Characterization of peanut phytochromes and their possible regulating roles in early peanut pod development

Engineering plant photoreceptors towards enhancing plant productivity

Light is a critical environmental factor that governs the growth and development of plants. Plants have specialised photoreceptor proteins, which allow them to sense both quality and quantity of light and drive a wide range of responses critical for optimising growth, resource use and adaptation to changes in environment. Understanding the role of these photoreceptors in plant biology has opened up potential avenues for engineering crops with enhanced productivity by engineering photoreceptor activity and/or action. The ability to manipulate plant genomes through genetic engineering and synthetic biology approaches offers the potential to unlock new agricultural innovations by fine-tuning photoreceptors or photoreceptor pathways that control plant traits of agronomic significance. Additionally, optogenetic tools which allow for precise, light-triggered control of plant responses are emerging as powerful technologies for real-time manipulation of plant cellular responses. As these technologies continue to develop, the integration of photoreceptor engineering and optogenetics into crop breeding programs could potentially revolutionise how plant researchers tackle challenges of plant productivity. Here we provide an overview on the roles of key photoreceptors in regulating agronomically important traits, the current state of plant photoreceptor engineering, the emerging use of optogenetics and synthetic biology, and the practical considerations of applying these approaches to crop improvement. This review seeks to highlight both opportunities and challenges in harnessing photoreceptor engineering approaches for enhancing plant productivity. In this review, we provide an overview on the roles of key photoreceptors in regulating agronomically important traits, the current state of plant photoreceptor engineering, the emerging use of optogenetics and synthetic biology, and the practical considerations of applying these approaches to crop improvement.

ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L

Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.

Genetic characterization of flowering and phytochrome genes in peanut (Arachis hypogaea L.) for early maturity

BACKGROUND

Peanut (Arachis hypogaea L.) production and cropping pattern is highly influenced by the climatic factors including temperature and rain pattern fluctuations. It is one of the most important cash crop in the rain fed areas of Pakistan and its production, under changing climatic conditions, that can be improved by developing short duration varieties. The present study was based on the molecular characterization of the maturity associated gene families in the peanut under two light conditions.

METHODS AND RESULTS

Genomic analysis based on the in silico study of important gene families for early maturity associated attributes like flowering time, their pattern, duration and photoperiodism was done for a comprehensive mapping of maturity related genes. Phytochromes genes Phy A, Phy B and Phy E and flowering genes FT2a, Ft5a and COL2 were selected for in silico characterization for protein based analysis including Multiple Sequence Alignment (MSA), and Neighbor Joining (NJ) tree. MSA and NJ trees of the peanut with Arabidopsis thaliana and Glycine max showed a clear picture of the phylogenetic relationship on the basis of selected gene proteins. Expression profile of phytochrome and flowering genes revealed that photoperiod conditions i.e. short and long days, have great influence on the Phy A, Phy B and Phy E, Ft2a, FT5a and COL2 gene expression pattern. In current study, the relative expression of all studied genes was found higher in short day light condition at flower initiation stage of the plants than in the long light day condition with exception of COL2 gene protein.

CONCLUSIONS

The molecular characterization based on the in silico study of the particular genes and qPCR based gene expression profiling of the selected genes provided an evidence of the role of these genes and their comparative analysis under two photoperiodic conditions.

Phylogenetic analysis of phytochrome A gene from Lablab purpureus (L.) Sweet

BACKGROUND

Phytochromes are the best characterized photoreceptors that perceive Red (R)/Far-Red (FR) signals and mediate key developmental responses in plants. It is well established that photoperiodic control of flowering is regulated by PHY A (phytochrome A) gene. So far, the members of PHY A gene family remains unexplored in Lablab purpureus, and therefore, their functions are still not deciphered. PHYA3 is the homologue of phytochrome A and known to be involved in dominant suppression of flowering under long day conditions by downregulating florigens in Glycine max. The present study is the first effort to identify and characterize any photoreceptor gene (PHYA3, in this study) in Lablab purpureus and decipher its phylogeny with related legumes.

RESULTS

PHYA3 was amplified in Lablab purpureus cv GNIB-21 (photo-insensitive and determinate) by utilizing primers designed from GmPHYA3 locus of Glycine max. This study was successful in partially characterizing PHYA3 in Lablab purpureus (LprPHYA3) which is 2 kb longer and belongs to exon 1 region of PHYA3 gene. Phylogenetic analysis of the nucleotide and protein sequences of PHYA genes through MEGA X delineated the conservation and evolution of Lablab purpureus PHYA3 (LprPHYA3) probably from PHYA genes of Vigna unguiculata, Glycine max and Vigna angularis. A conserved basic helix-loop-helix motif bHLH69 was predicted having DNA binding property. Domain analysis of GmPHYA protein and predicted partial protein sequence corresponding to exon-1 of LprPHYA3 revealed the presence of conserved domains (GAF and PAS domains) in Lablab purpureus similar to Glycine max.

CONCLUSION

Partial characterization of LprPHYA3 would facilitate the identification of complete gene in Lablab purpureus utilizing sequence information from phylogenetically related species of Fabaceae. This would allow screening of allelic variants for LprPHYA3 locus and their role in photoperiod responsive flowering. The present study could aid in modulating photoperiod responsive flowering in Lablab purpureus and other related legumes in near future through genome editing.

Genetic Improvement of Peanut (Arachis hypogea L.) Genotypes by Developing Short Duration Hybrids

Peanut, the only cash crop of rainfed areas of Pakistan, is facing immense challenges due to global warming. Climatic factors particularly the temperature fluctuations and rain pattern shift significantly impact the production and yield of peanut and unavailability of resilient varieties exacerbate this impact. To deal with the cropping pattern change and yield losses, due to climate vagaries, a study was conducted to develop early maturing hybrids using line into tester mating design. The F₁ hybrids from the parental lines were produced in the year 2018 using Line × Tester mating design and then grown in the field in the year 2019 for further evaluation. The hybrids were evaluated based on the early maturity and yield-related attributes in comparison with the parental lines. Based on the general combining ability estimate, line V-3 (Golden), was found as best parent with highly significant values for plant height, days to peg formation, days to maturity, number of pegs per plant, number of pods per plants, number of seeds per plant, 100 pod weight 100 seed weight. Similarly, tester V-7 (PI 635006 01 SD) showed highly significant results of GCA for days to germination, day to 50% flowering, plant height, days to peg formation, days to maturity, number of pegs per plant, number of pods per plants, number of seeds per plant, 100 kernel weight, shelling percentage. All the combinations were evaluated for specific combining ability and significant results were observed for V-3 × V-4 (Golden × PI 619175 01 SD) and V-1 × V-6 (BARI-2000 × PI 564846 01 SD) by developing or maturity and yield-related attributes. The hybrid combinations V-3 × V-5 (Golden × PI 635006 01 SD) followed by V-3 × V-6 showed highly significant results for mid parent heterosis and better parent heterosis for days to 50% flowering, plant height, days to peg formation, number of pegs, days to maturity, number of mature seeds per plant, shelling ratio, 100 pod weight and 100 kernel weight. These parents and hybrid combinations with early maturity genes and high yield attributes can further be used for the development of short duration variety.

The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.

Molecular Characterization and Expression Patterns of the HkSVP Gene Reveal Distinct Roles in Inflorescence Structure and Floral Organ Development in Hemerocallis fulva

SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that play a key role in regulating vital developmental processes in plants. Hemerocallis are perennial herbs that exhibit continuous flowering development and have been extensively used in landscaping. However, there are few reports on the regulatory mechanism of flowering in Hemerocallis. To better understand the molecular basis of floral formation of Hemerocallis, we identified and characterized the SVP-like gene HkSVP from the Hemerocallis cultivar 'Kanai Sensei'. Quantitative RT-PCR (qRT-PCR) indicated that HkSVP transcript was mainly expressed in the vegetative growth stage and had the highest expression in leaves, low expression in petals, pedicels and fruits, and no expression in pistils. The HkSVP encoded protein was localized in the nucleus of Arabidopsis protoplasts and the nucleus of onion epidermal cells. Yeast two hybrid assay revealed that HKSVP interacted with Hemerocallis AP1 and TFL1. Moreover, overexpression of HkSVP in Arabidopsis resulted in delayed flowering and abnormal phenotypes, including enriched trichomes, increased basal inflorescence branches and inhibition of inflorescence formation. These observations suggest that the HkSVP gene may play an important role in maintaining vegetative growth by participating in the construction of inflorescence structure and the development of flower organs.

Genome-wide identification of peanut PIF family genes and their potential roles in early pod development

Peanut is typically a geocarpic plant. The developing gynophore ('peg') in air could not swell normally until it buries into soil, indicating light-to-dark conversion is necessary for early pod development in peanut. As the subfamily of basic helix-loop-helix (bHLH) transcription factors, phytochrome interacting factors (PIFs) are key regulators involved in light signaling pathways, and play crucial roles in plant growth and development. In the current study, a total of 14 AhPIFs were identified in cultivated peanut genome (Arachis hypogaea L., AABB), while seven AdPIFs and six AiPIFs were discovered in the two wild diploids (A. duranensis (AA), A. ipaensis (BB)) respectively. Phylogenetic analysis revealed that peanut PIFs were clustered into four distinct clades, and members within the same subgroup had conserved motifs and displayed similar exon-intron distribution patterns. Gene synteny analysis indicated most of the PIFs exhibit one-to-one homology relationship between AA and BB subgenome in A. hypogaea, as well as among the three peanut species. Gene duplication detection showed that segmental duplication and purifying selection contributed to the expansion and evolution of peanut PIF gene family. Transcript profiles combined with subcellular localization analysis suggested AhPIF3A4 and AhPIF3B4 may possibly be involved in regulation of peanut early pod development. This study could further facilitate functional characterization of PIFs in peanut and other legumes.

Exploring the edible gum (galactomannan) biosynthesis and its regulation during pod developmental stages in clusterbean using comparative transcriptomic approach

Galactomannan is a polymer of high economic importance and is extracted from the seed endosperm of clusterbean (C. tetragonoloba). In the present study, we worked to reveal the stage-specific galactomannan biosynthesis and its regulation in clusterbean. Combined electron microscopy and biochemical analysis revealed high protein and gum content in RGC-936, while high oil bodies and low gum content in M-83. A comparative transcriptome study was performed between RGC-936 (high gum) and M-83 (low gum) varieties at three developmental stages viz. 25, 39, and 50 days after flowering (DAF). Total 209,525, 375,595 and 255,401 unigenes were found at 25, 39 and 50 DAF respectively. Differentially expressed genes (DEGs) analysis indicated a total of 5147 shared unigenes between the two genotypes. Overall expression levels of transcripts at 39DAF were higher than 50DAF and 25DAF. Besides, 691 (RGC-936) and 188 (M-83) candidate unigenes that encode for enzymes involved in the biosynthesis of galactomannan were identified and analyzed, and 15 key enzyme genes were experimentally validated by quantitative Real-Time PCR. Transcription factor (TF) WRKY was observed to be co-expressed with key genes of galactomannan biosynthesis at 39DAF. We conclude that WRKY might be a potential biotechnological target (subject to functional validation) for developing high gum content varieties.

Medicago PHYA promotes flowering, primary stem elongation and expression of flowering time genes in long days

BACKGROUND

Flowering time is an important trait for productivity in legumes, which include many food and fodder plants. Medicago truncatula (Medicago) is a model temperate legume used to study flowering time pathways. Like Arabidopsis thaliana (Arabidopsis), its flowering is promoted by extended periods of cold (vernalization, V), followed by warm long day (LD) photoperiods. However, Arabidopsis flowering-time genes such as the FLOWERING LOCUS C (FLC)/ MADS AFFECTING FLOWERING (MAF) clade are missing and CONSTANS-LIKE (CO-LIKE) genes do not appear to have a role in Medicago or Pisum sativum (pea). Another photoperiodic regulator, the red/far red photoreceptor PHYTOCHROME A (PHYA), promotes Arabidopsis flowering by stabilizing the CO protein in LD. Interestingly, despite the absence of CO-LIKE function in pea, PsPHYA plays a key role in promoting LD photoperiodic flowering and plant architecture. Medicago has one homolog of PHYA, MtPHYA, but its function is not known.

RESULTS

Genetic analysis of two MtPHYA Tnt1 insertion mutant alleles indicates that MtPHYA has an important role in promoting Medicago flowering and primary stem elongation in VLD and LD and in perception of far-red wavelengths in seedlings. MtPHYA positively regulates the expression of MtE1-like (MtE1L), a homologue of an important legume-specific flowering time gene, E1 in soybean and other Medicago LD-regulated flowering-time gene homologues, including the three FLOWERING LOCUS T-LIKE (FT-LIKE) genes, MtFTa1, MtFTb1 and MtFTb2 and the two FRUITFULL-LIKE (FUL-LIKE) genes MtFULa and MtFULb. MtPHYA also modulates the expression of the circadian clock genes, GIGANTEA (GI) and TIMING OF CAB EXPRESSION 1a (TOC1a). Genetic analyses indicate that Mtphya-1 Mte1l double mutants flowered at the same time as the single mutants. However, Mtphya-1 Mtfta1 double mutants had a weak additive effect in delaying flowering and in reduction of primary axis lengths beyond what was conferred by either of the single mutants.

CONCLUSION

MtPHYA has an important role in LD photoperiodic control of flowering, plant architecture and seedling de-etiolation under far-red wavelengths in Medicago. It promotes the expression of LD-induced flowering time genes and modulates clock-related genes. In addition to MtFTa1, MtPHYA likely regulates other targets during LD floral induction in Medicago.

Defining the function of SUMO system in pod development and abiotic stresses in Peanut

BACKGROUND

Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world's major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB).

RESULTS

Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses.

CONCLUSIONS

The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.