Inflorescence Development Research Articles

Transcriptional repressor AGL79 positively regulates flowering time in Arabidopsis

The MADS-box gene family is widely distributed in higher plants and the members of the angiosperm-specific APETALA1/FRUITFULL (AP1/FUL) subfamily plays important roles in the regulation of plant reproductive development. Recent studies revealed that the AP1/FUL subfamily member Dt2, VEGETATIVE1/PsFRUITFULc (VEG1/PsFULc) and MtFRUITFULc (MtFULc) are essential for the stem growth, branching and inflorescence development in legume species soybean (Glycine max), pea (Pisum sativum) and Medicago truncatula. However, the biological function of their homologue in Arabidopsis thaliana, AGAMOUS-LIKE 79 (AGL79), has not been well elucidated. In this study, we investigated the developmental roles of Arabidopsis AGL79 by CRISPR/Cas9-mutagenesis and molecular and physiological analyses. We found that AGL79 mainly acts as a transcriptional repressor and positively regulates Arabidopsis flowering time. We further revealed that AGL79 interacts with SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) and represses the expression of TERMINAL FLOWER 1 (TFL1). Our results demonstrated the AGL79-mediated flowering regulation in Arabidopsis and added an additional layer of complexity to the understanding of flowering time regulation in dicot plants.

The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice.

The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.

Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

Diversity of woodland strawberry inflorescences arises from heterochrony regulated by TERMINAL FLOWER 1 and FLOWERING LOCUS T.

A vast variety of inflorescence architectures have evolved in angiosperms. Here, we analyze the diversity and development of the woodland strawberry (Fragaria vesca) inflorescence. Contrary to historical classifications, we show that it is a closed thyrse: a compound inflorescence with determinate primary monopodial axis and lateral sympodial branches, thus combining features of racemes and cymes. We demonstrate that this architecture is generated by 2 types of inflorescence meristems differing in their geometry. We further show that woodland strawberry homologs of TERMINAL FLOWER 1 (FvTFL1) and FLOWERING LOCUS T (FvFT1) regulate the development of both the racemose and cymose components of the thyrse. Loss of functional FvTFL1 reduces the number of lateral branches of the main axis and iterations in the lateral branches but does not affect their cymose pattern. These changes can be enhanced or compensated by altering FvFT1 expression. We complement our experimental findings with a computational model that captures inflorescence development using a small set of rules. The model highlights the distinct regulation of the fate of the primary and higher-order meristems, and explains the phenotypic diversity among inflorescences in terms of heterochrony resulting from the opposite action of FvTFL1 and FvFT1 within the thyrse framework. Our results represent a detailed analysis of thyrse architecture development at the meristematic and molecular levels.

Relationship between the Growth of Current Shoot and the Development of Inflorescence and Vegetative Buds in Oncidesa Gower Ramsey ‘Honey Angel’ Leaf Axils

The flowering control of Oncidesa Gower Ramsey ‘Honey Angel’ is important and in-demand by the industry. Therefore, an understanding of the development of inflorescence and vegetative shoot from the leaf axils on the current shoot is required. The internode of a young Oncidesa current shoot between the 0th (at the base of the pseudobulb) and 1st (immediately above the pseudobulb) nodes can enlarge to form a pseudobulb, and the axillary bud on the 0th or -1st (immediately below the 0th node) node can differentiate into an inflorescence bud. The axillary buds on the lower nodes (-2nd to -4th nodes) can remain vegetative. In this study, we investigated the growth and anatomical features of axillary buds at various stages during the growth of the current shoot. We sampled the axillary buds on the 0th to -4th nodes from the current shoots when they were 10, 15, 20, 25, and 30 cm in length for sectioning and anatomical observations. Vegetative buds on the -2nd to -4th nodes grew faster and had more nodes than the inflorescence bud when the current shoot grew from 10 to 25 cm. However, when the current shoot elongated from 25 to 30 cm, the length and node number in the inflorescence bud on the 0th node increased and the inflorescence branch primordia were observable. The length and node number of the inflorescence bud became the same as that of the vegetative buds, which had no further growth, whereas the current shoot grew from 25 to 30 cm. The pseudobulb began to emerge from the leaf sheath (unsheathing) when the current shoot had reached 30 cm in length. Therefore, the time when the pseudobulb started to unsheathe from its subtending leaf was critical for the reproductive growth of Oncidesa Gower Ramsey ‘Honey Angel’ when growth acceleration of the inflorescence bud occurred. Evaluating the current shoot length can be a nondestructive method of estimating the developmental stage of the inflorescence bud.

Tomato APETALA2 family member SlTOE1 regulates inflorescence branching by repressing SISTER OF TM3.

Inflorescence architecture directly impacts yield potential in most crops. As a model of sympodial plants, tomato (Solanum lycopersicum) inflorescence exhibits highly structural plasticity. However, the genetic regulatory network of inflorescence architecture in tomato remains unclear. Here, we investigated a modulator of inflorescence branching in tomato, TARGET OF EAT1 (SlTOE1), an APETALA2 (AP2) family member found to be predominantly expressed in the floral meristem (FM) of tomato. sltoe1 knockout mutants displayed highly branched inflorescences and defective floral organs. Transcriptome analysis revealed that SISTER OF TM3 (STM3) and certain floral development-related genes were upregulated in the flower meristem of sltoe1. SlTOE1 could directly bind the promoters of STM3 and Tomato MADS-box gene 3 (TM3) to repress their transcription. Simultaneous mutation of STM3 and TM3 partially restored the inflorescence branching of the sltoe1cr mutants, suggesting that SlTOE1 regulates inflorescence development, at least in part through an SlTOE1STM3/TM3 module. Genetic analysis showed that SlTOE1 and ENHANCER OF JOINTLESS 2 (EJ2) additively regulate tomato inflorescence branching; their double mutants showed more extensive inflorescence branching. Our findings uncover a pathway controlling tomato inflorescence branching and offer deeper insight into the functions of AP2 subfamily members.

SUPERMAN strikes again in legumes.

The SUPERMAN (SUP) gene was described in Arabidopsis thaliana over 30 years ago. SUP was classified as a cadastral gene required to maintain the boundaries between reproductive organs, thus controlling stamen and carpel number in flowers. We summarize the information on the characterization of SUP orthologs in plant species other than Arabidopsis, focusing on the findings for the MtSUP, the ortholog in the legume Medicago truncatula. M. truncatula has been widely used as a model system to study the distinctive developmental traits of this family of plants, such as the existence of compound inflorescence and complex floral development. MtSUP participates in the complex genetic network controlling these developmental processes in legumes, sharing conserved functions with SUP. However, transcriptional divergence between SUP and MtSUP provided context-specific novel functions for a SUPERMAN ortholog in a legume species. MtSUP controls the number of flowers per inflorescence and the number of petals, stamens and carpels regulating the determinacy of ephemeral meristems that are unique in legumes. Results obtained in M. truncatula provided new insights to the knowledge of compound inflorescence and flower development in legumes. Since legumes are valuable crop species worldwide, with high nutritional value and important roles in sustainable agriculture and food security, new information on the genetic control of their compound inflorescence and floral development could be used for plant breeding.

Differential gene expression analysis of the resprouting process in Pinus canariensis provides new insights into a rare trait in conifers

Resprouting is crucial in population dynamics in response to wildfires or herbivory. This trait, common in angiosperms, is considered rare in conifers, being Pinus canariensis one of the few species able to resprout. We analyzed gene expression during wound-induced resprouting in 5 years-old Canarian pines. RNA was extracted at three different stages, including control samples from remote branches, representing immediate response to wounding (R0), resprouting initiation (R1), and elongation (R2), and then hybridized to a microarray designed with 15,000 cDNAs from Pinus canariensis transcriptome of meristematic activity. We found 1164 Differentially Expressed Genes (DEGs), of which 903 were significant in R0, 278 in R1, and 261 in R2. Genes related to defense- and stress-response were mainly found to be overexpressed at R0, while DEGs coding for transcription factors such as GROWTH-REGULATING FACTOR (GRF), FLOWERING-PROMOTING FACTOR (FPF), and the HOMEODOMAIN LEUCINE ZIPPER Class IV (HD-ZIP IV), mainly related to outgrowth processes and lateral organogenesis in plants, showed overexpression at R1 and R2, when new shoots were emerging. This data was compared to differential gene expression during apical growth in P. canariensis, suggesting similarities between vegetative apical growth and regulation of lateral shoot development in response to mechanical wounding, but also yielding 32 DEGs exclusively overexpressed at some point during resprouting stages (R1 and/or R2). The implication of such transcription factor families, with important roles in leaf and inflorescence development also in flowering plants, suggests underlying homologies between common lateral organogenesis processes in angiosperms and resprouting in gymnosperms.

Phenology of flowering and seed development of jernang rattan (Daemonorops spp.)

Abstract. Fridayanti N, Widajati E, Ilyas S, Budi SW, Palupi ER. 2023. Phenology of flowering and seed development of jernang rattan (Daemonorops spp.). Biodiversitas 24: 349-358. Jernang rattan has a high economic value due to its resin content in the exocarp, as the raw material of dyes, medicines, and cosmetics. The resin is highest in the immature fruit skin (exocarp); therefore, fruits are harvested before the seed is germinable. As a consequence, regeneration is very scarce, and the species is categorized as a rare plant. This research was aimed at investigating the flowering phenology and seed development of jernang rattan until they reach physiological maturity, when the viability and vigor are at their highest. The flowering phenology was observed based on Biologische Bundesanstalt Bundessortenamt and Chemische Industrie (BBCH), at the inflorescence stage, flowering stage, fruit development stage, and fruit ripening stage. The inflorescence development from flower bud until ready to bloom took 136.4 ±10.9 days for male plants and 141.6 ±16.4 days for female plants. The inflorescence of staminate flowers bloomed longer (29.4 ±2.7 days) than pistillate flowers (15.4 ± 4.0 days). Fruit abortion mostly occurs during the first six months of fruit development, coincides with the nuclear stage of endosperm, and the final seed set is 56%. It takes around 27 months of one reproduction cycle from the appearance of the inflorescence to seed maturity. The fruit reaches physiological maturity approximately at 22 MAA when the seed is of high viability and vigor, and harvesting at 22 MAA is best for seed production. It is recommended to set up a seed production area separated from the resin production area.

Reproductive development of common buckwheat (Fagopyrum esculentum Moench) and its wild relatives provides insights into their evolutionary biology.

Understanding the complex inflorescence architecture and developmental morphology of common buckwheat (Fagopyrum esculentum) is crucial for crop yield. However, most published descriptions of early flower and inflorescence development in Polygonaceae are based on light microscopy and often documented by line drawings. In Fagopyrum and many other Polygonaceae, an important inflorescence module is the thyrse, in which the primary axis never terminates in a flower and lateral cymes (monochasia) produce successively developing flowers of several orders. Each flower of a cyme is enclosed together with the next-order flower by a bilobed sheathing bract-like structure of controversial morphological nature. We explored patterns of flower structure and arrangement in buckwheat and its wild relatives, using comparative morphology, scanning electron microscopy and X-ray microtomography. Our data support interpretation of the sheathing bract as two congenitally fused phyllomes (prophylls), one of which subtends a next-order flower. In tepal-like bract, a homeotic mutant of F. esculentum, the bilobed sheathing bract-like organ acquires tepal-like features and is sometimes replaced by two distinct phyllomes. Wild representatives of F. esculentum (ssp. ancestrale) and most cultivars of common buckwheat possess an indeterminate growth type with lateral thyrses produced successively on the primary inflorescence axis until cessation of growth. In contrast, determinate cultivars of F. esculentum develop a terminal thyrse after producing lateral thyrses. In contrast to F. esculentum, the occurrence of a terminal thyrse does not guarantee a determinate growth pattern in F. tataricum. The number of lateral thyrses produced before the terminal thyrse on the main axis of F. tataricum varies from zero to c. 19. The nine stages of early flower development formally recognized here and our outline of basic terminology will facilitate more standardized and readily comparable descriptions in subsequent research on buckwheat biology. Non-trivial relative arrangements of tepals and bracteoles in Fagopyrum and some other Polygonaceae require investigation using refined approaches to mathematical modelling of flower development. Our data on inflorescence morphology and development suggest contrasting evolutionary patterns in the two main cultivated species of buckwheat, F. esculentum and F. tataricum. The genus Fagopyrum offers an excellent opportunity for evo-devo studies related to inflorescence architecture.

Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize

Increasing grain yield is required to meet the rapidly expanding demands for food, feed, and fuel. Inflorescence meristems are central to plant growth and development. However, the question concerning whether inflorescence development can be regulated to improve grain yield remains unclear. Here, we describe a naturally occurring single recessive mutation called fea5 that can increase grain yield in maize. Using bulk segregant analysis sequencing (BSA-seq), the candidate region was initially mapped to a large region on chromosome 4 (4.68 Mb-11.26 Mb). Transcriptome sequencing (RNA-seq) revealed a total of 1246 differentially expressed genes (DEGs), of which 835 were up-regulated and 411 were down-regulated. Further analysis revealed the enrichment of DEGs in phytohormone signal transduction. Consistently, phytohormone profiling indicated that auxin (IAA), jasmonic acid (JA), ethylene (ETH), and cytokinin (CK) levels increased significantly, whereas the gibberellin (GA) level decreased significantly in fea5. By integrating BSA-seq with RNA-seq, we identified Zm00001d048841 as the most likely candidate gene. Our results provide valuable insight into this new germplasm resource and the molecular mechanism underlying fasciated ears that produce a higher kernel row number in maize.

Carbohydrate Changes in the Pseudobulbs of Oncidesa Gower Ramsey ‘Honey Angel’ during Vegetative and Reproductive Growth

Pseudobulbs are carbohydrate storage organs in Oncidesa. A current pseudobulb forms on a developing vegetative shoot in each growth cycle and it becomes a back pseudobulb when the next vegetative shoot emerges. Both current and back pseudobulbs store carbohydrates, but their functions might differ because the inflorescence emerges from the new (current) shoot after the shoot has developed to a certain stage. This study investigated carbohydrate storage and use in current and back pseudobulbs. We analyzed carbohydrates in the current pseudobulb at five stages during inflorescence development. Glucose and fructose were the highest in the current pseudobulb in the first two stages, when the inflorescence was 10 to 35 cm tall. Then, both glucose and fructose decreased in the following stages to support inflorescence development, but starch increased at that time. In addition, we used Oncidesa with one or two new vegetative shoots to study the use of carbohydrates in pseudobulbs during growth cycles. In both plants with one or two shoots, glucose and fructose accumulated when current pseudobulbs formed, but plants with two new shoots had smaller current pseudobulbs and lower monosaccharide concentrations. Plants with two shoots also consumed more starch in all back pseudobulbs, whereas in the plants with one new shoot, starch only decreased significantly in the first back pseudobulb, which was closer to the new shoot. In addition, if an inflorescence did not develop in the previous growth cycle, new shoots used the monosaccharides that remained in the youngest back pseudobulb for growth; at the same time, starch accumulated in all back pseudobulbs. The current pseudobulb was the actively growing part. Its main carbohydrates were monosaccharides, which accounted for 25% of dry weight and Oncidesa used these carbohydrates mainly for inflorescence growth. After monosaccharides in the pseudobulb were used, the pseudobulb began to store starch. Back pseudobulbs, in which >50% of dry weight was starch, were the primary storage organs that supported new vegetative shoot growth and partly supported later inflorescence development that emerged from the new (current) shoot.

Characterization of a barley (Hordeum vulgare L.) mutant with multiple stem nodes and spikes and dwarf (msnsd) and fine-mapping of its causal gene.

Multiple nodes and dwarf mutants in barley are a valuable resource for identifying genes that control shoot branching, vegetative growth and development. In this study, physiological, microscopic and genetic analysis were conducted to characterize and fine-map the underling gene of a barley mutant with Multiple Stem Nodes and Spikes and Dwarf (msnsd), which was selected from EMS- and 60Co-treated barley cv. Edamai 934. The msnsd mutant had more stem nodes, lower plant height and a shorter plastochron than Edamai 934. Moreover, the mutant had two or more spikes on each tiller. Microscopic analysis showed that the dwarf phenotype of msnsd resulted from reduced cell lengths and cell numbers in the stem. Further physiological analysis showed that msnsd was GA3-deficient, with its plant height increasing after external GA3 application. Genetic analysis revealed that a single recessive nuclear gene, namely, HvMSNSD, controlled the msnsd phenotype. Using a segregating population derived from Harrington and the msnsd mutant, HvMSNSD was fine-mapped on chromosome 5H in a 200 kb interval using bulked segregant analysis (BSA) coupled with RNA-sequencing (BSR-seq), with a C-T substitution in the exon of HvTCP25 co-segregating with the msnsd phenotype. RNA-seq analysis showed that a gene encoding gibberellin 2-oxidase 8, a negative regulator of GA biosynthesis, was upregulated in the msnsd mutant. Several known genes related to inflorescence development that were also upregulated and enriched in the msnsd mutant. Collectively, we propose that HvMSNSD regulates the plastochron and morphology of reproductive organs, likely by coordinating GA homeostasis and changed expression of floral development related genes in barley. This study offers valuable insights into the molecular regulation of barley plant architecture and inflorescence development.

AN ALGORITHM FOR RESEARCH OF SUNFLOWER HYBRIDS PRODUCTIVITY UNDER CONDITIONS OF INSECT POLLINATION

The article summarizes the practical experience of five-year research on seed productivity of autofertile hybrids of sunflower Helianthus annuus L. in the presence and absence of insect pollination. The productivity of 21 sunflower hybrids from six producers «Pioneer», «Syngenta», «Euralis», «Limagrain», «MAS Seeds», «RAGT» - was studied. Experiments were conducted in the fields of the Continental Farmers Group agro-holding in the agroclimatic conditions of Western Ukraine. To exclude the effect of insect pollination, the heads of experimental plants were covered with bag isolators made of 50x40 cm polypropylene spunbond with a density of 30 g/m2 and the ability to adjust the strength of tying during inflorescence development. The heads of control plants were left open for free insect pollinators access. After full seed maturity, the isolators were removed from the experimental plants, and the heads of control plants were selected based on the identity of their diameters. The selected material was dried to an air-dry state and used for further research in laboratory conditions. Seed productivity was determined by indicators such as incompleteness of heads and seeds in different zones of the head disk, huskiness, 1000-seed weight, purity, biological yield, oil content, and protein content. Individual indicators of hybrid productivity were studied for the head disk within the outer, intermediate, and inner zones, each of which occupied one-third of its radius. To determine the incompleteness of seeds and huskiness in each zone of the head disk, 20 seeds were randomly selected from each zone and cleaned of seed coats. Analysis of oil content and protein content was carried out by a non-invasive method of NIR spectroscopy. The paired Wilcoxon criterion was used to determine statistically significant differences between control and experimental groups of plants under different pollination conditions. As a result of the conducted research, it was possible to develop an algorithm for determining quantitative and qualitative indicators of productivity of modern sunflower hybrids in the presence and absence of insect pollination

Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae.

The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.

NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer.

BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.

Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture.

Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.

Constructing the maize inflorescence regulatory network by using efficient tsCUT&Tag assay

Maize ear development determines the crop yield, and many important transcription factors (TFs) have been identified to function in this process. However, their transcriptional regulation mechanisms are still elusive. In this study, we generated the genome-wide DNA binding sites for 8 TFs which are known to function or highly expressed in inflorescence by applying the tsCUT&Tag method in maize leaf protoplast. We exposed a regulatory grid of 4 WUSCHEL-related homeobox (WOX) genes and revealed their potential regulatory mechanisms. In addition, a hierarchical regulation network for the determinacy and specification of maize inflorescence meristems were also constructed using the binding profiles of a floral development gene INDETERMINATE FLORAL APEX1 (IFA1) and 3 MADS-box genes. Our study provides an in-depth understanding and new insights of the regulatory mechanisms during maize inflorescence development.

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.