Transcriptome and Metabolome Analyses Reveal the Involvement of Multiple Pathways in Flowering Intensity in Mango

Transcriptome and metabolome analyses reveal that GA3ox regulates the dwarf trait in mango (Mangifera indica L.)

BACKGROUND

Mango is a tropical fruit with high economic value. The selection of suitable dwarf mango varieties is an important aspect of mango breeding. However, the mechanisms that regulate mango dwarfing remain unclear.

RESULTS

In this study, we compared the transcriptomes and metabolomes of mango varieties Guiqi (a dwarfed variety) and Jinhuang (an arborized variety). A total of 4,954 differentially expressed genes and 317 differentially abundant metabolites were identified between the two varieties, revealing the molecular mechanism of the gibberellin 3β-hydroxylase gene GA3ox in regulating dwarfing traits in mangoes using joint transcriptome and metabolome analyses. The results showed that differentially expressed genes were enriched in the diterpenoid biosynthesis pathway and that differentially abundant metabolites were annotated to their upstream pathway, the terpenoid backbone biosynthesis. A gene regulation network based on these two pathways was constructed, indicating the upregulation of the GA3ox gene and the accumulation of gibberellin in dwarfed mangoes. We then transferred the GA3ox gene to tobacco plants following the application of gibberellin, and the morphology and height of the transgenic tobacco plants largely recovered the phenotype.

CONCLUSIONS

These results demonstrated that GA3ox plays a role in the regulation of dwarf traits. Our study provides an important theoretical basis for studying the regulatory mechanisms underlying mango dwarfism to facilitate mango breeding.

Targeted Metabolites and Transcriptome Analysis Uncover the Putative Role of Auxin in Floral Sex Determination in Litchi chinensis Sonn

Litchi exhibits a large number of flowers, many flowering batches, and an inconsistent ratio of male and female flowers, frequently leading to a low fruit-setting rate. Floral sexual differentiation is a crucial phase in perennial trees to ensure optimal fruit production. However, the mechanism behind floral differentiation remains unclear. The objective of the study was to identify the role of auxin in floral differentiation at the transcriptional level. The results showed that the ratio of female flowers treated with naphthalene acetic acid (NAA) was significantly lower than that of the control stage (M0/F0). The levels of endogenous auxin and auxin metabolites were measured in male and female flowers at different stages of development. It was found that the levels of IAA, IAA-Glu, IAA-Asp, and IAA-Ala were significantly higher in male flowers compared to female flowers. Next-generation sequencing and modeling were employed to perform an in-depth transcriptome analysis on all flower buds in litchi 'Feizixiao' cultivars (Litchi chinensis Sonn.). Plant hormones were found to exert a significant impact on the litchi flowering process and flower proliferation. Specifically, a majority of differentially expressed genes (DEGs) related to the auxin pathway were noticeably increased during male flower bud differentiation. The current findings will enhance our comprehension of the process and control mechanism of litchi floral sexual differentiation. It also offers a theoretical foundation for implementing strategies to regulate flowering and enhance fruit production in litchi cultivation.

Population structure and genetic diversity of mango (Mangifera indica L.) germplasm resources as revealed by single-nucleotide polymorphism markers

Introduction

Mango is a vital horticultural fruit crop, and breeding is an essential strategy to enhance ongoing sustainability. Knowledge regarding population structure and genetic diversity in mango germplasm is essential for crop improvement.

Methods

A set of 284 mango accessions from different regions of the world were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction to generate genomic single-nucleotide polymorphism (SNP).

Results

After filtering, raw data containing 539.61 M reads were obtained. A total of 505,300 SLAFs were detected, of which, 205,299 were polymorphic. Finally, 29,136 SNPs were employed to dissect the population structure, genetic relationships, and genetic diversity. The 284 mango accessions were divided into two major groups: one group consisted mainly of mango accessions from Australia, the United States, Cuba, India, Caribbean, Israel, Pakistan, Guinea, Burma, China, and Sri Lanka, which belonged to the Indian type (P1); the other group contained mango accessions from the Philippines, Thailand, Indonesia, Vietnam, Cambodia, Malaysia, and Singapore, which belonged to Southeast Asian type (P2). Genetic diversity, principal component analysis (PCA), and population structure analyses revealed distinct accession clusters. Current results indicated that the proposed hybridization occurred widely between P1 and P2.

Discussion

Most of the accessions (80.99%) were of mixed ancestry, perhaps including multiple hybridization events and regional selection, which merits further investigation.

The roles of non-structural carbohydrates in fruiting: a review focusing on mango (Mangifera indica)

Reproductive development of fruiting trees, including mango (Mangifera indica L.), is limited by non-structural carbohydrates. Competition for sugars increases with cropping, and consequently, vegetative growth and replenishment of starch reserves may reduce with high yields, resulting in interannual production variability. While the effect of crop load on photosynthesis and the distribution of starch within the mango tree has been studied, the contribution of starch and sugars to different phases of reproductive development requires attention. This review focuses on mango and examines the roles of non-structural carbohydrates in fruiting trees to clarify the repercussions of crop load on reproductive development. Starch buffers the plant's carbon availability to regulate supply with demand, while sugars provide a direct resource for carbon translocation. Sugar signalling and interactions with phytohormones play a crucial role in flowering, fruit set, growth, ripening and retention, as well as regulating starch, sugar and secondary metabolites in fruit. The balance between the leaf and fruit biomass affects the availability and contributions of starch and sugars to fruiting. Crop load impacts photosynthesis and interactions between sources and sinks. As a result, the onset and rate of reproductive processes are affected, with repercussions for fruit size, composition, and the inter-annual bearing pattern.

Histone Deacetylase UvHST2 Is a Global Regulator of Secondary Metabolism in Ustilaginoidea virens

Ustilaginoidea virens, the causal agent of rice false smut, produces a large amount of mycotoxins, including ustilaginoidins and sorbicillinoids. However, little is known about the regulatory mechanism of mycotoxin biosynthesis inU. virens. Here, we demonstrate that the NAD+-dependent histone deacetylase UvHST2 negatively regulates ustilaginoidin biosynthesis. UvHst2 knockout caused retarded hypha growth and reduced conidiation and pathogenicity inU. virens. Transcriptome analysis revealed that the transcription factor genes, transporter genes, and other tailoring genes in eight biosynthetic gene clusters (BGCs) including ustilaginoidin and sorbicillinoid BGCs were upregulated in ΔUvhst2. Interestingly, the UvHst2 deletion affects alternative splicing. Metabolomics revealed that UvHST2 negatively regulates the biosynthesis of various mycotoxins including ustilaginoidins, sorbicillin, ochratoxin B, zearalenone, and O-M-sterigmatocystin. Combined transcriptome and metabolome analyses uncover that UvHST2 positively regulates pathogenicity but negatively modulates the expression of BGCs involved in secondary metabolism. Collectively, UvHST2 functions as a global regulator of secondary metabolism inU. virens.

Combined transcriptome and metabolome analysis reveal that the white and yellow mango pulp colors are associated with carotenoid and flavonoid accumulation, and phytohormone signaling

Mango (Mangifera indica L.) is a widely appreciated tropical fruit for its rich color and nutrition. However, knowledge on the molecular basis of color variation is limited. Here, we studied HY3 (yellowish-white pulp) and YX4 (yellow pulp), reaped with 24 h gap from the standard harvesting time. The carotenoids and total flavonoids increased with the advance of harvest time (YX4 > HY34). Transcriptome sequencing showed that higher expressions of the core carotenoid biosynthesis genes and flavonoid biosynthesis genes are correlated to their respective contents. The endogenous indole-3-acetic acid and jasmonic acid contents decreased but abscisic acid and ethylene contents increased with an increase in harvesting time (YX4 > HY34). Similar trends were observed for the corresponding genes. Our results indicate that the color differences are related to carotenoid and flavonoid contents, which in turn are influenced by phytohormone accumulation and signaling.

Integrated metabolome and transcriptome analysis provides insights on the floral scent formation in Hydrangea arborescens

Hydrangea (Hydrangea arborescens var. 'Annabelle') flowers are composed of sweet aroma sepals rather than true petals and can change color. Floral volatiles play important roles in plants, such as attracting pollinators, defending against herbivores, and signaling. However, the biosynthesis and regulatory mechanisms underlying fragrance formation in H. arborescens during flower development remain unknown. In this study, a combination of metabolite profiling and RNA sequencing (RNA-seq) was employed to identify genes associated with floral scent biosynthesis mechanisms in 'Annabelle' flowers at three developmental stages (F1, F2, and F3). The floral volatile data revealed that the 'Annabelle' volatile profile includes a total of 33 volatile organic compounds (VOCs), and VOCs were abundant during the F2 stage of flower development, followed by the F1 and F3 stages, respectively. Terpenoids and benzenoids/phenylpropanoids were abundant during the F2 and F1 stages, with the latter being the most abundant, whereas fatty acid derivatives and other compounds were found in large amount during the F3 stage. According to ultra performance liquid chromatography - tandem mass spectrometer (UPLC-MS/MS) analysis, benzene and substituted derivatives, carboxylic acids and derivatives, and fatty acyls play a significant role in the floral metabolite profile. The transcriptome data revealed a total of 17,461 differentially expressed genes (DEGs), with 7,585, 12,795, and 9,044 DEGs discovered between the F2 and F1, F3 and F1, and F2 and F3 stages, respectively. Several terpenoids and benzenoids/phenylpropanoids biosynthesis-related DEGs were identified, and GRAS/bHLH/MYB/AP2/WRKY were more abundant among transcription factors (TFs). Finally, DEGs interlinked with VOCs compounds were determined using cytoscape and k-means analysis. Our results paves the way for the discovery of new genes, critical data for future genetic studies, and a platform for the metabolic engineering of genes involved in the production of Hydrangea's signature floral fragrance.

Bamboo charcoal mediated plant secondary metabolites biosynthesis in tomato against South American tomato pinworm (Tuta absoluta)

Introduction

The south American tomato pinworm (Tuta absoluta), an invasive insect pest species, has established itself in more than 33 Chinese prefectures, where it is mainly damaging tomato crops. Immediate efforts have been initiated to find strategies to control this pest. Studies have shown that biochar (BC) amendment to soil can enhance plant growth and resistance to herbivory.

Methods

First, we quantified the morphological performance of tomato plants grown in different coconut bran and bamboo charcoal (v/v) combinations and selected the most beneficial one. Then we checked the T. absoluta survival on the tomato plants grown in the selected bamboo charcoal combination. Finally, we studied the leaf metabolite accumulation and gene expression changes in tomato plants after growing in the selected bamboo charcoal combination.

Results

We found that the 30:1 ratio of bamboo charcoal and coconut bran is the most beneficial to tomato growth as its amendment to soil increased tomato plant height, stem thickness, and chlorophyll content, whereas, the T. absoluta survival decreased. The metabolome profiles of BC tomato leaves showed an increased accumulation of flavonoids, terpenoids, and phenolic acids compared to CK. Transcriptome sequencing resulted in the identification of 244 differentially expressed genes. Most of the upregulated genes were associated with stress-related hub proteins, flavonoid biosynthesis, MAPK and phytohormone signaling, and terpenoid biosynthesis. Additionally, the expression of many genes related to signaling and defense was changed in response to the bamboo charcoal amendment.

Discussion

We conclude that bamboo charcoal induces biosynthesis of flavonoids, terpenoids, and phenolic acids, which improve plant growth and tolerance against T. absoluta, thus reducing the survival of destructive pests.

Molecular mechanisms of flowering phenology in trees

Flower initiation is a phenological developmental process strictly regulated in all flowering plants. Studies in Arabidopsis thaliana, a model plant organism in plant biology and genetics, and major cereal crops have provided fundamental knowledge and understanding of the underlying molecular mechanisms and regulation in annuals. However, this flowering process and underly molecular mechanisms in perennials are much more complicated than those in annuals and remain poorly understood and documented. In recent years, the increasing availability of perennial plant genomes and advances in biotechnology have allowed the identification and characterization of flowering-associated gene orthologs in perennials. In this review, we compared and summarized the recent progress in regulation of flowering time in perennial trees, with an emphasis on the perennial-specific regulatory mechanisms. Pleiotropic effects on tree growth habits such as juvenility, seasonal activity-dormancy growth, and the applications of tree flowering phenology are discussed.

Differential effects of low and high temperature stress on pollen germination and tube length of mango (Mangifera indica L.) genotypes

Mango flowering is highly sensitive to temperature changes. In this research, the maximum values of pollen germination rate (PGR), pollen tube length (PTL) and their cardinal temperatures (Tmin, Topt and Tmax) were estimated by using quadratic equation and modified bilinear model under the conditions of 14-36 °C. The pollen germination rate in four mango varieties ranged from 29.1% ('Apple mango') to 35.5% ('Renong No. 1'); the length of pollen tube ranged from 51.2 μm ('Deshehari') to 56.6 μm ('Jinhuang'). The cardinal temperatures ranges (Tmin, Topt and Tmax) of pollen germination were 20.3-22.8 °C, 26.7-30.6 °C and 30.4-34.3 °C, respectively; similarly, cardinal temperatures (Tmin, Topt and Tmax) of pollen tube growth were 20.3-21.2 °C, 27.9-32.1 °C and 30.2-34.4 °C respectively. Of those, 'Renong No. 1' could maintain relatively high pollen germination rate even at 30 °C, however, 'Deshehari' had the narrowest adaptive temperature range. These results were further confirmed by changes of superoxide dismutase, catalase activity and malondialdehyde content. These results showed that mango flowering was highly sensitive to temperature changes and there were significant differences in pollen germination rate and pollen tube length among different varieties. Current research results were of great significance for the introduction of new mango varieties in different ecological regions, the cultivation and management of mango at the flowering stage and the breeding of new mango varieties.

Comparative transcriptomics in alternate bearing cultivar Dashehari reveals the genetic model of flowering in mango

Flowering is a complex developmental process, with physiological and morphological phases influenced by a variety of external and internal factors. Interestingly, many mango cultivars tend to bear fruit biennially because of irregular flowering, and this has a negative impact on mango flowering and the subsequent yield, resulting in significant economic losses. In this article, transcriptome analysis was carried out on four tissues of mango cv. Dashehari (bearing tree leaf, shoot apex, inflorescence, and non-bearing tree leaf). De novo transcriptome assembly of RNA-seq reads of Dashehari using the Trinity pipeline generated 67,915 transcripts, with 25,776 genes identified. 85 flowering genes, represented by 179 transcripts, were differentially expressed in bearing vs. non-bearing leaf tissues. Gene set enrichment analysis of flowering genes identified significant upregulation of flowering related genes in inflorescence tissues compared to bearing leaf tissues. The flowering genes FT, CO, GI, ELF 4, FLD, FCA, AP1, LHY, and SCO1 were upregulated in the bearing leaf tissues. Pathway analysis of DEGs showed significant upregulation of phenylpropanoid and sucrose and starch pathways in non-bearing leaf tissue compared with bearing leaf tissue. The comparative transcriptome analysis performed in this study significantly increases the understanding of the molecular mechanisms driving the flowering process as well as alternative bearing in mango.