Overexpression of Arabidopsis FLOWERING LOCUS T (FT) gene improves floral development in cassava (Manihot esculenta, Crantz)

CRISPR/Cas9: an advanced platform for root and tuber crops improvement

Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.

Genome-wide identification of PEBP gene family in pineapple reveal its potential functions in flowering

Phosphatidylethanolamine binding protein (PEBP) plays an important role in regulating flowering time and morphogenesis of plants. However, the identification and functional analysis of PEBP gene in pineapple (AcPEBP) have not been systematically studied. The pineapple genome contained 11 PEBP family members, which were subsequently classified into three subfamilies (FT-like, TFL-like and MFT-like) based on phylogenetic relationships. The arrangement of these 11 shows an unequal pattern across the six chromosomes of pineapple the pineapple genome. The anticipated outcomes of the promoter cis-acting elements indicate that the PEBP gene is subject to regulation by diverse light signals and endogenous hormones such as ethylene. The findings from transcriptome examination and quantitative real-time polymerase chain reaction (qRT-PCR) indicate that FT-like members AcFT3 and AcFT4 display a heightened expression level, specifically within the floral structures. The expression of AcFT3 and AcFT4 increases sharply and remains at a high level after 4 days of ethylene induction, while the expression of AcFT7 and AcMFT1 decreases gradually during the flowering process. Additionally, AcFT3, AcFT4 and AcFT7 show specific expression in different floral organs of pineapple. These outcomes imply that members belonging to the FT-like subfamily may have a significant impact on the process of bud differentiation and flower development. Through transcriptional activation analysis, it was determined that AcFT4 possesses transcriptional activation capability and is situated in the nucleus and peripheral cytoplasm. Overexpression of AcFT4 in Arabidopsis resulted in the promotion of early flowering by 6-7 days. The protein interaction prediction network identified potential flower regulators, including CO, AP1, LFY and SOC1, that may interact with PEBP proteins. This study explores flower development in pineapple, thereby serving as a valuable reference for future research endeavors in this domain.

The Development of Thematic Core Collections in Cassava Based on Yield, Disease Resistance, and Root Quality Traits

Thematic collections (TCs), which are composed of genotypes with superior agronomic traits and reduced size, offer valuable opportunities for parental selection in plant breeding programs. Three TCs were created to focus on crucial attributes: root yield (CC_Yield), pest and disease resistance (CC_Disease), and root quality traits (CC_Root_quality). The genotypes were ranked using the best linear unbiased predictors (BLUP) method, and a truncated selection was implemented for each collection based on specific traits. The TCs exhibited minimal overlap, with each collection comprising 72 genotypes (CC_Disease), 63 genotypes (CC_Root_quality), and 64 genotypes (CC_Yield), representing 4%, 3.5%, and 3.5% of the total individuals in the entire collection, respectively. The Shannon-Weaver Diversity Index values generally varied but remained below 10% when compared to the entire collection. Most TCs exhibited observed heterozygosity, genetic diversity, and the inbreeding coefficient that closely resembled those of the entire collection, effectively retaining 90.76%, 88.10%, and 88.99% of the alleles present in the entire collection (CC_Disease, CC_Root_quality, and CC_Disease, respectively). A PCA of molecular and agro-morphological data revealed well-distributed and dispersed genotypes, while a discriminant analysis of principal components (DAPC) displayed a high discrimination capacity among the accessions within each collection. The strategies employed in this study hold significant potential for advancing crop improvement efforts.

Hormonal Regulation and Stimulation Response of Jatropha curcas L. Homolog Overexpression on Tobacco Leaf Growth by Transcriptome Analysis

The Flowering locus T (FT) gene encodes the florigen protein, which primarily regulates the flowering time in plants. Recent studies have shown that FT genes also significantly affect plant growth and development. The FT gene overexpression in plants promotes flowering and suppresses leaf and stem development. This study aimed to conduct a transcriptome analysis to investigate the multiple effects of Jatropha curcas L. homolog (JcFT) overexpression on leaf growth in tobacco plants. The findings revealed that JcFT overexpression affected various biological processes during leaf development, including plant hormone levels and signal transduction, lipid oxidation metabolism, terpenoid metabolism, and the jasmonic-acid-mediated signaling pathway. These results suggested that the effects of FT overexpression in plants were complex and multifaceted, and the combination of these factors might contribute to a reduction in the leaf size. This study comprehensively analyzed the effects of JcFT on leaf development at the transcriptome level and provided new insights into the function of FT and its homologous genes.

Top and Side Lighting Induce Morphophysiological Improvements in Korean Ginseng Sprouts (Panax ginseng C.A. Meyer) Grown from One-Year-Old Roots

Nowadays, not only the roots, but also leaves and flowers of ginseng are increasingly popular ingredients in supplements for healthcare products and traditional medicine. The cultivation of the shade-loving crop, ginseng, is very demanding in terms of the light environment. Along with the intensity and duration, light direction is another important factor in regulating plant morphophysiology. In the current study, three lighting directions-top (T), side (S), or top + side (TS)-with an intensity of 30 ± 5 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) were employed. Generally, compared with the single T lighting, the composite lighting direction, TS, was more effective in shaping the ginseng with improved characteristics, including shortened, thick shoots; enlarged, thick leaves; more leaf trichomes; earlier flower bud formation; and enhanced photosynthesis. The single S light resulted in the worst growth parameters and strongly inhibited the flower bud formation, leading to the latest flower bud observation. Additionally, the S lighting acted as a positive factor in increasing the leaf thickness and number of trichomes on the leaf adaxial surface. However, the participation of the T lighting weakened these traits. Overall, the TS lighting was the optimal direction for improving the growth and development traits in ginseng. This preliminary research may provide new ideas and orientations in ginseng cultivation lodging resistance and improving the supply of ginseng roots, leaves, and flowers to the market.

Flowering and fruit-set in cassava under extended red-light photoperiod supplemented with plant-growth regulators and pruning

BACKGROUND

Cassava (Manihot esculenta Crantz) is staple food and major source of calories for over 500 million people in sub-Saharan Africa. The crop is also a source of income for smallholder farmers, and has increasing potential for industrial utilization. However, breeding efforts to match the increasing demand of cassava are impeded by its inability to flower, delayed or unsynchronized flowering, low proportion of female flowers and high fruit abortions. To overcome these sexual reproductive bottlenecks, this study investigated the effectiveness of using red lights to extend the photoperiod (RLE), as a gateway to enhancing flowering and fruit set under field conditions.

MATERIALS AND METHODS

Panels of cassava genotypes, with non- or late and early flowering response, 10 in each case, were subjected to RLE from dusk to dawn. RLE was further evaluated at low (LL), medium (ML) and high (HL) red light intensities, at ~  ≤ 0.5; 1.0 and 1.5PFD (Photon Flux Density) in µmol m^-2 s^-1 respectively. Additionally, the effect of a cytokinin and anti-ethylene as plant growth regulators (PGR) and pruning under RLE treatment were examined.

RESULTS

RLE stimulated earlier flower initiation in all genotypes, by up to 2 months in the late-flowering genotypes. Height and number of nodes at first branching, particularly in the late-flowering genotypes were also reduced, by over 50%. Number and proportion of pistillate flowers more than doubled, while number of fruits and seeds also increased. Number of branching levels during the crop season also increased by about three. Earlier flowering in many genotypes was most elicited at LL to ML intensities. Additive effects on flower numbers were detected between RLE, PGR and pruning applications. PGR and pruning treatments further increased number and proportion of pistillate flowers and fruits. Plants subjected to PGR and pruning, developed bisexual flowers and exhibited feminization of staminate flowers. Pruning at first branching resulted in higher pistillate flower induction than at second branching.

CONCLUSIONS

These results indicate that RLE improves flowering in cassava, and its effectiveness is enhanced when PGR and pruning are applied. Thus, deployment of these technologies in breeding programs could significantly enhance cassava hybridizations and thus cassava breeding efficiency and impact.

Flower-inducing technology facilitates speed breeding in cassava

Cassava is a tropical crop that provides daily carbohydrates to more than 800 million people. New cassava cultivars with improved yield, disease resistance, and food quality are critical to end hunger and reduce poverty in the tropics. However, the progress of new cultivar development has been dragged down by difficulties obtaining flowers from desired parental plants to enable designed crosses. Inducing early flowering and increasing seed production are crucial to improving the efficiency of developing farmer-preferred cultivars. In the present study, we used breeding progenitors to evaluate the effectiveness of flower-inducing technology, including photoperiod extension, pruning, and plant growth regulators. Photoperiod extension significantly reduced the time to flowering in all 150 breeding progenitors, especially late-flowering progenitors which were reduced from 6-7 months to 3-4 months. Seed production was increased by using the combination of pruning and plant growth regulators. Combining photoperiod extension with pruning and the PGR 6-benzyladenine (synthetic cytokinin) produced significantly more fruits and seeds than only photoperiod extension and pruning. Another growth regulator, silver thiosulfate, commonly used to block the action of ethylene, did not show a significant effect on fruit or seed production when combined with pruning. The present study validated a protocol for flower induction in cassava breeding programs and discussed factors to consider in implementing the technology. By inducing early flowering and increasing seed production, the protocol helped move one step further for speed breeding in cassava.

Multiple transcriptome comparisons reveal the essential roles of FLOWERING LOCUS T in floral initiation and SOC1 and SVP in floral activation in blueberry

The flowering mechanisms, especially chilling requirement-regulated flowering, in deciduous woody crops remain to be elucidated. Flower buds of northern highbush blueberry cultivar Aurora require approximately 1,000 chilling hours to bloom. Overexpression of a blueberry FLOWERING LOCUS T (VcFT) enabled precocious flowering of transgenic “Aurora” mainly in non-terminated apical buds during flower bud formation, meanwhile, most of the mature flower buds could not break until they received enough chilling hours. In this study, we highlighted two groups of differentially expressed genes (DEGs) in flower buds caused by VcFT overexpression (VcFT-OX) and full chilling. We compared the two groups of DEGs with a focus on flowering pathway genes. We found: 1) In non-chilled flower buds, VcFT-OX drove a high VcFT expression and repressed expression of a major MADS-box gene, blueberry SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (VcSOC1) resulting an increased VcFT/VcSOC1 expression ratio; 2) In fully chilled flower buds that are ready to break, the chilling upregulated VcSOC1 expression in non-transgenic “Aurora” and repressed VcFT expression in VcFT-OX “Aurora”, and each resulted in a decreased ratio of VcFT to VcSOC1; additionally, expression of a blueberry SHORT VEGETATIVE PHASE (VcSVP) was upregulated in chilled flower buds of both transgenic and non-transgenic’ “Aurora”. Together with additional analysis of VcFT and VcSOC1 in the transcriptome data of other genotypes and tissues, we provide evidence to support that VcFT expression plays a significant role in promoting floral initiation and that VcSOC1 expression is a key floral activator. We thus propose a new hypothesis on blueberry flowering mechanism, of which the ratios of VcFT-to-VcSOC1 at transcript levels in the flowering pathways determine flower bud formation and bud breaking. Generally, an increased VcFT/VcSOC1 ratio or increased VcSOC1 in leaf promotes precocious flowering and flower bud formation, and a decreased VcFT/VcSOC1 ratio with increased VcSOC1 in fully chilled flower buds contributes to flower bud breaking.

PEBP Signaling Network in Tubers and Tuberous Root Crops

Tubers and tuberous root crops are essential carbohydrate sources and staple foods for humans, second only to cereals. The developmental phase transition, including floral initiation and underground storage organ formation, is controlled by complex signaling processes involving the integration of environmental and endogenous cues. FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1/CENTRORADIALIS (TFL1/CEN), members of the phosphatidylethanolamine-binding protein (PEBP) gene family, play a central role in this developmental phase transition process. FT and FT-like proteins have a function to promote developmental phase transition, while TFL1/CEN act oppositely. The balance between FT and TFL1/CEN is critical to ensure a successful plant life cycle. Here, we present a summarized review of the role and signaling network of PEBP in floral initiation and underground storage organ formation, specifically in tubers and tuberous root crops. Lastly, we point out several questions that need to be answered in order to have a more complete understanding of the PEBP signaling network, which is crucial for the agronomical improvement of tubers and tuberous crops.

Long-day photoperiod and cool temperature induce flowering in cassava: Expression of signaling genes

Cassava is a staple food crop in the tropics, and is of particular importance in Africa. Recent development of genomic selection technology have improved the speed of cassava breeding; however, cassava flower initiation and development remains a bottleneck. The objectives of the current studies were to elucidate the effect of photoperiod, temperature and their interactions on the time of flowering and flower development in controlled environments, and to use RNA-sequencing to identify transcriptome expression underlying these environmental responses. Compared to a normal tropical day-length of 12 h, increasing the photoperiod by 4 h or decreasing the air temperature from 34/31 to 22°/19°C (day/night) substantially hastened the time to flowering. For both photoperiod and temperature, the environment most favorable for flowering was opposite the one for storage root harvest index. There was a pronounced treatment interaction: at warm day-time temperatures, percent flowering was low, and photoperiod had little effect. In contrast, at cooler temperatures, percent flowering increased, and long-day (LD) photoperiod had a strong effect in hastening flowering. In response to temperature, many differentially expressed genes in the sugar, phase-change, and flowering-time-integrator pathways had expression/flowering patterns in the same direction as in Arabidopsis (positive or negative) even though the effect of temperature on flowering operates in the reverse direction in cassava compared to Arabidopsis. Three trehalose-6-phosphate-synthase-1 (TPS1) genes and four members of the SPL gene family had significantly increased expression at cool temperature, suggesting sugar signaling roles in flower induction. In response to LD photoperiod, regulatory genes were expressed as in Arabidopsis and other LD flowering plants. Several hormone-related genes were expressed in response to both photoperiod and temperature. In summary, these findings provide insight on photoperiod and temperature responses and underlying gene expression that may assist breeding programs to manipulate flowering for more rapid crop improvement.

Heterologous expression of flowering locus T promotes flowering but does not affect diurnal movement in the legume Lotus japonicus

Flowering locus T (FT) is known to promote flowering in response to photoperiodic conditions and has recently been shown to contribute to other phenomenon, such as diurnal stomatal movement. In legumes, FTs are classified into three subtypes, though the role of each subtype is not well defined. It has been reported that when FT of Lotus japonicus (LjFT) is heterologously expressed in Arabidopsis, LjFT functions as a mobile florigen to promote flowering, similar to Arabidopsis FT (AtFT). In this study, we expressed AtFT in L. japonicus using the SUC2 promoter and showed that heterologous expression of AtFT was able to promote flowering in the plant. We also showed that AtFT expression does not affect stomatal closing nor nyctinastic leaf movement. These findings contribute to our understanding of flower development and have potential application to breeding or plant biotechnology.

Field transcriptome analysis reveals a molecular mechanism for cassava-flowering in a mountainous environment in Southeast Asia

The field survey in this article showed in 'KU50', a popular variety and late-branching type of cassava in Southeast Asia, that flowering rarely occurs in normal-field conditions in Southeast Asia but is strongly induced in the dry season in the mountainous region. Flowering time is correlated with the expression patterns of MeFT1 and homologs of Arabidopsis GI, PHYA, and NF-Ys. Cassava (Manihot esculenta Crantz) is a tropical crop that is propagated vegetatively rather than sexually by seed. Flowering rarely occurs in the erect-type variety grown in Southeast Asia, but it is known that cassava produces flowers every year in mountainous regions. Data pertaining to the effect of environmental factors on flowering time and gene expression in cassava, however, is limited. The aim of the present study was to determine the kinds of environmental conditions that regulate flowering time in cassava and the underlying molecular mechanisms. The flowering status of KU50, a popular variety in Southeast Asia and late-branching type of cassava, was monitored in six fields in Vietnam and Cambodia. At non-flowering and flowering field locations in North Vietnam, the two FLOWERING LOCUS T (FT)-like genes, MeFT1 and MeFT2, were characterized by qPCR, and the pattern of expression of flowering-related genes and genes responsive to environmental signals were analyzed by using RNA sequencing data from time-series samples. Results indicate that cassava flowering was induced in the dry season in the mountain region, and that flowering time was correlated with the expression of MeFT1, and homologs of Arabidopsis GI, PHYA, and NF-Ys. Based upon these data, we hypothesize that floral induction in cassava is triggered by some conditions present in the mountain regions during the dry season.

Lighting from Top and Side Enhances Photosynthesis and Plant Performance by Improving Light Usage Efficiency

Light is a critical environmental factor that influences plant growth and development, ranging from seed germination to flowering and fruiting. This study was carried out to explore how the optimal combination of various lighting directions increases the light usage efficiency and influences the plant morphophysiology, by investigating the plant growth parameters, leaf anatomy, epidermal morphology, stomatal properties, chlorophyll content, key physiological changes, and correlated gene expressions. In closed-type plant growth chambers, rooted cuttings of two chrysanthemum (Chrysanthemum morifolium Ramat.) cultivars, “Pearl Egg” and “Gaya Glory”, were subjected to a 10-h photoperiod with 600 μmol∙m⁻²·s⁻¹ photosynthetic photon flux density (PPFD) provided by light-emitting diodes (LEDs) in each light-direction combination (top (1/1) (T), top (1/2) + side (1/2) (TS), top (1/2) + bottom (1/2) (TB), side (1/2) + bottom (1/2) (SB), and top (1/3) + side (1/3) + bottom (1/3) (TSB)). The TS lighting significantly enhanced the morphophysiological performance, compared to the other lighting direction combinations. Notably, the excellent branch formation and earlier flowering were induced by the TS lighting in both “Pearl Egg” and “Gaya Glory” plants.

Cassava mosaic disease and its management in Southeast Asia

Key message

Status of the current outbreak of cassava mosaic disease (CMD) in Southeast Asia was reviewed. Healthy cassava seed production and dissemination systems have been established in Vietnam and Cambodia, along with integrated disease and pest management systems, to combat the outbreak.

Abstract

Cassava (Manihot esculenta Crantz) is one of the most important edible crops in tropical and subtropical regions. Recently, invasive insect pests and diseases have resulted in serious losses to cassava in Southeast Asia. In this review we discuss the current outbreak of cassava mosaic disease (CMD) caused by the Sri Lankan cassava mosaic virus (SLCMV) in Southeast Asia, and summarize similarities between SLCMV and other cassava mosaic begomoviruses. A SATREPS (Science and Technology Research Partnership for Sustainable Development) project “Development and dissemination of sustainable production systems based on invasive pest management of cassava in Vietnam, Cambodia and Thailand”, was launched in 2016, which has been funded by The Japan International Cooperation Agency (JICA) and The Japan Science and Technology Agency (JST), Japan. The objectives of SATREPS were to establish healthy seed production and dissemination systems for cassava in south Vietnam and Cambodia, and to develop management systems for plant diseases and insect pests of cassava. To achieve these goals, model systems of healthy seed production in Vietnam and Cambodia have been developed incorporating CMD-resistant planting materials through international networks with The International Center for Tropical Agriculture (CIAT) and The International Institute of Tropical Agriculture (IITA).

Supplementary Information

The online version contains supplementary material available at 10.1007/s11103-021-01168-2.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Reproductive barriers in cassava: Factors and implications for genetic improvement

Cassava breeding is hampered by high flower abortion rates that prevent efficient recombination among promising clones. To better understand the factors causing flower abortion and propose strategies to overcome them, we 1) analyzed the reproductive barriers to intraspecific crossing, 2) evaluated pollen-pistil interactions to maximize hand pollination efficiency, and 3) identified the population structure of elite parental clones. From 2016 to 2018, the abortion and fertilization rates of 5,748 hand crossings involving 91 parents and 157 progenies were estimated. We used 16,300 single nucleotide polymorphism markers to study the parents’ population structure via discriminant analysis of principal components, and three clusters were identified. To test for male and female effects, we used a mixed model in which the environment (month and year) was fixed, while female and male (nested to female) were random effects. Regardless of the population structure, significant parental effects were identified for abortion and fertilization rates, suggesting the existence of reproductive barriers among certain cassava clones. Matching ability between cassava parents was significant for pollen grains that adhered to the stigma surface, germinated pollen grains, and the number of fertilized ovules. Non-additive genetic effects were important to the inheritance of these traits. Pollen viability and pollen-pistil interactions in cross- and self-pollination were also investigated to characterize pollen-stigma compatibility. Various events related to pollen tube growth dynamics indicated fertilization abnormalities. These abnormalities included the reticulated deposition of callose in the pollen tube, pollen tube growth cessation in a specific region of the stylet, and low pollen grain germination rate. Generally, pollen viability and stigma receptivity varied depending on the clone and flowering stage and were lost during flowering. This study provides novel insights into cassava reproduction that can assist in practical crossing and maximize the recombination of contrasting clones.

Side Lighting Enhances Morphophysiology by Inducing More Branching and Flowering in Chrysanthemum Grown in Controlled Environment

Light is one of the most important factors that influence plant growth and development. This study was conducted to examine how lighting direction affects plant morphophysiology by investigating plant growth parameters, leaf anatomy, epidermal cell elongation, stomatal properties, chloroplast arrangement, and physiological changes. In closed-type plant factory units, the rooted cuttings of two chrysanthemum (Chrysanthemum morifolium Ramat.) cultivars, ‘Gaya Glory’ and ‘Pearl Egg’, were subjected to a 10 h photoperiod with a 300 μmol∙m⁻²∙s⁻¹ photosynthetic photon flux density (PPFD) provided by light-emitting diodes (LEDs) from three directions relative to the plant including the top, side, and bottom. Compared to the top or bottom lighting, the side lighting greatly enhanced the plant growth, improved the leaf internal structure and chloroplast arrangement, induced small stomata with a higher density, and promoted stomatal opening, which is associated with an increased stomatal conductance and photosynthetic efficiency. It is worth noting that the side lighting significantly enhanced the induction of branching and flowering for both cultivars., The plants grown with side lighting consistently exhibited the greatest physiological performance. We conclude that the lighting direction had a profound effect on the morphophysiological characteristics of chrysanthemum, and that side lighting dramatically promoted their growth and development, especially in their branching and flowering.

Global identification of long non-coding RNAs involved in the induction of spinach flowering

Background

Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait.

Results

In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs.

Conclusions

This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07989-1.

Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes

Cassava is an important food security crop in tropical regions of the world. Cassava improvement by breeding is limited by its delayed and poor production of flowers, such that cassava flowering under field conditions indirectly lengthens the breeding cycle. By studying genotype and environment interaction under two Nigerian field conditions (Ubiaja and Ibadan) and three controlled temperature conditions (22°C/18°C, 28/24°C and 34/30°C (day/night)), we found that while early flowering genotypes flowered at similar times and rates under all growing conditions (unfavorable and favorable field and controlled-temperature environments), late flowering genotypes were environmentally sensitive such that they were substantially delayed in unfavorable environments. On the basis of nodes-to-flower, flowering of late genotypes approached the flowering time of early flowering genotypes under relatively cool Ubiaja field conditions and in growth chambers at 22°C, whereas warmer temperatures elicited a delaying effect. Analysis of transcriptomes from leaves of field and controlled-temperature environments revealed that conditions which promote early flowering in cassava have low expression of the flowering repressor gene TEMPRANILLO 1 (TEM1), before and after flowering. Expression data of field plants showed that the balance between flower stimulatory and inhibitory signaling appeared to correlate with flowering time across the environments and genotypes.

Flower Development in Cassava Is Feminized by Cytokinin, While Proliferation Is Stimulated by Anti-Ethylene and Pruning: Transcriptome Responses

Cassava, a tropical storage-root crop, is a major source of food security for millions in the tropics. Cassava breeding, however, is hindered by the poor development of flowers and a low ratio of female flowers to male flowers. To advance the understanding of the mechanistic factors regulating cassava flowering, combinations of plant growth regulators (PGRs) and pruning treatments were examined for their effectiveness in improving flower production and fruit set in field conditions. Pruning the fork-type branches, which arise at the shoot apex immediately below newly formed inflorescences, stimulated inflorescence and floral development. The anti-ethylene PGR silver thiosulfate (STS) also increased flower abundance. Both pruning and STS increased flower numbers while having minimal influence on sex ratios. In contrast, the cytokinin benzyladenine (BA) feminized flowers without increasing flower abundance. Combining pruning and STS treatments led to an additive increase in flower abundance; with the addition of BA, over 80% of flowers were females. This three-way treatment combination of pruning+STS+BA also led to an increase in fruit number. Transcriptomic analysis of gene expression in tissues of the apical region and developing inflorescence revealed that the enhancement of flower development by STS+BA was accompanied by downregulation of several genes associated with repression of flowering, including homologs of TEMPRANILLO1 (TEM1), GA receptor GID1b, and ABA signaling genes ABI1 and PP2CA. We conclude that flower-enhancing treatments with pruning, STS, and BA create widespread changes in the network of hormone signaling and regulatory factors beyond ethylene and cytokinin.

Molecular cloning and expression analysis of sucrose phosphate synthase genes in cassava (Manihot esculenta Crantz)

Sucrose phosphate synthase (SPS), a key rate-limiting enzyme in the sucrose biosynthesis pathway in plants, is encoded by a multi-gene family. Until recently, the identification and characterization of the SPS gene family have been performed for dozens of plant species; however, few studies have involved a comprehensive analysis of the SPS family members in tropical crops, such as cassava (Manihot esculenta Crantz). In the current study, five SPS genes (MeSPS1, MeSPS2, MeSPS3, MeSPS4, and MeSPS5) were isolated from cassava, and their sequence characteristics were comprehensively characterized. These MeSPS genes were found distributed on five chromosomes (Chr2, Chr14, Chr15, Chr16, and Chr18). Phylogenetic analysis showed that the MeSPS protein sequences were clustered into three families, together with other SPS sequences from both dicot and monocot species (families A, B, and C). The spatio-temporal expression pattern analysis of MeSPS genes showed a tissue-specific and partially overlapping expression pattern, with the genes mainly expressed in source tissues during cassava growth and development. Correlation analysis revealed that the expression of MeSPS genes correlated positively with root starch content, indicating that the expression of MeSPS genes might accelerate the rate of starch accumulation in the roots of cassava plants.

Prospects for the accelerated improvement of the resilient crop quinoa

Crops tolerant to drought and salt stress may be developed by two approaches. First, major crops may be improved by introducing genes from tolerant plants. For example, many major crops have wild relatives that are more tolerant to drought and high salinity than the cultivated crops, and, once deciphered, the underlying resilience mechanisms could be genetically manipulated to produce crops with improved tolerance. Secondly, some minor (orphan) crops cultivated in marginal areas are already drought and salt tolerant. Improving the agronomic performance of these crops may be an effective way to increase crop and food diversity, and an alternative to engineering tolerance in major crops. Quinoa (Chenopodium quinoa Willd.), a nutritious minor crop that tolerates drought and salinity better than most other crops, is an ideal candidate for both of these approaches. Although quinoa has yet to reach its potential as a fully domesticated crop, breeding efforts to improve the plant have been limited. Molecular and genetic techniques combined with traditional breeding are likely to change this picture. Here we analyse protein-coding sequences in the quinoa genome that are orthologous to domestication genes in established crops. Mutating only a limited number of such genes by targeted mutagenesis appears to be a promising route for accelerating the improvement of quinoa and generating a nutritious high-yielding crop that can meet the future demand for food production in a changing climate.

Flowering in Persian walnut: patterns of gene expression during flower development

BACKGROUND

Flower development and sufficient fruit set are important parameters with respect to walnut yield. Knowledge about flowering genes of fruit trees can help to conduct better molecular breeding programs. Therefore, this study was carried out to investigate the expression pattern of some flowering genes (FT, SOC1, CAL, LFY and TFL1) in Persian walnut (cv. Chandler) during the growing season and winter dormancy.

RESULTS

The results showed that walnut flower induction and initiation in Shahmirzad, Iran occurred in early June and late September, respectively. After meeting chilling and heat requirement, flower differentiation and anthesis occurred in late-March and mid-April to early-May, respectively. Study of flowering gene expression showed that the expression of the FT gene increased in three stages including before breaking of bud dormancy, from late March to late April (coincided with flower differentiation and anthesis) and from late May to mid-June (coincided with flower induction). Like FT, the expression of SOC1 gene increased during flower induction and initiation (mid-May to early-August) as well as flower anthesis (mid-April to early-May). LFY and CAL genes as floral meristem identity genes are activated by FT and SOC1 genes. In contrast with flowering stimulus genes, TFL1 showed overexpression during winter dormancy which prevented flowering.

CONCLUSION

The expression of FT gene activated downstream floral meristem identity genes including SOC1, CAL and LFY which consequently led to release bud dormancy as well as flower anthesis and induction. Also, TFL1 as a flowering inhibitor gene in walnut showed overexpression during the bud dormancy. Chilling accumulation reduced TFL1 gene expression and increased the expression of flowering genes which ultimately led to overcome dormancy.

Transgenic overexpression of endogenous FLOWERING LOCUS T-like gene MeFT1 produces early flowering in cassava

Endogenous FLOWERING LOCUS T homolog MeFT1 was transgenically overexpressed under control of a strong constitutive promoter in cassava cultivar 60444 to determine its role in regulation of flowering and as a potential tool to accelerate cassava breeding. Early profuse flowering was recorded in-vitro in all ten transgenic plant lines recovered, causing eight lines to die within 21 days of culture. The two surviving transgenic plant lines flowered early and profusely commencing as soon as 14 days after establishment in soil in the greenhouse. Both transgenic lines sustained early flowering across the vegetative propagation cycle, with first flowering recorded 30–50 days after planting stakes compared to 90 days for non-transgenic controls. Transgenic plant lines completed five flowering cycles within 200 days in the greenhouse as opposed to twice flowering event in the controls. Constitutive overexpression of MeFT1 generated fully mature male and female flowers and produced a bushy phenotype due to significantly increased flowering-induced branching. Flower induction by MeFT1 overexpression was not graft-transmissible and negatively affected storage root development. Accelerated flowering in transgenic plants was associated with significantly increased mRNA levels of MeFT1 and the three floral meristem identity genes MeAP1, MeLFY and MeSOC1 in shoot apical tissues. These findings imply that MeFT1 encodes flower induction and triggers flowering by recruiting downstream floral meristem identity genes.

Identification of FT family genes that respond to photoperiod, temperature and genotype in relation to flowering in cassava (Manihot esculenta, Crantz)

Cassava is a starch-storing root crop that is an important source of dietary energy in tropical regions of the world. Genetic improvement of cassava by breeding is hindered by late flowering and sparse flower production in lines that are needed as parents. To advance understanding of regulatory mechanisms in cassava, this work sought to identify and characterize homologs of the FLOWERING LOCUS T (FT) gene. Ten members of the phosphatidylethanolamine-binding protein gene family, to which FT belongs, were obtained from the cassava genome database. Phylogenetic and sequence analysis of these proteins was used to identify two putative FT homologs which had amino acid sequences at key positions in accordance with those predicted for functional FTs. Expression of these ten genes was determined in mature leaves, immature leaves, flower buds, fibrous roots, storage roots and stem. The FT transcripts were expressed in mature leaves, as expected for their possible role in leaf-to-apical meristem signaling. In growth chamber studies, plants flowered earlier in long-day photoperiod than in short-day photoperiod. Expression studies indicated that while MeFT1 was expressed in leaves without a clear-cut photoperiod response, MeFT2 was expressed in a photoperiod-dependent manner, consistent with its involvement in photoperiodic control of flowering. In growth chambers that subjected plants to a range of temperatures from 22 to 34 °C, flowering was delayed by warmer temperatures although MeFT1 and MeFT2 expression declined in only one genotype, indicating other factors regulate this response. The earliest flowering genotype, IBA980002, had high levels of MeFT1 and MeFT2 expression, suggesting that both homologs contribute to earliness of this genotype.

An optimized isolation protocol yields high-quality RNA from cassava tissues (Manihot esculenta Crantz)

We developed and modified a precise, rapid, and reproducible protocol isolating high-quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170-600 μg·g^-1) using low-cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A ₂₆₀ : A ₂₈₀ ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase-polymerase chain reaction or RNA sequencing) in cassava molecular breeding.

Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea

Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.

Grafting as a strategy to increase flowering of cassava

In cassava (Manihot esculenta Crantz), transferring genes via genetic breeding depends on crosses between contrasting progenitors, which is often limited by the low flowering rate of many genotypes. The main purpose of this work was to evaluate the effect of grafting on floral induction of cassava. For this, three genotypes were used: 1) BRS Formosa: a genotype with low flowering rate; 2) BGM0823: a genotype with high flowering rate; and 3) FLA05-02: a genotype of M. esculenta ssp. flabellifolia with high flowering rate. Cleft grafting was performed to generate the following treatments: Self-grafting of: 1) BGM0823 (Self-0823); 2) BRS Formosa (Self-Formosa); and 3) FLA05-02 (Self-FLA); and grafting of the genotypes, with the first being the scion and the second the rootstock: 4) BGM0823 × BRS Formosa; 5) BGM0823 × FLA05-02; 6) FLA05-02 × BRS Formosa; 7) FLA05-02 × BGM0823; 8) BRS Formosa × BGM0823; 9) BRS Formosa × FLA05-02; and also ungrafted treatments: 10) BGM0823; 11) BRS Formosa; and 12) FLA05-02. The results showed a 201% increase in the production of male flowers, 560% of female flowers and 400% of fruits in BRS Formosa grafted on BGM0823. BGM0823 (rootstock) also increased fruit production by 190% of FLA05-02. The grafted cassava plants exhibited an increase on the shoot production, although there was no change in the fresh root yield. The grafting of genotypes with high flowering rates can induce flowering in genotypes with low flowering rates.