Distyly is a reproductive system, characterized by the presence of two floral morphs, which promotes outcrossing via physical and biochemical means. In distylous , the mating type of the S-morph is determined by two genes: (male) and (female). Despite the importance of these -genes, it is likely that additional genes are involved in the distylous syndrome. Here, we use comparative mass spectrometry analysis to identify differentially expressed proteins in a series of self-compatible mutants and wildtype distylous members of . Our analysis identified a member of the family that overwhelmingly correlated with L-morph male mating type. Exploration of the large datasets and previously published work led to the proposal that differential ROS levels in the pistil may contribute towards the self-incompatibility response. To support this hypothesis, we generated a co-expression network for whole flower buds from self-compatible and WT . This network led to the identification of a series of ROS and auxin-related genes that correlated with self-compatibility. We update previously proposed SI response models to reflect how ROS, jasmonic acid, and brassinosteroid signaling likely establish the S-morph female self-incompatibility response. Overall, this work has identified genes potentially related to self-compatibility and has provided a foundation for future empirical work investigating the basis of the SI response in .

Trichomes are found on almost all terrestrial plants and are derived from epidermal cells. Nonglandular trichomes (NGTs) protect plants from environmental stress, such as pest and pathogen invasion, reduce water loss, and increase resistance to abiotic stressors, including UV radiation, cold, and extreme temperatures. Trichomes provide an excellent model system for studying the growth and differentiation of plant cells. Although several such genes that govern the specification and patterning of trichomes have been molecularly characterized in a few model plants, including , most aspects of trichome initiation remain unclear. In this review, we summarize the structural and morphological characteristics of NGTs in diverse crops as well as report recent investigations providing insights into the regulation of NGT formation in plants. We also discuss how NGTs help plants resist various abiotic factors that impose multiple stresses on plant life. This review provides a foundation for understanding the valuable role of NGTs in protecting plants from multiple stresses.

The reproductive cycle of interior lodgepole pine spans approximately 26 months, with seed cones initiating in late summer, followed by pollen conelets emerging the next spring when pollination occurs. Fertilization and cone maturation occur in the subsequent spring and fall. Successful pollination, critical for seed conelet retention, requires an ~80% success rate. In June 2020, 30 pine clones (genotypes), with contrasting conelet abortion rates, were selected from a production seed orchard in Alberta, Canada. Sixty conelets per clone (30 aborted and 30 healthy) were collected for synchrotron radiation-based microcomputed tomography (SR-μCT) analysis. A subset of two contrasting clones (1401 and 596) was selected for detailed study. Conelets were transported to the Canadian Light Source in Saskatoon, Saskatchewan, for SR-μCT Phase Contrast Imaging (PCI), where samples were mounted and scanned using a PCO Edge 5.5 sCMOS camera and analyzed using Avizo software to visualize internal structures. Results showed that healthy conelets in clones 1401 and 596 had greater tissue volume (248.8 and 251.9 mm, respectively) and more organized cavity spaces than aborted conelets (64.7 and 102.1 mm, respectively), with differential internal air space volume (clone 1401: 8.7 mm in aborted vs. 17.5 mm in healthy; clone 596: 6.9 mm in aborted vs. 11.5 mm in healthy). Overall, SR-μCT imaging demonstrated significant advantages over traditional methods of visualization by providing a nondestructive, high-resolution analysis of internal structures. In addition, this technology enhances our understanding of pine reproductive processes, improving management practices in seed orchards-the delivery system for tree improvement programs.

One class of enzymes that plant pathogens employ to manipulate innate immunity and physiology of the infected cells is host-targeted ADP-ribosyltransferases. The bacterial pathogen uses its Type III secretion system to inject several effector proteins with ADP-ribosyltransferase activity into plant cells. One of them, AvrRpm1, ADP-ribosylates the plasma membrane-associated RPM1-INTERACTING PROTEIN 4 (RIN4) in and to attenuate targeted secretion of defense-promoting compounds. Substrate identification of host-targeted ADP-ribosyltransferases is complicated by the biochemical lability of the protein modification during plant protein extraction and in several cases requires prior knowledge of plant immune signaling pathways that are impaired by the ADP-ribosylating Type III effector. Using the AvrRpm1-RIN4 pair as a proof of concept, we present an untargeted proteomics workflow for enrichment and detection of ADP-ribosylated proteins and peptides from plant cell extracts that in several cases provides site resolution for the modification.

SnRK1 is an evolutionarily conserved protein kinase belonging to the SNF1/AMPK family of protein kinases that is central to adjusting growth in response to the energy status. Numerous studies have shown adaptive and developmental roles of SnRK1, but the understanding of the SnRK1 signaling network in monocots is limited. Using CRISPR/Cas9 mutagenesis to target the functional kinase subunits in rice, we carried out comprehensive phenotypic, transcriptomic, proteomic, and phosphoproteomic analyses of rice mutants displaying growth defects under normal and starvation conditions. These analyses revealed the role of SnRK1 signaling in controlling growth and stress-related processes in both energy-sufficient and energy-limited conditions and pointed to the subfunctionalization of SnRK1 kinase subunit genes. In addition to the classical protein targets of SnRK1, phosphoproteomics revealed novel targets including the key components of intracellular membrane trafficking, ethylene signaling, and ion transport. The upregulation of stress-related processes and suppression of growth-related processes in mutants correlated with their phenotypic defects. Overall, this study highlights a dual role of SnRK1 as a promoter of growth under favorable conditions and a critical regulator of adaptive response under stress conditions.

Vis. is an endemic species distributed along the eastern coast of the Adriatic Sea. In this study, the leaf structure as observed by light and electron microscopy, the phytochemical composition of the volatile organic compounds, and the cytotoxic activity of are presented. The secretory ducts located above and within the phloem and below the xylem part of the vascular bundle represent the first description of the leaf secretory structures of . The essential oil and hydrosol were extracted from air-dried leaves by Clevenger distillation and analyzed by gas chromatography-mass spectrometry, combined with headspace solid-phase microextraction of volatiles from the hydrosol and fresh plant material. α-Amorphene, β-caryophyllene, germacrene D, β-cadinene, and α-copaene were the most abundant sesquiterpenes in the essential oil and fresh plant material. Among the monoterpenes, α-pinene was most abundant in the essential oil, limonene in fresh plant material, and α-terpineol in the hydrosol. Moderate cytotoxic activity of the methanolic extract of , with higher inhibition of cell division observed in the human cervical cancer and osteosarcoma cell lines, and weaker activity in the healthy retinal pigmented epithelial and colon cancer cell lines, was detected using the MTS-based assay. With these results, we aim to highlight the potential of endemic plants, emphasizing the importance of studying species such as and their contributions to biodiversity and human health as sources of bioactive compounds.

Crossover recombination is a pivotal event that takes place during meiosis of germinal cells, leading to the rearrangement of parental chromosomes and generating novel allele combinations, thereby enhancing genetic diversity. This process holds significant importance for plant breeders as it enables the transfer of gene variants from one variety to another. Recent studies have explored diverse strategies to predict recombination events along chromosomes in key plant species, employing various types of genome features. In this study, the relationship between genome structure, quantified using k-mers, and crossover recombination is investigated. To facilitate this analysis, the Python package is introduced; it uses frequency chaos game representation (FCGR) to count k-mers from genome fasta files and adds them as column features for subsequent analysis. This package is used to explore the genomes of one model and five crop plant species, namely, Arabidopsis, bean, maize, rice, sorghum, and tomato. The investigation reveals both positive and negative trends between 3-mers, 2-mers, and recombination rates. Furthermore, the information derived from k-mers was used to train regression-based machine learning models for predicting recombination rates along chromosomes. The results demonstrate the efficacy of using k-mer for predicting purposes, particularly for sorghum and tomato datasets, highlighting linear relationships between several k-mers and recombination events. We hope that this predictive strategy based on genomic sequence information can be useful for the development of new plant crosses.

Baill. is a species that thrives in warm, humid climates with consistently moist soil conditions. With rising global temperatures and an increasing frequency of droughts, the natural habitat of Baill. is facing severe threats. In-depth investigation of the molecular mechanisms underlying Baill.'s response to drought stress is crucial for the conservation of this rare species and the enhancement of its environmental adaptability. This study systematically analyzed the drought stress response of Baill. under varying light conditions through transcriptome data analysis. The results showed that under different light conditions, Baill. responded to drought stress by regulating its internal osmotic balance via the "response to mannitol" pathway. Notably, the molecular mechanisms by which Baill. responds to drought stress vary significantly under different light conditions. Compared with high light intensity, Baill. under shaded conditions responded to drought stress by upregulating glycosyltransferase-related pathways. In addition, three soil drought-related pathway genes (SDRPGs) (, , and ) involved in the regulation of drought stress in Baill. were identified, and both ABA and SA were found to influence their expression. As a key environmental factor, air humidification may enhance the drought stress adaptability of Baill. by modulating ABA biosynthesis. The SDRPGs and signaling pathways identified in this study may serve as important candidate targets, providing theoretical guidance and scientific reference for the genetic improvement of drought resistance in Baill. and the long-term conservation of rare plant resources.

Powdery mildew (PM), mainly caused by , is a severe destructive disease that threatens the production of cucurbit crops globally. Heterologous transformation has shown that the gene (suppressor of the G2 allele of skp1) improved PM resistance in tobacco. However, the function of the gene in pumpkins () is largely unknown. Herein, transient overexpression in pumpkin cotyledons inhibited the spore germination and mycelia growth of by inducing an increase in salicylic acid (SA) content, and exogenous SA intensified the inhibitory effect of the gene on the growth of . The β-glucuronidase activity of cotyledons transformed with the promoter was induced by PM and signaling molecules (gibberellic acid, ethephon, SA, abscisic acid, and methyl jasmonate). The yeast one-hybrid assay verified that transcription factor CmWRKY21, CmWRKY31, and CmWRKY75 proteins interact with the promoter. Transactivation analysis revealed that CmWRKY21 and CmWRKY31 significantly triggered the expression of driven by the promoter under PM. Furthermore, transient co-overexpression of / and enhanced the inhibitory effect on the growth of . In conclusion, the gene is a PM resistance gene in pumpkin and is transcriptionally regulated by CmWRKY21 and CmWRKY31. Our study provides a reference for resistance breeding of pumpkins.

RNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted long non-coding (lnc) RNA-seq or targeted amplicon-seq, involve high costs, complex workflows, and limited accessibility. To address these limitations, I developed a rapid and cost-effective long-read sequencing approach, termed Target-Indexed-PCR (TIP) sequencing, for digital quantification of RNA editing and intron retention events in targeted chloroplast transcripts. This method combines multiplexed high-fidelity PCR amplification with Oxford Nanopore sequencing and custom in-house Perl and Python scripts for streamlined data processing, including barcode-based demultiplexing, strand reorientation, alignment to a pseudo-genome, manual editing-site inspection, and splicing variant identification. As a proof of concept, TIP sequencing was applied to and transcripts, two chloroplast () genes with the highest number of known editing sites in . These transcripts were analyzed both in an inducible CRISPR interference (iCRISPRi) system targeting , a key RNA-editing factor, and in transgenic lines with either overexpression or co-suppression silencing. My findings revealed dose- and development-dependent impacts of on C-to-U editing efficiency. Moreover, I identified an accumulation of intron-retaining transcripts, specifically in Dex-treated iCRISPRi lines and in both overexpression and silencing rosette leaves, indicating impaired chloroplast splicing functions when expression is perturbed beyond an as-yet-undefined threshold. The platform achieves single-molecule resolution, robust reproducibility, and high read coverage across biological replicates at a fraction of the cost of lncRNA-seq. Collectively, this study establishes TIP sequencing as a versatile, scalable, and affordable tool for targeted post-transcriptional analysis in plant organelles and expands our understanding of 's role in chloroplast RNA maturation. By overcoming key limitations of existing approaches, TIP sequencing enables routine, site-specific quantification of post-transcriptional regulation in organelles, including RNA editing and splicing, making it broadly accessible to researchers studying plastid biology, stress responses, and organelle-nucleus communication.

This beginner's guide is intended for plant biologists new to network analysis. Here, we introduce key concepts and resources for researchers interested in incorporating network analysis into research, either as a stand-alone component for generating hypotheses or as a framework for examining and visualizing experimental results. Network analysis provides a powerful tool to predict gene functions. Advances in and reduced costs for systems biology techniques, such as genomics, transcriptomics, and proteomics, have generated abundant omics data for plants; however, the functional annotation of plant genes lags. Therefore, predictions from network analysis can be a starting point to annotate genes and ultimately elucidate genotype-phenotype relationships. In this paper, we introduce networks and compare network-building resources available for plant biologists, including databases and software for network analysis. We then compare four databases available for plant biologists in more detail: AraNet, GeneMANIA, ATTED-II, and STRING. AraNet and GeneMANIA are functional association networks, ATTED-II is a gene coexpression database, and STRING is a protein-protein interaction database. AraNet and ATTED-II are plant-specific databases that can analyze multiple plant species, whereas GeneMANIA builds networks for and nonplant species and STRING for multiple species. Finally, we compare the performance of the four databases in predicting known and probable gene functions of the Nuclear Factor-Y (NF-Y) genes. We conclude that plant biologists have an invaluable resource in these databases and discuss how users can decide which type of database to use depending on their research question.

[This corrects the article DOI: 10.1002/pld3.70081.].

Flowering dogwood ( L.) and Asian dogwood ( F. Buerger ex Hance) are popular deciduous ornamental trees native to a wide range of the eastern and southeastern United States and East Asia, respectively. Anthocyanin pigments enhance desirable pink or dark red colored bracts in dogwoods. Although anthocyanin biosynthesis is one of the best-studied biological processes in nature, genomic and genetic resources to understand the molecular regulation of its synthesis in dogwoods are still lacking. Two classes of genes control anthocyanin production; both structural genes and MYB transcription factors may function as positive or negative regulators of anthocyanin biosynthesis. To reveal the molecular mechanisms that govern color production in ornamental dogwoods, mature bracts of three cultivars of (white bracts: "Cloud Nine"; red bracts: "Cherokee Brave," and "Cherokee Chief") and two cultivars of (light green bracts: "Greensleeves" and midtone pink bracts "Rosy Teacups") were sampled when color was maximally visible. Differential gene expression analysis of the RNAseq data identified 1156 differentially expressed genes in and 1396 in . Phylogenetic analysis with functional orthologues in other plants grouped the candidate R2R3-MYB identified in this study into two distinct subgroups. , , and 2 belong to Subgroup 4, whereas and clustered in Subgroup 5. Genes in the former group repress anthocyanin and proanthocyanidin synthesis in flowering and Asian dogwoods, whereas genes in the latter increase it. Our study contributes to understanding processes behind anthocyanin production and lays the foundation for the future development of molecular markers for faster development of desirable red-bracted dogwoods.

Programmed cell death (PCD) mediates plant development and environmental interactions. Photosynthesis-derived singlet oxygen (O) is one of key reactive oxygen species (ROS) implicated in acclimation and PCD responses to environmental stress conditions. Using cell suspension culture system, we characterized the PCD induced by Rose Bengal (RB), a photosensitizer generating O₂ upon light exposure. Obtained results reiterated that RB-induced PCD is light and chloroplast dependent. Further, we demonstrate that PCD induced by RB involves calcium signaling and mitochondria, thus sharing common features with other forms of regulated cell death in plants. The PCD induced by RB was associated with early transcriptional reprogramming, involving switching off the primary metabolism and activation of stress response and cell death related pathways (e.g., oxidative stress, hypoxia, immunity, and salicylic acid). The constructed gene regulatory network featured O-responsive genes and suggested involvement of transcription factor in retrograde regulation of RB-induced PCD. Interestingly, treatment with RB also induced light independent toxicity, showing features of uncontrolled, necrotic cell death. Presented findings highlight RB as a valuable tool for studying O-induced PCD that may advance future work on chloroplast-mediated oxidative stress responses and enhancing plant resilience to climate change-related stressors through targeted modulation of ROS pathways.

Resistance to 2-methyl-4-chloro-phenoxyacetic acid (MCPA) was recently confirmed in a population of green pigweed () from Dresden, Ontario, Canada, with a resistance factor of 4.4. Resistance to synthetic auxin herbicides in species has previously been linked to non-target site resistance mechanisms with low-level resistance factors (< 10). Based on this information, an investigation into the mechanism of resistance to MCPA was conducted in this population of green pigweed. No significant differences in absorption, translocation, and metabolism of C-MCPA existed between the resistant and a susceptible population of green pigweed. An RNA-Sequencing experiment to identify differentially expressed genes also confirmed this result. Genes that were differentially expressed in the resistant population were linked to target site modifications. A single nucleotide polymorphism (SNP) conferring a leucine to phenylalanine substitution was identified in auxin response factor (ARF) 9. This mutation may be in the Phox and Bem1p (PB1) domain in ARF9, which facilitates the interaction between ARFs and Aux/IAA repressor proteins. The results demonstrate that the mechanism of resistance to MCPA is not a non-target site mechanism and may be linked to a target site modification. Specifically, a SNP in ARF9 could disrupt the interaction between ARF9 and other Aux/IAAs, which could prevent ubiquitination of Aux/IAAs and subsequent lethal action of MCPA.

Microalgae are promising sources to sustainably meet the global needs for energy and products. Algae grow under different trophic conditions, where nutritional status regulates biosynthetic pathways, energy production, and growth. The green alga has strong economic potential because it co-produces biofuel precursors and the high-value antioxidant astaxanthin while accumulating biomass when grown mixotrophically. As an emerging reference alga for photosynthesis, metabolism, and bioproduction, needs a defined, optimized medium to standardize experiments during fast growth for batch cultivation. Because the interplay of glucose treatment (+Glc) and mineral deficiency influences photosynthesis, growth, and the production of lipids and astaxanthin, we designed a replete nutrient medium tailored to the cellular ionome. We combined inductively coupled plasma mass spectrometry (ICP-MS) and +Glc growth curves to determine a medium that is nutrient replete for at least 5 days of +Glc logarithmic growth. We found that there are high nutritional needs for phosphorus and sulfur during mixotrophy. Iron was the only element measured for which the cellular concentration correlated with exogenous concentration and was iteratively adjusted until the cellular ionome was consistent through the logarithmic growth phase. This -Optimized Ratio of Elements (CORE) medium supports fast growth and high biomass and lipid accumulation without causing excess nutrient toxicity. This defined, nutrient-replete standard is important for future investigations and can be adapted for other species to support high biomass for batch cultivation. The method used to develop CORE medium shows how ionomics informs replicable media design and may be applied in industrial settings to inform cost-effective biofuel production.

Weedy rice, a wild relative of cultivated rice, is highly stress-resistant and proliferates in paddy fields. In this study, 353 weedy rice accessions were analyzed to identify salt-tolerance genes using population evolution analysis, phenotypic screening, genome-wide association studies (GWAS), transcriptome analysis, haplotype characterization, gene knockout experiments, and Na and K ion flux assays. Population structure analysis classified the accessions into six distinct groups. Three salt-tolerant accessions-HW131, HW136, and HW119-were identified based on leaf rolling degree (LRD), leaf withering degree (LWD), chlorophyll content (ChlC), and nitrogen content (NC) traits. GWAS and transcriptome data pinpointed and as candidate salt-tolerance genes. Haplotype analysis and qPCR confirmed two major haplotypes: AHap2 and BHap1. A 2-bp deletion (TC) at position 818 bp in was associated with severe salt sensitivity (phenotypic grade 7), whereas the wild-type exhibited strong tolerance (grade1). Knockout mutants exhibited significantly increased Na and K flux across mesophyll cell membranes compared to wild-type plants, validating () as a crucial salt-tolerance gene. This study provides novel genetic insights into salt-stress adaptation in weedy rice, paving the way for breeding enhanced salt-tolerant varieties.

Plant diseases caused by pathogenic microorganisms result in significant damage to agriculture. Lactic acid bacteria (LAB), in particular strains of (), are used as one of the biocontrol methods against plant pathogenic bacteria due to high antagonistic activity associated with their metabolic potential. We have investigated the influence of nutrient medium components (various carbon and nitrogen sources) and cultivation conditions (temperature, duration, and pH) of strains on the level of their antagonistic activity against the test strains of plant pathogenic bacteria. The antimicrobial activity of LAB supernatants was maximal in the presence of 3% (30 g/L) sucrose as the main carbon source and 1% (10 g/L) tyrosine as the main nitrogen source in the nutrient medium against all investigated test strains of PPB. However, the use of such a carbon source as galactose or arabinose led to a decrease or even absence of antimicrobial properties of LAB against phytopathogenic bacteria. The optimal conditions for cultivation of lactobacilli were determined: cultivation temperature +30 ± 1°C, pH 7.8, and duration 72 h. Strains of and caused zones of inhibition in test pathogens from 298 to 291 mm. Whereas during 24-h cultivation of LAB strains, their antagonistic activity was significantly lower, and the zones of inhibition decreased by 30%. The duration and temperature had a significant effect on increasing the antagonistic activity of strains, in contrast to the pH of the medium ( ≥ 0.05).

In apple (), flowering is repressed by the phytohormone gibberellin (GA) and high temperatures (> 27°C), but the molecular mechanisms underlying this repression remain unknown. In (Arabidopsis), GA and temperature signaling converge on DELLA protein regulation, with both factors promoting DELLA degradation through independent 26S proteasome-mediated pathways. Here, we tested whether high-temperature-induced DELLA degradation is conserved in apple. Using the heterologous systems Arabidopsis and , we characterized the function of the apple DELLA protein DELLA REPRESSOR OF ga1-3 (MdRGL1a) and found that high temperatures promote its degradation via a 26S proteasome-dependent mechanism. Additionally, MdRGL1a interacts with apple orthologs of Arabidopsis CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and SUPPRESSOR OF phyA-105 2 (SPA2), components of an E3 ubiquitin ligase complex that mediates protein ubiquitination and degradation. These findings suggest a conserved mechanism of temperature-induced DELLA degradation between apple and Arabidopsis. The degradation of MdRGL1a may underlie flowering suppression in apple under high temperatures, providing molecular insights that could aid in developing strategies to stabilize apple and other crop production in the face of climate change.

Phototropic bending of plants towards a light source allows them to position their photosynthetic tissues to optimize light capture. In light-grown (de-etiolated) seedlings, phototropic bending of the hypocotyl is inhibited by light with a high red:far-red ratio (HRFR) and high levels of blue light (HBL). This occurs via activation of the phytochrome B (phyB) and cryptochrome 1 (cry1) photoreceptor signaling pathways. Both phyB and cry1 act upstream of PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors, which are required for hypocotyl bending in light-grown seedlings. Presently, it is not known whether other pathways are involved in the inhibition of PIF-mediated phototropism in light-grown seedlings. To address this, we conducted a screen to identify mutants with increased phototropic bending relative to wild type in HRFR + HBL conditions. Through this screen, we identified EARLY FLOWERING 3 (ELF3), a member of the Evening Complex (EC), as a key inhibitor of phototropic bending in green seedlings. We show that both ELF3 and LUX, another component of the EC, inhibit phototropic bending upstream of PIF4/PIF5. Furthermore, we show that phototropic bending in seedlings is subject to circadian regulation in an ELF3-dependent manner. Finally, we provide evidence that ELF3 in the grass also affects phototropism but in an opposite way than in .

Anthocyanins are pigments that contribute to plant defense and adaptation to environmental stresses. Given their antioxidant properties and positive impacts on human health, enhancing anthocyanin biosynthesis in plants holds significant economic importance. In potato, several genotypes produce a high amount of anthocyanins, but the molecular mechanisms underlying the genotypic variation of anthocyanin content remain poorly understood. Here, key genes that may determine the genotype-dependent capacity for anthocyanin biosynthesis were analyzed. Anthocyanin content in tubers from five genotypes was measured, and Heimeiren and Desiree, exhibiting high and low anthocyanin content, respectively, were selected. We were unable to identify any evidence of differing activity in anthocyanin biosynthesis enzymes based on single amino acid polymorphism analysis between the two genotypes. However, transcriptome sequencing coupled with prediction of gene function identified 27 candidate genes showing different expression levels in tubers of these genotypes. We additionally verified expression patterns of these genes and found that four genes encoding flavanone 3-hydroxylase, flavonoid 3',5'-hydroxylase, anthocyanin synthase (ANS), and anthocyanin O-methyltransferase (AOMT) were strong candidates for high accumulation of anthocyanins in Heimeiren. Particularly, ANS and AOMT are strong candidates increasing anthocyanin content in the tuber flesh. These results imply that genotype-dependent variations of anthocyanin biosynthesis may be due to difference of gene expression, but not enzymatic activities. Our study suggests key anthocyanin biosynthesis genes showing different expression levels in high- and low-anthocyanin genotypes, offering potential for the metabolic engineering of potatoes to increase anthocyanin content.