Meristem Differentiation Research Articles

Evolutionary origin and functional investigation of the widely conserved plant PEBP gene STEPMOTHER OF FT AND TFL1 (SMFT).

Genes of the family PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS (PEBP) have been intensely studied in plants for their role in cell (re)programming and meristem differentiation. Recently, sporadic reports of the presence of a new type of PEBP in plants became available, highly similar to the YY-PEBPs of prokaryotes. A comprehensive investigation of their spread, origin, and function revealed conservation across the plant kingdom. The YY-PEBP clade in plants seems to have resulted from a single Horizontal Gene Transfer (HGT) episode from a prokaryotic organism to an ancestral streptophyte. YY-PEBPs are also present in other eukaryotes, such as certain fungi, diatoms, and rotifers, and these cases derive from independent HGT events. Reciprocally, the occurrence of the eukaryotic CETS/RKIP type PEBPs (CR-PEBPs) was noticed in bacteria of the genus Nocardia, showing that HGT has occurred as well from eukaryotes to prokaryotes. Based on these observations, we propose that the current model of the PEBP family in plants needs to be updated with the clade STEPMOTHER OF FT AND TFL1 (SMFT). SMFT genes not only share high sequence conservation but also show specific expression in homologous plant structures that serve as propagules. Functional analysis of Arabidopsis smft mutant lines pointed to a function for this gene in regulating seed germination, both concerning primary dormancy release and in response to adverse high-temperature conditions. Overall, our study reveals an increasing complexity in the evolutionary history of the PEBP gene family, unlocking new potential in understanding the evolution and functional spectrum of these important key regulatory genes.

Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots.

Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.

Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation

Maize develops separate ear and tassel inflorescences with initially similar morphology but ultimately different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely unclear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel, we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. We identified 16 diverse gene clusters with differential spatiotemporal expression patterns and revealed biased regulation of redox, programmed cell death, and hormone signals during meristem differentiation between ear and tassel. Notably, based on their dynamic expression patterns, we revealed the roles of two RNA-binding proteins in regulating inflorescence meristem activity and axillary meristem formation. Moreover, using the transcriptional profiles of 53 910 single cells, we uncovered the cellular heterogeneity between ear and tassel florets. We found that multiple signals associated with either enhanced cell death or reduced growth are responsible for tassel pistil suppression, while part of the gibberellic acid signal may act non-cell-autonomously to regulate ear stamen arrest during sex differentiation. We further showed that the pistil-protection gene SILKLESS 1 (SK1) functions antagonistically to the known pistil-suppression genes through regulating common molecular pathways, and constructed a regulatory network for pistil-fate determination. Collectively, our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation for identifying new regulators and pathways for maize hybrid breeding and improvement.

ALTERED MERISTEM PROGRAM1 sustains cellular differentiation by limiting HD-ZIP III transcription factor gene expression.

Plants show remarkable developmental and regenerative plasticity through the sustained activity of stem cells in meristems. Under certain conditions, pluripotency can even be reestablished in cells that have already entered differentiation. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis (Arabidopsis thaliana) causes a set of hypertrophic phenotypes, indicating a defect in the suppression of pluripotency. A role of AMP1 in the miRNA-mediated inhibition of translation has previously been reported; however, how this activity is related to its developmental functions is unclear. Here, we examined the functional interaction between AMP1 and the Class III homeodomain-leucine zipper (HD-ZIP III) transcription factors, which are miRNA-controlled determinants of shoot meristem specification. We found that the HD-ZIP III transcriptional output is enhanced in the amp1 mutant and that plant lines with increased HD-ZIP III activity not only developed amp1 mutant-like phenotypes but also showed a synergistic genetic interaction with the mutant. Conversely, the reduction of HD-ZIP III function suppressed the shoot hypertrophy defects of the amp1 mutant. We further provide evidence that the expression domains of HD-ZIP III family members are expanded in the amp1 mutant and that this misexpression occurs at the transcriptional level and does not involve the function of miRNA165/166. Finally, amp1 mutant-specific phenotypes cannot be mimicked by a general inhibition of miRNA function in the AMP1 expression domain. These findings lead us to a model in which AMP1 restricts cellular pluripotency upstream of HD-ZIP III proteins, and this control appears to be not directly mediated by the canonical miRNA pathway.

Expression patterns and evidence of the expansion of Nicotiana tabacum L. TALE genes in the Solanaceae family

AbstractThe three-amino-acid-loop-extension (TALE) proteins are a class of transcription factors that regulate meristem differentiation during plant growth and development. In this study, we identified a total of 45 members of the tobacco TALE (NtTALE) transcription factor family. Based on domain type, the NtTALE genes were divided into BELL subfamily and KNOX subfamily. Cis-acting element analysis showed that the NtTALE gene promoters had a variety of response elements, including light-responsive elements, hormonal and abiotic stresses responsive elements, plant development related elements. Among the 45 NtTALE genes, the expression patterns of various plant tissues at different stages were different, 10 responded to alkali stress, 19 responded to dehydration treatment, 14 responded to cold stress, two responded to salt stress, and 17 responded to Ralstonia solanacearum infection. Phylogenetic analysis showed that the number of TALE genes in Nicotiana was significantly expanded compared with that in other Solanaceae. The KNOXIII subfamily members (NtTALE29, NtTALE45) were found only in Nicotiana tabacum. This study provides a theoretical basis for further research on the biological function of NtTALE genes.

Rice ins(3)P synthase1 (RINO1) participates in embryonic development by regulating inositol-associated changes in auxin synthesis and its distribution.

The breeding of low phytic acid (LPA) crops is widely considered an effective strategy to improve crop nutrition, but the LPA crops usually have inferior seed germination performance. To clarify the reason for the suboptimal seed performance of LPA rice, this study investigated the impact of reduced seed phytic acid (InsP6) content in rice ins(3)P synthase1 (EC 5.5.1.4, RINO1), one of the key targets for engineering LPA rice, knockouton cellular differentiation in seed embryos and its relation to myo-inositol metabolism and auxin signalling during embryogenesis. The results indicated that the homozygotes of RINO1 knockout could initiate differentiation at the early stage of embryogenesis but failed to form normal differentiation of plumule and radicle primordia. The loss of RINO1 function disrupted vesicle trafficking and auxin signalling due to the significantly lowered phosphatidylinositides (PIs) concentration in seed embryos, thereby leading to the defects of seed embryos without the recognizable differentiation of shoot apex meristem (SAM) and radicle apex meristem (RAM) for the homozygotes of RINO1 knockout. The abnormal embryo phenotype of RINO1 homozygotes was partially rescued by exogenous spraying of inositol and indole-3-acetic acid (IAA) in rice panicle. Thus, RINO1 is crucial for both seed InsP6 biosynthesis and embryonic development. The lower phosphatidylinositol (4,5)-bisphosphate (PI (4,5) P2) concentration and the disorder auxin distribution induced by insufficient inositol supply in seed embryos were among the regulatory switch steps leading to aberrant embryogenesis and failure of seed germination in RINO1 knockout.

HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development.

The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.

Arabidopsis cyclophilins direct intracellular transport of mobile mRNA via organelle hitchhiking.

Plants convert external cues into mobile mRNAs to synchronize meristematic differentiation with environmental dynamics. These mRNAs are selectively transported to intercellular pores, plasmodesmata (PD), for cell-to-cell movement. However, how plants recognize and deliver mobile mRNAs to PD remains unknown. Here we show that mobile mRNAs hitchhike on organelle trafficking to transport towards PD. Perturbed cytoskeleton organization or organelle trafficking severely disrupts the subcellular distribution of mobile mRNAs. Arabidopsis rotamase cyclophilins (ROCs), which are organelle-localized RNA-binding proteins, specifically bind mobile mRNAs on the surface of organelles to direct intracellular transport. Arabidopsis roc mutants exhibit phenotype alterations and disruptions in the transport of mobile mRNAs. These findings suggest that ROCs play a crucial role in facilitating the systemic delivery of mobile mRNAs. Our results highlight that an RNA-binding protein-mediated hitchhiking system is specifically recruited to orient plant mobile mRNAs for intercellular transport.

Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics.

The intricate morphology of the flower is primarily established within floral meristems in which floral organs will be defined and from where the developing flower will emerge. Floral meristem development involves multiscale-level regulation, including lineage and positional mechanisms for establishing cell-type identity, and transcriptional regulation mediated by changes in the chromatin environment. However, many key aspects of floral meristem development remain to be determined, such as: 1) the exact role of cellular location in connecting transcriptional inputs to morphological outcomes, and 2) the precise interactions between transcription factors and chromatin regulators underlying the transcriptional networks that regulate the transition from cell proliferation to differentiation during floral meristem development. Here, we highlight recent studies addressing these points through newly developed spatial reconstruction techniques and high-resolution transcription factor-chromatin environment interactions in the model plant Arabidopsis thaliana. Specifically, we feature studies that reconstructed 3D gene expression atlases of the floral meristem. We also discuss how the precise timing of floral meristem specification, floral organ patterning, and floral meristem termination is determined through temporally defined epigenetic dynamics for fine-tuning of gene expression. These studies offer fresh insights into the well-established principles of floral meristem development and outline the potential for further advances in this field in an age of integrated, powerful, multiscale resolution approaches.

Genome-wide identification of the CclKNOX gene family and functional characterization of CclKNOX3 and CclKNOX5 in citrus shoot development

KNOTTED1-LIKE HOMEOBOX (KNOX) genes are a relatively conserved gene family in plants, and have important regulatory functions in the morphological development of plants. In this study, a total of 9 KNOX proteins were found from citrus and divided into two classes, Class I and Class II. Subsequently, their gene structures, protein characteristics and sequence features were analyzed. Spatial expression analysis showed that most of the genes exhibited a constitutive expression pattern in different tissues of Citrus clementina. Interestingly, the expression pattern of CclKNOX3 was different from other Class I members, as it was mainly expressed in stems, lateral buds and shoot tips. Overexpression of CclKNOX3 led to strong differentiation of shoot apical meristem and curled leaves in transgenic tobacco and lemon. In addition, CclKNOX3 was found to interact with CclKNOX5, localized in the nucleus and have transcriptional inhibitory activity. Further transgenic analysis found that 35S:CclKNOX5 transgenic tobacco showed similar phenotype with 35S:CclKNOX3. Furthermore, yeast one hybrid and luciferase assay confirmed that CclKNOX3 and CclKNOX5 were regulated by CclKNOX4. This study expands our knowledge about the citrus KNOX family and provides valuable informations for future studies on shoot developmental regulation.

Arabidopsis leaf-expressed AGAMOUS-LIKE 24 mRNA systemically specifies floral meristem differentiation.

Plants can record external stimuli in mobile mRNAs and systemically deliver them to distal tissues to adjust development. Despite the identification of thousands of mobile mRNAs, the functional relevance of mobile mRNAs remains limited. Many mobile mRNAs are synthesized in the source cells that perceive environmental stimuli, but specifically exert their functions upon transportation to the recipient cells. However, the translation of mobile mRNA-encoded protein in the source cells could locally activate downstream target genes. How plants avoid ectopic functions of mobile mRNAs in the source cells to achieve tissue specificity remains to be elucidated. Here, we show that Arabidopsis AGAMOUS-LIKE 24 (AGL24) is a mobile mRNA whose movement is necessary and sufficient to specify floral organ identity. Although AGL24 mRNA is expressed in vegetative tissues, AGL24 protein exclusively accumulates in the shoot apex. In leaves, AGL24 proteins are degraded to avoid ectopically activating its downstream target genes. Our results reveal how selective protein degradation in source cells provides a strategy to limit the local effects associated with proteins encoded by mobile mRNAs, which ensures that mobile mRNAs specifically trigger systemic responses only in recipient tissues.

Genome-Wide Analysis of WOX Multigene Family in Sunflower (Helianthus annuus L.).

The WUSCHEL-related homeobox (WOX) is a family of specific transcription factors involved in plant development and response to stress, characterized by the presence of a homeodomain. This study represents the first comprehensive characterization of the WOX family in a member of the Asteraceae family, the sunflower (H. annuus L.). Overall, we identified 18 putative HaWOX genes divided by phylogenetic analysis in three major clades (i.e., ancient, intermediate, and WUS). These genes showed conserved structural and functional motifs. Moreover, HaWOX has homogeneously distributed on H. annuus chromosomes. In particular, 10 genes originated after whole segment duplication events, underpinning a possible evolution of this family along with the sunflower genome. In addition, gene expression analysis evidenced a specific pattern of regulation of the putative 18 HaWOX during embryo growth and in ovule and inflorescence meristem differentiation, suggesting a pivotal role for this multigenic family in sunflower development. The results obtained in this work improved the understanding of the WOX multigenic family, providing a resource for future study on functional analysis in an economically valuable species such as sunflower.

Discriminant analysis for estimating meristematic differentiation point based on morphometric indicators in banana (Musa AAA)

In the banana crop, leaf area is a fundamental trait for production; however, monitoring this variable during a cycle is difficult due to the structural characteristics of the plant, and a method for its determination is necessary. Therefore, the objective of this research was to propose a model for estimating total leaf area by measuring the cross-sectional area of the pseudostem to identify when meristematic differentiation occurs. In plants between F10 and flowering, functional leaves were measured for length, width, and dry mass. Cross-sectional area was calculated every 10 cm from the base to 70 cm, at ⅓, ½ of the plant height and up to the last pair of leaves. From the principal components, the cross-sectional measurement at 50 cm was selected, obtaining a nonlinear model for indirect estimation of leaf area. Subsequently, Fisher’s linear discriminant analysis was used with the parameters associated with the number of leaves emitted and the estimated leaf area to obtain the cutoff point as the centroid of the extracted components. As an indicator for the approximate identification of the moment of meristem differentiation, the emission of leaf 12 was generated, which determines the phenological stage (vegetative-reproductive) of the plant. The results describe tools to follow up the growth in the productive units to facilitate crop monitoring, allowing the generation of differential production approaches.

Paradigm and Framework of WUS-CLV Feedback Loop in Stem Cell Niche for SAM Maintenance and Cell Identity Transition

Shoot apical meristem (SAM) consists of stem cells that act as a reservoir for the aerial growth. It plays an important role in the differential architectural development in plants. SAM actively performs parallel functions by maintaining the pluripotent of stem cells and continuous organogenesis throughout the plant’s life cycle. Molecular mechanisms regulating the signaling networks of this dual function of the SAM have been progressively understood. In the SAM, the feedback loop of WUSCHEL (WUS)-CLAVATA (CLV) has been found to be the key regulator in stabilizing stem cell proliferation and differentiation. In general, WUS migrates into central zone (CZ) from organizing center (OC) and activates the expression of CLV3 by binding to the promoter elements. CLV3 acts as a ligand to interact with the CLV1, leucine rich repeats (LRR) receptor-like kinase (RLK) and LRR receptor-like protein CLV2, and protein kinase coryne (CRN) (CLV2/CRN) to restrict WUS transcription to the OC. Evolution of CLV3 is one of the main factors contributing to the transformation of two-dimensional (2D) to 3D plants. WUS-CLV loop is involved in several pathways and networks that integrate on meristem maintenance and cell identity transition. WUS-CLV maintains stem cells with simultaneous differentiation signals by the spatial-temporal signaling of the phytohormones. WUS-CLV loop has an interaction with reactive oxygen species (ROS), an important signaling molecules regulating cell proliferation and developmental transition. WUS also forms feedback loop with AGAMOUS (AG) for differentiation, proliferation, and termination of floral meristem. These loops might also involve in interaction with vernalization and its regulatory factors that oversees the precise timing of flowering after exposure to cold temperatures. In this review, we highlight the evolutionary and developmental importance of the WUS-CLV feedback loop on SAM maintenance and cell identity transition for inflorescence and floral meristem development.

Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.

Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum

La and La-related proteins (LARPs) are RNA-binding proteins regulating gene expression. Here, identification and molecular evolution of La and LARP gene family were performed in 16 plant species. Firstly, 188 La and LARP genes were identified. Based on phylogenetic tree and gene structure, they can be divided into three categories: La, LARP1 and LARP6. LARP1 can be further divided into LARP1-L and LARP1-S sub-categories. Compared with the LARP1-S, one additional DM15 domain was found in the C-terminal of LARP1-L. La and LARP genes are mainly distributed at both ends of chromosomes with a relatively consistent distribution position in A and D genomes of Gossypium hirsutum. Las and LARPs of G. hirsutum probably came from cruciferae, and gene recombination and chromosome structure variation occurred in G. hirsutum during evolution. The expression patterns and the distribution of cis-acting elements were also analyzed. The results showed that Las and LARPs respond to some abiotic stresses and hormone stimulation. The protein interaction network indicated that La and LARP proteins may be involved in meristem differentiation, hormone signal transduction, and post-translational modification. This study will provide a basis for the further functional and evolutional study of this gene family.

Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity.

The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley transcriptome and leaf chlorophyll content under 8h conditions, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. This might lead to a cascade of suspended sink-source activities, which ultimately delay organ development and differentiation in barley shoot meristems under short photoperiods.

Auxin-regulated timing of transition from vegetative to reproductive growth in rapeseed (Brassica napus L.) under different nitrogen application rates.

Accelerating the differentiation of floral meristem (FM) from shoot apical meristems (SAM) which determines the conversion from vegetative to reproductive growth is of great significance for the production of rapeseed (Brassica napus L.). In this research, the mechanisms of different nitrogen (N) application rates (low N, N1; normal N, N2; and high N, N3) on different FM development stages triggering the regulation of FM differentiation genes through the auxin biosynthetic and signal transduction were investigated. We found that the stage of FM differentiation, which was identified through a stereomicroscope and scanning electron microscope, came 4 and 7 days earlier under high N rate than under normal and low N levels, with the seed yield increased by 11.1 and 22.6%, respectively. Analysis of the auxin and its derivatives contents showed that the main biosynthesis way of auxin was the indole acetaldehyde oxime (IAOx) pathway, with 3-Indole acetonitrile dramatically accumulated during FM differentiation. At the same time, an obvious decrease of IAA contents at each FM differentiation stage was detected, and then gradually rose. Results of the expression of genes involved in auxin biosynthesis, auxin signaling transduction, and FM identification under five FM differentiation stages and three nitrogen application rates showed that genes involved in auxin biosynthesis were regulated before the FM differentiation stage, while the regulation of FM identity genes appeared mainly at the middle and later periods of the five stages, and the regulation level of genes varied under different N rates. Taken together, a high nitrogen rate could accelerate the initiation of FM differentiation, and auxin involved a lot in this regulation.

Transcriptome Analysis to Explore the Cause of the Formation of Different Inflorescences in Tomato

The number of inflorescence branches is an important agronomic character of tomato. The meristem differentiation and development pattern of tomato inflorescence is complex and its regulation mechanism is very different from those of other model plants. Therefore, in order to explore the cause of tomato inflorescence branching, transcriptome analysis was conducted on two kinds of tomato inflorescences (single racemes and compound inflorescences). According to the transcriptome data analysis, there were many DEGs of tomato inflorescences at early, middle, and late stages. Then, GO and KEGG enrichments of DEGs were performed. DEGs are mainly enriched in metabolic pathways, biohormone signaling, and cell cycle pathways. According to previous studies, DEGs were mainly enriched in metabolic pathways, and FALSIFLORA (FA) and ANANTHA (AN) genes were the most notable of 41 DEGs related to inflorescence branching. This study not only provides a theoretical basis for understanding inflorescence branching, but also provides a new idea for the follow-up study of inflorescence.

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.