RNA-sequencing analysis reveals betalains metabolism in the leaf of Amaranthus tricolor L

Emerging Trends in Secondary Metabolite Research in Caryophyllales: Betalains and Their Roles in Plant Adaptation and Defense Mechanisms

Betalains, a distinctive group of nitrogen-containing pigments exclusive to the Caryophyllales order, possess diverse biological activities such as antioxidant, anti-inflammatory, and antimicrobial properties, making them highly valuable for applications in food, nutraceutical, and pharmaceutical industries. This Review provides a comprehensive analysis of betalain biosynthesis, structural diversity, and ecological significance, highlighting their roles in enhancing stress resilience, adaptation mechanisms, and plant evolutionary strategies. The evolutionary development of betalains is explored, revealing their emergence through gene duplication events and providing insights into their mutual exclusivity with anthocyanins. This study utilizes comparative genetics and advanced molecular tools to uncover the intricate regulatory networks involving transcription factors such as MYB, bHLH, WRKY, and SPL, which govern betalain biosynthesis. Furthermore, the Review discusses innovative transgenic studies that introduce betalains into non-native species, demonstrating their potential to enhance stress tolerance and boost agricultural productivity. While significant progress has been made in understanding betalain biosynthesis pathways, the evolutionary relationships with anthocyanins and the specific ecological functions of betalains in plants remain areas of ongoing exploration. Future research directions include integrating chemotaxonomic studies, molecular phylogenetics, and multiomics approaches to unravel the full spectrum of betalain functions and regulatory mechanisms. Such studies are essential to deepening our understanding of these vibrant pigments and their evolutionary implications, offering new opportunities for biotechnological innovations and sustainable agricultural practices. This Review stands out by combining genetic, ecological, and evolutionary perspectives, providing novel insights into the multifunctionality of betalains and their potential to drive future advancements in plant science and biotechnology.

Amaranth Plants with Various Color Phenotypes Recruit Different Soil Microorganisms in the Rhizosphere

To explore and utilize the abundant soil microorganisms and their beneficial functions, high-throughput sequencing technology was used to analyze soil microbial compositions in the rhizosphere of red and green amaranth varieties. The results showed that significant differences in soil microbial composition could be found in the rhizosphere of amaranth plants with different color phenotypes. Firstly, soil bacterial compositions in the rhizosphere were significantly different between red and green amaranths. Among them, Streptomyces, Pseudonocardia, Pseudolabrys, Acidibacter, norank_ f_ Micropepsaceae, Bradyrhizobium, and Nocardioides were the unique dominant soil bacterial genera in the rhizosphere of red amaranth. In contrast, Conexibacter, norank_f_norank_o_norank_c_TK10, and norank_f_ norank_o_ norank_ c_AD3 were the special dominant soil bacterial genera in the rhizosphere of green amaranth. Additionally, even though the soil fungal compositions in the rhizosphere were not significantly different between red and green amaranths, the abundance of the dominant soil fungal genera in the rhizosphere showed significant differences between red and green amaranths. For example, unclassified_k__Fungi, Fusarium, Cladophialophora, unclassified_c__Sordariomycetes and unclassified_p__Chytridiomycota significantly enriched as the dominant soil fungal genera in the rhizosphere of the red amaranth. In contrast, Aspergillues only significantly enriched as the dominant soil fungal genus in the rhizosphere of green amaranth. All of the above results indicated that amaranth with various color phenotypes exactly recruited different microorganisms in rhizosphere, and the enrichments of soil microorganisms in the rhizosphere could be speculated in contributing to amaranth color formations.

Genome-Wide Identification of the Cation/Proton Antiporter (CPA) Gene Family and Functional Analysis of AtrNHX8 under Salt Stress

Amaranthus tricolor is an important vegetable, and its quality is affected by salt stress. Cation/proton antiporters (CPA) contribute to plant development and tolerance to salt stress. In this study, 35 CPA genes were identified from a genome database for A. tricolor, including 9 NHX, 5 KEA, and 21 CPA2 genes. Furthermore, in A. tricolor, the expression levels of most AtrNHX genes were higher at a low salinity level (50 or 100 mM NaCl) than in the control or 200 mM NaCl treatment. Levels of most AtrNHX genes were elevated in the stem. Moreover, AtrNHX8 was homologous to AtNHX4, which is involved in the regulation of sodium homeostasis and salt stress response. After AtrNHX8 overexpression in Arabidopsis thaliana, seed germination was better, and the flowering time was earlier than that of wild-type plants. Additionally, the overexpression of AtrNHX8 in A. thaliana improved salt tolerance. These results reveal the roles of AtrNHX genes under salt stress and provide valuable information on this gene family in amaranth.

Amaranth's Growth and Physiological Responses to Salt Stress and the Functional Analysis of AtrTCP1 Gene

Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50-200 mmol·L-1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L-1, while it was promoted at 50 mmol·L-1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L-1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene.

Identification of WRKY gene family members in amaranth based on a transcriptome database and functional analysis of AtrWRKY42-2 in betalain metabolism

Introduction

WRKY TFs (WRKY transcription factors) contribute to the synthesis of secondary metabolites in plants. Betalains are natural pigments that do not coexist with anthocyanins within the same plant. Amaranthus tricolor ('Suxian No.1') is an important leaf vegetable rich in betalains. However, the WRKY family members in amaranth and their roles in betalain synthesis and metabolism are still unclear.

Methods

To elucidate the molecular characteristics of the amaranth WRKY gene family and its role in betalain synthesis, WRKY gene family members were screened and identified using amaranth transcriptome data, and their physicochemical properties, conserved domains, phylogenetic relationships, and conserved motifs were analyzed using bioinformatics methods.

Results

In total, 72 WRKY family members were identified from the amaranth transcriptome. Three WRKY genes involved in betalain synthesis were screened in the phylogenetic analysis of WRKY TFs. RT-qPCR showed that the expression levels of these three genes in red amaranth 'Suxian No.1' were higher than those in green amaranth 'Suxian No.2' and also showed that the expression level of AtrWRKY42 gene short-spliced transcript AtrWRKY42-2 in Amaranth 'Suxian No.1' was higher than that of the complete sequence AtrWRKY42-1, so the short-spliced transcript AtrWRKY42-2 was mainly expressed in 'Suxian No.2' amaranth. Moreover, the total expression levels of AtrWRKY42-1 and AtrWRKY42-2 were down-regulated after GA3 treatment, so AtrWRKY42-2 was identified as a candidate gene. Therefore, the short splice variant AtrWRKY42-2 cDNA sequence, gDNA sequence, and promoter sequence of AtrWRKY42 were cloned, and the PRI 101-AN-AtrWRKY42-2-EGFP vector was constructed to evaluate subcellular localization, revealing that AtrWRKY42-2 is located in the nucleus. The overexpression vector pRI 101-AN-AtrWRKY42-2-EGFP and VIGS (virus-induced gene silencing) vector pTRV2-AtrWRKY42-2 were transferred into leaves of 'Suxian No.1' by an Agrobacterium-mediated method. The results showed that AtrWRKY42-2 overexpression could promote the expression of AtrCYP76AD1 and increase betalain synthesis. A yeast one-hybrid assay demonstrated that AtrWRKY42-2 could bind to the AtrCYP76AD1 promoter to regulate betalain synthesis.

Discussion

This study lays a foundation for further exploring the function of AtrWRKY42-2 in betalain metabolism.

Comparative Transcriptomic Analysis of the Metabolism of Betalains and Flavonoids in Red Amaranth Hypocotyl under Blue Light and Dark Conditions

Amaranth plants contain abundant betalains and flavonoids. Anthocyanins are important flavonoids; however, they cannot coexist in the same plant with betalains. Blue light influences metabolite synthesis and hypocotyl elongation; accordingly, analyses of its effects on betalain and flavonoid biosynthesis in Amaranthus tricolor may provide insight into the distribution of these plant pigments. We analyzed the betalain and flavonoid content and transcriptome profiles in amaranth hypocotyls under blue light and dark conditions. Furthermore, we analyzed the expression patterns of key genes related to betalains and flavonoids. Amaranth hypocotyls were shorter and redder and showed higher betalain and flavonoid content under blue light than in dark conditions. Key genes involved in the synthesis of betalains and flavonoids were upregulated under blue light. The gene encoding DELLA was also upregulated. These results suggest that blue light favors the synthesis of both betalains and flavonoids via the suppression of bioactive gibberellin and the promotion of DELLA protein accumulation, which also suppresses hypocotyl elongation. The metabolite profiles differed between plants under blue light and dark conditions. These findings improve our understanding of the environmental cues and molecular mechanisms underlying pigment variation in Amaranthus.

Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis

Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi-C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1, located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution.

Amaranth as a natural food colorant source: Survey of germplasm and optimization of extraction methods for betalain pigments

Growing consumer demands for healthier foods have evoked trends in the food industry to replace synthetically produced colorants with naturally derived alternatives. Anthocyanins currently comprise the bulk of the natural colorant market, but betalains offer advantages where anthocyanins have limits. Amaranthus species are appealing betalain sources given their extensive pigmentation patterns and recognized food status around the world. An advantage of amaranths as natural food colorants is that, when grown as leafy vegetables, water extracts would be compliant with U.S. Food and Drug Administration guidelines as "vegetable juice" colorants. Thus, we developed a methodology based on U.S. FDA guidelines to investigate betalain diversity among forty-eight amaranth accessions grown as leafy vegetables. Total betacyanin concentrations ranged from 4.7 to 478.8 mg/100 g dry weight, with amaranthin and isoamaranthin identified as major constituents. Our findings will guide future research on amaranths to determine economic viability and suitability for growing natural colorant markets.

A short-term cooling of root-zone temperature increases bioactive compounds in baby leaf Amaranthus tricolor L

Leafy vegetables that are offered as seedling leaves with petioles are referred to as baby leaf vegetables. One of the most nutritious baby leaves, amaranth (Amaranthus tricolor L.), contains several bioactive compounds and nutrients. Here, we investigated the growth and quality of baby leaf amaranth using a variety of short-term cooling root-zone temperatures (RZT; 5, 10, 15, and 20°C), periods (1, 3, 5, and 7 days), and combinations thereof. We observed that exposing amaranth seedlings to RZT treatments at 5 and 10°C for 1-3 days increased the antioxidant capacity and the concentrations of bioactive compounds, such as betalain, anthocyanin, phenolic, flavonoid, and ascorbic acid; however, extending the treatment period to 7 days decreased them and adversely affected growth. For RZT treatments at 20°C, leaf photosynthetic pigments, bioactive compounds, nutrients, and antioxidant capacity increased gradually as the treatment period was extended to 7 days. The integration of RZTs at 5 and 10°C for one day preceded or followed by an RZT treatment at 20°C for 2 days had varied effects on the growth and quality of amaranth leaves. After one day of RZT treatment at 5°C followed by 2 days of RZT treatment at 20°C, the highest concentrations of bioactive compounds, nutrients, and antioxidant capacity were 1.4-3.0, 1.7, and 1.7 times higher, respectively, than those of the control, and growth was not impaired. The short-term cooling RZT treatments under controlled environments were demonstrated to be adequate conditions for the improvement of target bioactive compounds in amaranth baby leaf without causing leaf abnormality or growth impairment.

Natural or light-induced pigment accumulation in grain amaranths coincides with enhanced resistance against insect herbivory

MAIN CONCLUSION

Increased resistance to insect herbivory in grain amaranth plants is associated with increased betalain pigmentation, either naturally acquired or accumulated in response to blue-red light irradiation. Betalains are water-soluble pigments characteristic of plants of the Caryophyllales order. Their abiotic stress-induced accumulation is believed to protect against oxidative damage, while their defensive function against biotic aggressors is scarce. A previous observation of induced betalain-biosynthetic gene expression in stressed grain amaranth plants led to the proposal that these pigments play a defensive role against insect herbivory. This study provided further support for this premise. First, a comparison of "green" and "red" Amaranthus cruentus phenotypes showed that the latter suffered less insect herbivory damage. Coincidentally, growth and vitality of Manduca sexta larvae were more severely affected when fed on red-leafed A. cruentus plants or on an artificial diet supplemented with red-leaf pigment extracts. Second, the exposure of A. cruentus and A. caudatus plants, having contrasting pigmentation phenotypes, to light enriched in the blue and red wavelength spectra led to pigment accumulation throughout the plant and to increased resistance to insect herbivory. These events were accompanied by the induced expression of known betalain-biosynthetic genes, including uncharacterized DODA genes believed to participate in this biosynthetic pathway in a still undefined way. Finally, transient co-expression of different combinations of betalain-biosynthetic genes in Nicotiana benthamiana led to detectable accumulation of betalamic acid and betanidin. This outcome supported the participation of certain AhDODA and other genes in the grain amaranth betalain-biosynthetic pathway.

Defining Color Change in Pitaya: A Close Look at Betacyanin Synthesis Genes in Stenocereus queretaroensis

Betalains are tyrosine-derived plant pigments present in several species of the Caryophyllales order. Betalains are classified in red betacyanins and yellow betaxanthins and are implicated in plant stress tolerance and visual attraction for pollinators. The compounds are used as natural colorants in many industries. Today, there is little information on betalain biosynthesis with several key enzymes that remain unknown on plants of the Caryophyllales order. Omic tools have proven to be very useful in gaining insights into various molecular mechanisms. In this study, we used suspension cells from fruits of the cactus Stenocereus queretaroensis. Two growing conditions were used to perform RNA-seq and differential expression analysis to help identify betalain biosynthesis-related genes. We found 98 differential expressed genes related to aromatic amino acids and betalain biosynthesis pathways. Interestingly, we found that only one gene of the betalain synthesis pathway was differentially expressed. The rest of the genes belong to the aromatic amino acid pathway, including hydroxy phenylpyruvate-related genes, suggesting the possibility of an alternative biosynthetic pathway similar to that observed in legumes.

Elucidation of the core betalain biosynthesis pathway in Amaranthus tricolor

Amaranthus tricolor L., a vegetable Amaranthus species, is an economically important crop containing large amounts of betalains. Betalains are natural antioxidants and can be classified into betacyanins and betaxanthins, with red and yellow colors, respectively. A. tricolor cultivars with varying betalain contents, leading to striking red to green coloration, have been commercially produced. However, the molecular differences underlying betalain biosynthesis in various cultivars of A. tricolor remain largely unknown. In this study, A. tricolor cultivars with different colors were chosen for comparative transcriptome analysis. The elevated expression of AmCYP76AD1 in a red-leaf cultivar of A. tricolor was proposed to play a key role in producing red betalain pigments. The functions of AmCYP76AD1, AmDODAα1, AmDODAα2, and AmcDOPA5GT were also characterized through the heterologous engineering of betalain pigments in Nicotiana benthamiana. Moreover, high and low L-DOPA 4,5-dioxygenase activities of AmDODAα1 and AmDODAα2, respectively, were confirmed through in vitro enzymatic assays. Thus, comparative transcriptome analysis combined with functional and enzymatic studies allowed the construction of a core betalain biosynthesis pathway of A. tricolor. These results not only provide novel insights into betalain biosynthesis and evolution in A. tricolor but also provide a basal framework for examining genes related to betalain biosynthesis among different species of Amaranthaceae.

Research Progress of Betalain in Response to Adverse Stresses and Evolutionary Relationship Compared with Anthocyanin

Betalains are applicable to many aspects of life, and their properties, characteristics, extraction and biosynthesis process have been thoroughly studied. Although betalains are functionally similar to anthocyanins and can substitute for them to provide pigments for plant color, it is rare to study the roles of betalains in plant responses to adverse environmental conditions. Owing to their antioxidant capability to remove excess reactive oxygen species (ROS) in plants and humans, betalains have attracted much attention due to their bioactivity. In addition, betalains can also act as osmotic substances to regulate osmotic pressure in plants and play important roles in plant responses to adverse environmental conditions. The study of the physiological evolution of betalains is almost complete but remains complicated because the evolutionary relationship between betalains and anthocyanins is still uncertain. In this review, to provide a reference for the in-depth study of betalains compared with anthocyanins, the biochemical properties, biosynthesis process and roles of betalains in response to environmental stress are reviewed, and the relationship between betalains and anthocyanins is discussed.