive expression patterns observed in T. miscellus emphasize the importance of reciprocal origins in promoting the genetic diversity of polyploids.

CRb and PbBa8.1 Synergically Increases Resistant Genes Expression upon Infection of Plasmodiophora brassicae in Brassica napus.

PbBa8.1 and CRb are two clubroot-resistant genes that are important for canola breeding in China. Previously, we combined these resistant genes and developed a pyramid-based, homozygous recurrent inbred line (618R), the results of which showed strong resistance to Plasmodiophora brassicae field isolates; however, the genetic mechanisms of resistance were unclear. In the present work, we conducted comparative RNA sequencing (RNA-Seq) analysis between 618R and its parental lines (305R and 409R) in order to uncover the transcriptomic response of the superior defense mechanisms of 618R and to determine how these two different resistant genes coordinate with each other. Here, we elucidated that the number and expression of differentially expressed genes (DEGs) in 618R are significantly higher than in the parental lines, and PbBa8.1 shares more DEGs and plays a dominant role in the pyramided line. The common DEGs among the lines largely exhibit non-additive expression patterns and enrichment in resistance pathways. Among the enriched pathways, plant–pathogen interaction, plant hormone signaling transduction, and secondary metabolites are the key observation. However, the expressions of the salicylic acid (SA) signaling pathway and reactive oxygen species (ROS) appear to be crucial regulatory components in defense response. Our findings provide comprehensive transcriptomic insight into understanding the interactions of resistance gene pyramids in single lines and can facilitate the breeding of improved resistance in Brassica napus.

Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae).

Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina. The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.

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.

Non-additive expression of awn development regulatory genes in the bread wheat lines with introgressions from Amblyopyrum muticum

Aim. Nonadditive expression of homeotic genes is considered to cause the development of nonparental phenotypes in the plants of hybrid origin. Previously, orthologs of rice and barley awn development regulators TaTOB1, TaDL, TaKNOX3, and TaETT2 were identified in the bread wheat genome sequence. Nonadditive expression of these regulators can be the reason for the emergence of non-parental terminally awned phenotypes among the bread wheat lines with introgressions from Amblyopyrum muticum Methods. Gene expression was identified with end-point detection RT-qPCR Results. Introgressive lines have expression of TaTOB1, TaKNOX3, and TaETT2 at the lower level compared to parents. As orthologs of TaTOB1 and TaKNOX3 are negative regulators of awn development in rice and barley, their reduced expression could have caused the appearance of terminally awned plants among introgressive lines. Neverthless, the reduced expression of the genes wasn’t specific to the lines with non-parental phenotype. Conclusions. Due to the lack of correlation between reduced expression of the genes studied and non-parental phenotype of the introgressive lines, the role of nonadditive expression of TaTOB1, TaKNOX3, and TaETT2 in the development of this phenotype is not clear. Keywords: amphidiploids, non-additive expression, developmental genetics, awns.

Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An\u2019nong 591 under heat stress

BackgroundHeterosis is the superior performance of F1 hybrids relative to their parental lines for a wide range of traits. In this study, expression profiling and heterosis associated genes were analyzed by RNA sequencing (RNA-Seq) in seedlings of the maize hybrid An’nong 591 and its parental lines under control and heat stress conditions.ResultsThrough performing nine pairwise comparisons, the maximum number of differentially expressed genes (DEGs) was detected between the two parental lines, and the minimum number was identified between the F1 hybrid and the paternal lines under both conditions, which suggested greater genetic contribution of the paternal line to heat stress tolerance. Gene Ontology (GO) enrichment analysis of the 4518 common DEGs indicated that GO terms associated with diverse stress responses and photosynthesis were highly overrepresented in the 76 significant terms of the biological process category. A total of 3970 and 7653 genes exhibited nonadditive expression under control and heat stress, respectively. Among these genes, 2253 (56.8%) genes overlapped, suggesting that nonadditive genes tend to be conserved in expression. In addition, 5400 nonadditive genes were found to be specific for heat stress condition, and further GO analysis indicated that terms associated with stress responses were significantly overrepresented, and 60 genes were assigned to the GO term response to heat. Pathway enrichment analysis indicated that 113 genes were involved in spliceosome metabolic pathways. Nineteen of the 33 overlapping genes assigned to the GO term response to heat showed significantly higher number of alternative splicing (AS) events under heat stress than under control conditions, suggesting that AS of these genes play an important role in response to heat stress.ConclusionsThis study reveals the transcriptomic divergence of the maize F1 hybrid and its parental lines under control and heat stress conditions, and provides insight into the underlying molecular mechanisms of heterosis and the response to heat stress in maize.

Nonadditive and allele-specific expression of insulin-like growth factor 1 in Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (O. aureus, ♂) hybrids.

Hybrid Nile tilapia (Oreochromis niloticus, ♀) × blue tilapia (O. aureus, ♂) is a widely cultured tilapia variety due to its growth vigor compared to the parent species. As a peptide hormone, insulin-like growth factor 1 (IGF-1) plays a critical role in regulating somatic growth. The present study focuses on the expression characteristics of IGF-1 in hybrid tilapia. The cloned complete open reading frame of IGF-1 in hybrid tilapia is 549 bp in length, encoding a protein of 182 amino acids. The deduced protein is highly similar to that of Nile tilapia and blue tilapia. IGF-1 was found to be primarily expressed in the liver and muscle in the hybrid; lower expression levels were found in other tissues such as the intestine, spleen, and head-kidney. Increased mRNA expression was observed in the liver and muscle of the hybrid compared to Nile tilapia and blue tilapia, indicating a nonadditive expression pattern in the hybrid. An IGF-1 SNP site (397 site: C in Nile tilapia, G in blue tilapia) for differentiating the Nile tilapia or blue tilapia subgenome in hybrids was identified. Pyrosequencing analysis of the liver transcriptome indicated that most of the hybrids (9 of 10 individuals) predominantly expressed the G allele, demonstrating bias of the blue tilapia subgenome. The present study provides novel data indicating, for the first time, overall gene expression of IGF-1 and allele-specific expression in hybrid tilapia.

Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development

Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their F1 hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into ∼30 000 genes that are expressed in at least one tissue of one inbred and an additional ∼10 000 ″silent" genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (∼74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single parent expression. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis- and trans-regulatory variation. Genes with cis-regulatory variation often exhibit additive expression and tend to have more consistent regulatory variation throughout development. In contrast, genes with trans-regulatory variation are enriched for non-additive patterns and often show tissue-specific differential expression. Taken together, this study provides a deeper understanding of regulatory variation and the degree of additive gene expression throughout maize development. The dynamic nature of differential expression, additivity, and regulatory variation imply abundant variability for tissue-specific regulatory mechanisms and suggest that connections between transcriptome and phenome will require expression data from multiple tissues.