mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses

This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.

hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools

Bread wheat (Triticum aestivum L.) is a globally important food crop, which was domesticated about 8-10,000 years ago. Bread wheat is an allopolyploid, and it evolved from two hybridization events of three species. To widen the genetic base in breeding, bread wheat has been re-synthesized by crossing durum wheat (Triticum turgidum ssp. durum) and goat grass (Aegilops tauschii Coss), leading to so-called synthetic hexaploid wheat (SHW). We applied the quantitative genetics tools of "hybrid prediction"-originally developed for the prediction of wheat hybrids generated from different heterotic groups - to a situation of allopolyploidization. Our use-case predicts the phenotypes of SHW for three quantitatively inherited global wheat diseases, namely tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB). Our results revealed prediction abilities comparable to studies in 'traditional' elite or hybrid wheat. Prediction abilities were highest using a marker model and performing random cross-validation, predicting the performance of untested SHW (0.483 for SB to 0.730 for TS). When testing parents not necessarily used in SHW, combination prediction abilities were slightly lower (0.378 for SB to 0.718 for TS), yet still promising. Despite the limited phenotypic data, our results provide a general example for predictive models targeting an allopolyploidization event and a method that can guide the use of genetic resources available in gene banks.

Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid

Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.

Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry

Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.

Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae)

Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.

The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants

Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.

Downregulation of the expression of subgenomic chromosome A7 genes promotes plant height in resynthesized allopolyploid Brassica napus

KEY MESSAGE

Homoeolog expression bias and the gene dosage effect induce downregulation of genes on chromosome A7, causing a significant increase in the plant height of resynthesized allopolyploid Brassica napus. Gene expression levels in allopolyploid plants are not equivalent to the simple average of the expression levels in the parents and are associated with several non-additive expression phenomena, including homoeolog expression bias. However, hardly any information is available on the effect of homoeolog expression bias on traits. Here, we studied the effects of gene expression-related characteristics on agronomic traits using six isogenic resynthesized Brassica napus lines across the first ten generations. We found a group of genes located on chromosome A7 whose expression levels were significantly negatively correlated with plant height. They were expressed at significantly lower levels than their homoeologous genes, owing to allopolyploidy rather than inheritance from parents. Homoeolog expression bias resulted in resynthesized allopolyploids with a plant height similar to their female Brassica oleracea parent, but significantly higher than that of the male Brassica rapa parent. Notably, aneuploid lines carrying monosomic and trisomic chromosome A7 had the highest and lowest plant heights, respectively, due to changes in the expression bias of homoeologous genes because of alterations in the gene dosage. These findings suggest that the downregulation of the expression of homoeologous genes on a single chromosome can result in the partial improvement of traits to a significant extent in the nascent allopolyploid B. napus.

A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale genome assembly for the genus Orinus (Orinus kokonorica as representative) and preform comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and the two subgenomes of O. kokonorica display neither fractionation bias nor global homoeolog expression dominance. We find substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes may have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations and extensive SVs between orthologs of flower and rhizome related genes may contribute to the morphological differences between the two genera. Our results provide new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.

Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat

Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analysis and epigenome profiling via hidden Markov model in common wheat, we detect a large proportion of enhancer-like elements (ELEs) derived from TEs producing nascent noncoding transcripts, namely ELE-RNAs, which are well indicative of the regulatory activity of ELEs. Quantifying ELE-RNA transcriptome across typical developmental stages reveals that TE-initiated ELE-RNAs are mainly from RLG_famc7.3 specifically expanded in subgenome A. Acquisition of spike-specific transcription factor binding likely confers spike-specific expression of RLG_famc7.3-initiated ELE-RNAs. Knockdown of RLG_famc7.3-initiated ELE-RNAs resulted in global downregulation of spike-specific genes and abnormal spike development. These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.

Integrated agronomic, physiological, microstructure, and whole-transcriptome analyses reveal the role of biomass accumulation and quality formation during Se biofortification in alfalfa

Se-biofortified agricultural products receive considerable interest due to the worldwide severity of selenium (Se) deficiency. Alfalfa (Medicago sativa L.), the king of forage, has a large biomass, a high protein content, and a high level of adaptability, making it a good resource for Se biofortification. Analyses of agronomic, quality, physiological, and microstructure results indicated the mechanism of biomass increase and quality development in alfalfa during Se treatment. Se treatment effectively increased Se content, biomass accumulation, and protein levels in alfalfa. The enhancement of antioxidant capacity contributes to the maintenance of low levels of reactive oxygen species (ROS), which, in turn, serves to increase alfalfa's stress resistance and the stability of its intracellular environment. An increase in the rate of photosynthesis contributes to the accumulation of biomass in alfalfa. To conduct a more comprehensive investigation of the regulatory networks induced by Se treatment, the transcriptome sequencing of non-coding RNA (ncRNA) was employed to compare 100 mg/kg Se treatment and control groups. The analysis identified 1,414, 62, and 5 genes as DE-long non-coding RNAs (DE-lncRNA), DE-microRNAs (DE-miRNA), and DE-circular RNA (DE-circRNA), respectively. The function of miRNA-related regulatory networks during Se biofortification in alfalfa was investigated. Subsequent enrichment analysis revealed significant involvement of transcription factors, DNA replication and repair mechanisms, photosynthesis, carbohydrate metabolism, and protein processing. The antioxidant capacity and protein accumulation of alfalfa were regulated by the modulation of signal transduction, the glyoxalase pathway, proteostasis, and circRNA/lncRNA-related regulatory networks. The findings offer new perspectives on the regulatory mechanisms of Se in plant growth, biomass accumulation, and stress responses, and propose potential strategies for enhancing its utilization in the agricultural sector.

Impact of the acquired subgenome on the transcriptional landscape in Brettanomyces bruxellensis allopolyploids

Gene expression variation can provide an overview of the changes in regulatory networks that underlie phenotypic diversity. Certain evolutionary trajectories such as polyploidization events can have an impact on the transcriptional landscape. Interestingly, the evolution of the yeast species Brettanomyces bruxellensis has been punctuated by diverse allopolyploidization events leading to the coexistence of a primary diploid genome associated with various haploid acquired genomes. To assess the impact of these events on gene expression, we generated and compared the transcriptomes of a set of 87 B. bruxellensis isolates, selected as being representative of the genomic diversity of this species. Our analysis revealed that acquired subgenomes strongly impact the transcriptional patterns and allow discrimination of allopolyploid populations. In addition, clear transcriptional signatures related to specific populations have been revealed. The transcriptional variations observed are related to some specific biological processes such as transmembrane transport and amino acids metabolism. Moreover, we also found that the acquired subgenome causes the overexpression of some genes involved in the production of flavor-impacting secondary metabolites, especially in isolates of the beer population.

Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice

Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.

Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis.

Low impact of polyploidization on the transcriptome of synthetic allohexaploid wheat

BACKGROUND

Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) less than 10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. The scale of the consequences of polyploidization, and their mechanism of establishment, remain uncertain.

RESULTS

Here we sampled several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect any massive reprogramming in gene expression, with only around 1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of this differential expression is located on the D subgenome, without consistency in the direction of the expression change. Homoeolog expression bias in synthetic wheat is similar to the pattern observed in the parents. Both differential expression and homoeolog bias are tissue-specific. While up to three families of transposable elements became upregulated in wheat synthetics, their position and distance are not significantly associated with expression changes in proximal genes.

DISCUSSION

While only a few genes change their expression pattern after polyploidization, they can be involved in agronomically important pathways. Alternative parental combinations can lead to opposite changes on the same subset of D-located genes, which is relevant for harnessing new diversity in wheat breeding. Tissue specificity of the polyploidization-triggered expression changes indicates the remodelling of transcriptomes in synthetic wheat is plastic and likely caused by regulome interactions rather than permanent changes. We discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal.

CONCLUSIONS

Transcriptomic response to polyploidization in synthetic AABBDD wheat is modest and much lower than some previous estimates. Homoeolog expression bias in wheat allohexaploids is mostly attributed to parental legacy, with polyploidy having a mild balancing effect.

Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response

Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3'-UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and downregulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.

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

KEY MESSAGE

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

Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat

Synthetic hexaploid wheat (SHW) lines are created as pre-breeding germplasm to diversify the D subgenome of hexaploid wheat and capitalize upon the untapped genetic diversity of the Aegilops tauschii gene pool. However, the phenotypes observed in the Ae. tauschii parents are not always recovered in the SHW lines, possibly due to inter-subgenome interactions. To elucidate this post-polyploidization genome reprogramming phenomenon, we performed RNA-seq of four SHW lines and their corresponding tetraploid and diploid parents, across ten tissues and three biological replicates. Homoeologue expression bias (HEB) analysis using more than 18,000 triads suggests massive suppression of homoeoalleles of the D subgenome in SHWs. Comparative transcriptome analysis of the whole-genome gene set further corroborated this finding. Alternative splicing analysis of the high-confidence genes indicates an additional layer of complexity where all five splice events are identified, and retained intron is predominant. Homoeologue expression upon resynthesis of hexaploid wheat has implications to the usage and handling of this germplasm in breeding as it relates to capturing the effects of epistatic interaction across subgenomes upon polyploidization. Special considerations must be given to this germplasm in pre-breeding activities to consider the extent of the inter-subgenome interactions on gene expression and their impact on traits for crop improvement.

Comparative analysis of Fusarium crown rot resistance in synthetic hexaploid wheats and their parental genotypes

BACKGROUND

Fusarium crown rot (FCR) is a chronic disease of cereals worldwide. Compared with tetraploid wheat, hexaploid wheat is more resistant to FCR infection. The underlying reasons for the differences are still not clear. In this study, we compared FCR responses of 10 synthetic hexaploid wheats (SHWs) and their tetraploid and diploid parents. We then performed transcriptome analysis to uncover the molecular mechanism of FCR on these SHWs and their parents.

RESULTS

We observed higher levels of FCR resistance in the SHWs compared with their tetraploid parents. The transcriptome analysis suggested that multiple defense pathways responsive to FCR infection were upregulated in the SHWs. Notably, phenylalanine ammonia lyase (PAL) genes, involved in lignin and salicylic acid (SA) biosynthesis, exhibited a higher level of expression to FCR infection in the SHWs. Physiological and biochemical analysis validated that PAL activity and SA and lignin contents of the stem bases were higher in SHWs than in their tetraploid parents.

CONCLUSION

Overall, these findings imply that improved FCR resistance in SHWs compared with their tetraploid parents is probably related to higher levels of response on PAL-mediated lignin and SA biosynthesis pathways.

Subgenome-dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors

Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both resynthesized and natural lines of polyploid Brassica napus, along with the progenitors Brassica rapa and Brassica oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12 709 DAS events) and lower in resynthesized B. napus (8863 DAS events). Natural B. napus had more upregulated events and fewer downregulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus, this resulted in a disproportionate C subgenome contribution to the pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in resynthesized and natural B. napus.

The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat

Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.

Transcriptomic Analysis Reveals Panicle Heterosis in an Elite Hybrid Rice ZZY10 and Its Parental Lines

Heterosis is the phenomenon in which some hybrid traits are superior to those of their parents. Most studies have analyzed the heterosis of agronomic traits of crops; however, heterosis of the panicles can improve yield and is important for crop breeding. Therefore, a systematic study of panicle heterosis is needed, especially during the reproductive stage. RNA sequencing (RNA Seq) and transcriptome analysis are suitable for further study of heterosis. Using the Illumina Nova Seq platform, the transcriptome of ZhongZheYou 10 (ZZY10), an elite rice hybrid, the maintainer line ZhongZhe B (ZZB), and the restorer line Z7-10 were analyzed at the heading date in Hangzhou, 2022. 581 million high-quality short reads were obtained by sequencing and were aligned against the Nipponbare reference genome. A total of 9000 differential expression genes were found between the hybrids and their parents (DG_HP). Of the DG_HP, 60.71% were up-regulated and 39.29% were down-regulated in the hybrid. Comparative transcriptome analysis revealed that 5235 and 3765 DG_HP were between ZZY10 and ZhongZhe B and between ZZY10 and Z7-10, respectively. This result is consistent with the transcriptome profile of ZZY10 and was similar to Z7-10. The expression patterns of DG_HP mainly exhibited over-dominance, under-dominance, and additivity. Among the DG_HP-involved GO terms, pathways such as photosynthesis, DNA integration, cell wall modification, thylakoid, and photosystem were significant. 21 DG_HP, which were involved in photosynthesis, and 17 random DG_HP were selected for qRT-PCR validation. The up-regulated PsbQ and down-regulated subunits of PSI and PSII and photosynthetic electron transport in the photosynthesis pathway were observed in our study. Extensive transcriptome data were obtained by RNA-Seq, providing a comprehensive overview of panicle transcriptomes at the heading stage in a heterotic hybrid.

The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits

Orychophragmus violaceus, referred to as "eryuelan" (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ∼1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceus identified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceus was phylogenetically close to the Brassica genus, and tetraploidy in O. violaceus occurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus.

Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat

Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades. Fifty-six consensus meta-QTLs (MQTLs) were detected, unevenly distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5D, 6A, 6D, 7B, and 7D. The confidence interval (CI) of the identified MQTLs was 0.18 to 15.07 cM, with an average of 5.74 cM, and 3.17-times narrower than that of the original QTLs. A total of 30 MQTLs were aligned with marker-trait associations (MTAs) reported in genome-wide association studies (GWAS) for chlorophyll traits in wheat. Based on MQTL-flanking marker information and homology analyses combined with RNA-seq data, 136 putative candidate genes were identified in MQTL regions, involved in porphyrin metabolism, photosynthesis, terpene biosynthesis, glyoxylate and dicarboxylate metabolism, and secondary metabolites. The results of this study contribute to the understanding of the genetic basis for controlling chlorophyll traits and can be used in breeding wheat with high photosynthetic efficiency.

Dynamic patterns of gene expression and regulatory variation in the maize seed coat

BACKGROUND

Seed size is an important factor contributing to maize yield, but its molecular mechanism remains unclear. The seed coat, which serves as one of the three components of the maize grain, determines seed size to a certain extent. The seed coat also shares the maternal genotype and is an ideal material for studying heterosis.

RESULTS

In this study, the self-pollinated seeds of the maize hybrid Yudan888 and its parental lines were continuously collected from 0 day after pollination (DAP) to 15 DAP for phenotyping, cytological observation and RNA-seq. The phenotypic data showed that 3 DAP and 8 DAP are the best time points to study maize seed coat heterosis. Cytological observations indicated that maize seed coat heterosis might be the result of the coordination between cell number and cell size. Furthermore, the RNA-seq results showed that the nonadditive genes changed significantly between 3 and 8 DAP. However, the number of genes expressed additively was not significantly different. Our findings suggest that seed coat heterosis in hybrid is the result of nonadditive expression caused by dynamic changes in genes at different time points during seed expansion and seed coat development. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that genes related to DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation contributed significantly to hybrid seed coat heterosis.

CONCLUSION

Maize seed coat phenotyping allowed us to infer that 3 DAP and 8 DAP are important time points in the study of seed coat heterosis. Our findings provide evidence for genes involved in DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation in hybrid with high or low parental expression as major contributors to hybrid seed coat heterosis.

Does one subgenome become dominant in the formation and evolution of a polyploid?

BACKGROUND

Polyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution.

SCOPE

In addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered.

CONCLUSIONS

Contrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.

Recent allopolyploidy alters Spartina microRNA expression in response to xenobiotic-induced stress

Environmental contamination by xenobiotics represents a major threat for natural ecosystems and public health. In response, xenobiotic detoxification is a fundamental trait of organisms for developmental plasticity and stress tolerance, but the underlying molecular mechanisms remain poorly understood in plants. To decipher this process, we explored the consequences of allopolyploidy on xenobiotic tolerance in the genus Spartina Schreb. Specifically, we focused on microRNAs (miRNAs) owing to their central function in the regulation of gene expression patterns, including responses to stress. Small RNA-Seq was conducted on the parents S. alterniflora and S. maritima, their F1 hybrid S. x townsendii and the allopolyploid S. anglica under phenanthrene-induced stress (phe), a model Polycyclic Aromatic Hydrocarbon (PAH) compound. Differentially expressed miRNAs in response to phe were specifically identified within species. In complement, the respective impacts of hybridization and genome doubling were detected, through changes in miRNA expression patterns between S. x townsendii, S. anglica and the parents. The results support the impact of allopolyploidy in miRNA-guided regulation of plant response to phe. In total, we identified 17 phe-responsive miRNAs in Spartina among up-regulated MIR156 and down-regulated MIR159. We also describe novel phe-responsive miRNAs as putative Spartina-specific gene expression regulators in response to stress. Functional validation using Arabidopsis (L.) Heynh. T-DNA lines inserted in homologous MIR genes was performed, and the divergence of phe-responsive miRNA regulatory networks between Arabidopsis and Spartina was discussed.

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

Genetic Improvement and Application Practices of Synthetic Hexaploid Wheat

Synthetic hexaploid wheat (SHW) is a useful genetic resource that can be used to improve the performance of common wheat by transferring favorable genes from a wide range of tetraploid or diploid donors. From the perspectives of physiology, cultivation, and molecular genetics, the use of SHW has the potential to increase wheat yield. Moreover, genomic variation and recombination were enhanced in newly formed SHW, which could generate more genovariation or new gene combinations compared to ancestral genomes. Accordingly, we presented a breeding strategy for the application of SHW-the 'large population with limited backcrossing method'-and we pyramided stripe rust resistance and big-spike-related QTLs/genes from SHW into new high-yield cultivars, which represents an important genetic basis of big-spike wheat in southwestern China. For further breeding applications of SHW-derived cultivars, we used the 'recombinant inbred line-based breeding method' that combines both phenotypic and genotypic evaluations to pyramid multi-spike and pre-harvest sprouting resistance QTLs/genes from other germplasms to SHW-derived cultivars; consequently, we created record-breaking high-yield wheat in southwestern China. To meet upcoming environmental challenges and continuous global demand for wheat production, SHW with broad genetic resources from wild donor species will play a major role in wheat breeding.

Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats

Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.

Subgenome-biased expression and functional diversification of a Na+/H+ antiporter homoeologs in salt tolerance of polyploid wheat

Common wheat (Triticum aestivum, BBAADD) is an allohexaploid species combines the D genome from Ae. tauschii and with the AB genomes from tetraploid wheat (Triticum turgidum). Compared with tetraploid wheat, hexaploid wheat has wide-ranging adaptability to environmental adversity such as salt stress. However, little is known about the molecular basis underlying this trait. The plasma membrane Na⁺/H⁺ transporter Salt Overly Sensitive 1 (SOS1) is a key determinant of salt tolerance in plants. Here we show that the upregulation of TaSOS1 expression is positively correlated with salt tolerance variation in polyploid wheat. Furthermore, both transcriptional analysis and GUS staining on transgenic plants indicated TaSOS1-A and TaSOS1-B exhibited higher basal expression in roots and leaves in normal conditions and further up-regulated under salt stress; while TaSOS1-D showed markedly lower expression in roots and leaves under normal conditions, but significant up-regulated in roots but not leaves under salt stress. Moreover, transgenic studies in Arabidopsis demonstrate that three TaSOS1 homoeologs display different contribution to salt tolerance and TaSOS1-D plays the prominent role in salt stress. Our findings provide insights into the subgenomic homoeologs variation potential to broad adaptability of natural polyploidy wheat, which might effective for genetic improvement of salinity tolerance in wheat and other crops.

Biased gene expression reveals the contribution of subgenome to altitude adaptation in allopolyploid Isoetes sinensis

Allopolyploids are believed to inherit the genetic characteristics of its progenitors and exhibit stronger adaptability and vigor. The allotetraploid Isoetes sinensis was formed by the natural hybridization and polyploidization of two diploid progenitors, Isoetes taiwanensis and Isoetes yunguiensis, and was believed to have the potential to adapt to plateau environments. To explore the expression pattern of homoeologous genes and their contributions to altitude adaptation, we transplanted natural allotetraploid I. sinensis (TnTnYnYn) along the altitude gradient for a long-term, and harvested them in summer and winter, respectively. One year after transplanting, it still lived well, even in the extreme environment of the Qinghai-Tibet Plateau. Then, we performed high-throughput RNA sequencing to measure their gene expression level. A total of 7801 homoeologous genes were expressed, among which 5786 were identified as shared expression in different altitudes and seasons. We further found that altitude variations could change the subgenome bias trend of I. sinensis, but season could not. Moreover, the functions of uniquely expressed genes indicated that temperature might be an important restrictive factor during the adaptation process. Through the analysis of DEGs and uniquely expressed genes, we found that Y subgenome provided more contributions to high altitude adaptation than T subgenome. These adaptive traits to high altitude may be inherited from its plateau progenitor I. yunguiensis. Through weighted gene co-expression network analysis, pentatricopeptide repeats gene family and glycerophospholipid metabolism pathway were considered to play important roles in high-altitude adaptation. Totally, this study will enrich our understanding of allopolyploid in environmental adaptation.

Acetylome reprograming participates in the establishment of fruit metabolism during polyploidization in citrus

Polyploidization leads to novel phenotypes and is a major force in evolution. However, the relationship between the evolution of new traits and variations in the post-translational modifications (PTM) of proteins during polyploidization has not been studied. Acetylation of lysine residues is a common protein PTM that plays a critical regulatory role in central metabolism. To test whether changes in metabolism in citrus fruit is associated with the reprogramming of lysine acetylation (Kac) in non-histone proteins during allotetraploidization, we performed a global acetylome analysis of fruits from a synthetic allotetraploid citrus and its diploid parents. A total of 4,175 Kac sites were identified on 1,640 proteins involved in a wide range of fruit traits. In the allotetraploid, parental dominance (i.e. resemblance to one of the two parents) in specific fruit traits, such as fruit acidity and flavonol metabolism, was highly associated with parental Kac level dominance in pertinent enzymes. This association is due to Kac-mediated regulation of enzyme activity. Moreover, protein Kac probably contributes to the discordance between the transcriptomic and proteomic variations during allotetraploidization. The acetylome reprogramming can be partially explained by the expression pattern of several lysine deacetylases (KDACs). Overexpression of silent information regulator 2 (CgSRT2) and histone deacetylase 8 (CgHDA8) diverted metabolic flux from primary metabolism to secondary metabolism and partially restored a metabolic status to the allotetraploid, which expressed attenuated levels of CgSRT2 and CgHDA8. Additionally, KDAC inhibitor treatment greatly altered metabolism in citrus fruit. Collectively, these findings reveal the important role of acetylome reprogramming in trait evolution during polyploidization.

Comparative transcriptomic reveals the molecular mechanism of maize hybrid Zhengdan538 in response to water deficit

Heterosis, known as one of the most successful strategies for increasing grain yield and abiotic/biotic stress tolerance, has been widely exploited in maize breeding. However, the underlying molecular processes are still to be elucidated. The maize hybrid "Zhengdan538" shows high tolerance to drought stress. The transcriptomes of the seedling leaves of its parents, "ZhengA88" and "ZhengT22" and their reciprocal F₁ hybrid under well-watered and water deficit conditions, were analyzed by RNA sequencing (RNA-Seq). Transcriptome profiling of the reciprocal hybrid revealed 2994-4692 differentially expressed genes (DEGs) under well-watered and water-deficit conditions, which were identified by comparing with their parents. The reciprocal hybrid was more closely related to the parental line "ZhengT22" than to the parental line "ZhengA88" in terms of gene expression patterns under water-deficit condition. Furthermore, genes showed expression level dominance (ELD), especially the high-parental ELD (Class 3 and 5), accounted for the largest proportion of DEGs between the reciprocal F₁ hybrid and their parental lines under water deficit. These ELD genes mainly participated in photosynthesis, energy biosynthesis, and metabolism processes. The results indicated that ELD genes played important roles in hybrid tolerance to water deficit. Moreover, a set of important drought-responsive transcription factors were found to be encoded by the identified ELD genes and are thought to function in improving drought tolerance in maize hybrid plants. Our results provide a better understanding of the molecular mechanism of drought tolerance in hybrid maize.

The dynamics of lncRNAs transcription in interspecific F1 allotriploid hybrids between Brassica species

Interspecific hybridization is the intrinsic forces behind genome evolution. Long non-coding RNAs (lncRNAs) are important for plant biological processes regulation. However, it is unclear that these non-coding fractions are impacted by interspecific hybridization. Here we examined the profiles of lncRNAs by comparing them with coding genes in Brassica napus, three accessions of Brassica rapa, and their F₁ hybrids. 6206 high-confidential lncRNAs were identified in F ₁ hybrids and their parentals, and the lncRNAs transcriptome in the F₁ hybrids was reprogrammed by the genome shock. Notably, genome-wide unbalanced of lncRNAs were observed between A_n and A_r subgenomes, ELD (Expression Level Dominance) was biased toward the A_n -genome in F₁ hybrids, and ELD of non-conserved lncRNAs was more than conserved lncRNAs. Our findings demonstrate that the reprogramed lncRNAs acts as important role in enhancing plant plasticity, leading to the acquisition of desirable traits in polyploid Brassica species.

Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses

BACKGROUND

Zoysiagrass (Zoysia spp.) is a warm-season turfgrass. It is widely used as turfgrasses throughout the world, offers good turf qualities, including salt tolerance, resistance to drought and heat. However, the underlying genetic mechanism of zoysiagrass responsive to salt stress remains largely unexplored.

RESULTS

In present study, we performed a whole-genome comparative analysis for ten plant genomes. Evolutionary analysis revealed that Chloridoideae diverged from Panicoideae approximately 33.7 million years ago (Mya), and the phylogenetic relationship among three zoysiagrasses species suggested that Zoysia matrella may represent an interspecific hybrid between Zoysia japonica and Zoysia pacifica. Genomic synteny indicated that Zoysia underwent a genus-specific whole-genome duplication (WGD) event approximately 20.8 Mya. The expression bais of homologous genes between the two subgenomes suggested that the B subgenome of Z. japonica contributes to salt tolerance. In additon, comparative genomic analyses revealed that the salt adaptation of Zoysia is likely attributable to the expanded cytochrome P450 and ABA biosynthetic gene families. Furthermore, we further found that many duplicated genes from the extra WGD event exhibited distinct functional divergence in response to salt stress using transcriptomic analysis, suggesting that this WGD event contributed to strong resistance to salt stress.

CONCLUSIONS

Here, our results revealed that expanded cytochrome P450 and ABA biosynthetic gene families, and many of those duplicated genes from recent zoysia-specific WGD event contributed to salt adaptation of zoysiagrass, which provided insight into the genetic underpinning of salt adaptation and valuable information for further studies on salt stress-related traits in Zoysia.

Cross-kingdom transcriptomic trends in the evolution of hybrid gene expression

Hybridization is a route to speciation that occurs widely across the eukaryote tree of life. The success of allopolyploids (hybrid species with increased ploidy) and homoploid hybrids (with unchanged ploidy) is well documented. However, their formation and establishment is not straightforward, with a suite of near‐instantaneous and longer term biological repercussions faced by the new species. Central to these challenges is the rewiring of gene regulatory networks following the merger of distinct genomes inherited from both parental species. Research on the evolution of hybrid gene expression has largely involved studies on a single hybrid species or a few gene families. Here, we present the first standardized transcriptome‐wide study exploring the fates of genes following hybridization across three kingdoms: animals, plants and fungi. Within each kingdom, we pair an allopolyploid system with a closely related homoploid hybrid to decouple the influence of increased ploidy from genome merger. Genome merger, not changes in ploidy, has the greatest effect on posthybridization expression patterns across all study systems. Strikingly, we find that differentially expressed genes in parent species preferentially switch to more similar expression in hybrids across all kingdoms, likely as a consequence of regulatory trans‐acting cross‐talk within the hybrid nucleus. We also highlight the prevalence of gene loss or silencing among extremely differentially expressed genes in hybrid species across all kingdoms. These shared patterns suggest that the evolutionary process of hybridization leads to common high‐level expression outcomes, regardless of the particular species or kingdom.

Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization

Hybridization is useful to enhance the yield potential of agronomic crops in the world. Cotton has genome doubling due to the allotetraploid process and hybridization in coordination with duplicated genome can produce more yield and adaptability. Therefore, the expression of homoeologous gene pairs between hybrids and inbred parents is vital to characterize the genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (an average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus

BACKGROUND

Heterosis is an important biological phenomenon in which the hybrids exceed the parents in many traits. However, the molecular mechanism underlying seedling heterosis remains unclear.

RESULTS

In the present study, we analyzed the leaf transcriptomes of strong hybrids (AM, HM) and weak hybrids (CM, HW) and their parents (A, C, H, M, and W) at two periods. Phenotypically, hybrids had obvious biomass heterosis at the seedling stage, with statistically significant differences between the strong and weak hybrids. The transcriptomic analysis demonstrated that the number of differentially expressed genes (DEGs) between parents was the highest. Further analysis showed that most DEGs were biased toward parental expression. The biological processes of the two periods were significantly enriched in the plant hormone signal transduction and photosynthetic pathways. In the plant hormone signaling pathway, DEG expression was high in hybrids, with expression differences between strong and weak hybrids. In addition, DEGs related to cell size were identified. Similar changes were observed during photosynthesis. The enhanced leaf area of hybrids generated an increase in photosynthetic products, which was consistent with the phenotype of the biomass. Weighted gene co-expression network analysis of different hybrids and parents revealed that hub genes in vigorous hybrid were mainly enriched in the plant hormone signal transduction and regulation of plant hormones.

CONCLUSION

Plant hormone signaling and photosynthesis pathways, as well as differential expression of plant cell size-related genes, jointly regulate the dynamic changes between strong and weak hybrids and the generation of seedling-stage heterosis. This study may elucidate the molecular mechanism underlying early biomass heterosis and help enhance canola yield.

Expression Analysis of TCP Transcription Factor Family in Autopolyploids of Chrysanthemum nankingense

Autopolyploids often exhibit plant characteristics different from their diploid ancestors and are frequently associated with altered genes expression controlling growth and development. TCP is a unique transcription factor family in plants that is closely related to plant growth and development. Based on transcriptome sequencing of Chrysanthemum nankingense, 23 full-length TCP genes were cloned. The expression of CnTCP9 was most variable in tetraploids, at least threefold greater than diploids. Due to the lack of a C. nankingense transgenic system, we overexpressed CnTCP9 in Arabidopsis thaliana (Col-0) and Chrysanthemum morifolium. Overexpression of CnTCP9 caused enlargement of leaves in A. thaliana and petals in C. morifolium, and the expression of genes downstream of the GA pathway in C. morifolium were increased. Our results suggest that autopolyploidization of C. nankingense led to differential expression of TCP family genes, thereby affecting plant characteristics by the GA pathway. This study improves the understanding of enlarged plant size after autopolyploidization.

Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the Invasive Sphagneticola trilobata and the Native S. calendulacea in South China, and Implications for Its Invasiveness

The role of hybridization is significant in biological invasion, and thermotolerance is a trait critical to range expansions. The South American Sphagneticola trilobata is now widespread in South China, threatening the native S. calendulacea by competition and hybridization. Furthermore, upon formation, their F1 hybrid can quickly replace both parents. In this study, the three taxa were used as a model to investigate the consequences of hybridization on cold tolerance, particularly the effect of subgenome dominance in the hybrid. Upon chilling treatments, physiological responses and transcriptome profiles were compared across different temperature points to understand their differential responses to cold. While both parents showed divergent responses, the hybrid’s responses showed an overall resemblance to S. calendulacea, but the contribution of homeolog expression bias to cold stress was not readily evident in the F1 hybrid possibly due to inherent bias that comes with the sampling location. Our findings provided insights into the role of gene expression in differential cold tolerance, and further contribute to predicting the invasive potential of other hybrids between S. trilobata and its congeners around the world.

Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress

Maize (Zea mays) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to drought stress in maize roots is unclear. In our study, we found 375 miRNAs in the roots of 16 inbred lines. Of the 16 lines, zma-MIR168, zma-MIR156, and zma-MIR166 were highly expressed, whereas zma-MIR399, zma-MIR2218, and zma-MIR2275 exhibited low expression levels. The expression patterns of miRNA in parental lines and their derived RILs are different. Over 50% of miRNAs exhibited a lower expression in recombinant inbred lines than in parents. The expression of 50 miRNAs was significantly altered under water stress (WS) in at least three inbred lines, and the expression of miRNAs in drought-tolerant lines changed markedly. To better understand the reasons for miRNA response to drought, the degree of histone modifications for miRNA genes was estimated. The methylation level of H3K4 and H3K9 in miRNA precursor regions changed more noticeably after WS, but no such phenomenon was seen for DNA methylation and m6A modification. After the prediction of miRNA targets using psRNATarget and psRobot, we used correlation analysis and qRT-PCR to further investigate the relationship between miRNAs and target genes. We found that 87 miRNA–target pairs were significantly negatively correlated. In addition, a weighted gene co-expression network analysis using miRNAs, as well as their predicted targets, was conducted to reveal that miR159, miR394, and miR319 may be related to maize root growth. The results demonstrated that miRNAs might play essential roles in the response to drought stress.

Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species

Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.

Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms

Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.

Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.

Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.)

In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder's MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified. Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999-2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder's MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.

Improvement and Re-Evolution of Tetraploid Wheat for Global Environmental Challenge and Diversity Consumption Demand

Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.

Gene expression profiling reveals transcription factor networks and subgenome bias during Brassica napus seed development

We profiled the global gene expression landscape across the reproductive lifecycle of Brassica napus. Comparative analysis of this nascent amphidiploid revealed the contribution of each subgenome to plant reproduction. Whole-genome transcription factor networks identified BZIP11 as a transcriptional regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in a similar reduction in gene activity of predicted gene targets, and a reproductive-lethal phenotype. Global mRNA profiling revealed lower accumulation of Cⁿ subgenome transcripts relative to the Aⁿ subgenome. Subgenome-specific transcription factor networks identified distinct transcription factor families enriched in each of the Aⁿ and Cⁿ subgenomes early in seed development. Analysis of laser-microdissected seed subregions further reveal subgenome expression dynamics in the embryo, endosperm and seed coat of early stage seeds. Transcription factors predicted to be regulators encoded by the Aⁿ subgenome are expressed primarily in the seed coat, whereas regulators encoded by the Cⁿ subgenome were expressed primarily in the embryo. Data suggest subgenome bias are characteristic features of the B. napus seed throughout development, and that such bias might not be universal across the embryo, endosperm and seed coat of the developing seed. Transcriptional networks spanning both the Aⁿ and Cⁿ genomes of the whole B. napus seed can identify valuable targets for seed development research and that -omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.