BMC Plant Biology

Improving photosynthesis is a promising approach to enhance sugar beet productivity. However, genetic variation in leaf photosynthesis and its relationship with disease resistance remain underexplored. We evaluated 98 sugar beet genotypes representing different breeding categories, including commercial F1 hybrids, seed-parent lines, and pollinator lines, in Hokkaido, northern Japan. Leaf gas exchange was measured during early growth under field conditions around the infection period of Cercospora leaf spot (CLS). To account for fluctuating irradiance during large-scale phenotyping, we applied a multilevel mixed-effects light-response model to estimate genotype-specific photosynthetic characteristics. Substantial genotypic variations in photosynthetic characteristics were detected. F1 hybrids exhibited higher photosynthetic capacity than breeding lines, whereas differences among breeding categories were unclear due to large within-category variation. Some breeding lines exhibited photosynthetic rates higher than those of hybrids, indicating exploitable genetic resources within the present genetic panel. We did not detect statistically significant trade-off between leaf photosynthesis and CLS resistance among 98 genotypes; in a subset of 19 genotypes analysed in detail, the relationship was even synergistic. Our results highlight the genetic diversity of leaf photosynthesis and its category-dependent structure, and suggest that selection for enhanced photosynthesis can proceed without substantial trade-off with CLS resistance. HighlightLeaf photosynthesis of 98 sugar beet genotypes showed significant genetic variation and dependence on breeding category. Active photosynthesis incurred minimal trade-off with Cercospora leaf spot resistance.

Quality attributes play a pivotal role in determining consumers acceptability and market value of food crops. Dioscorea alata is a major yam species for food security in tropical areas, but our understanding of the genetic factors underlying tuber culinary traits is limited. This study aimed at elucidating the genetic basis of key culinary attributes, including dry matter content, cooking time, boiled yam hardness, and moldability, through genome-wide association studies (GWAS). Phenotypic assessments revealed notable variations among the D. alata genotypes across two locations as well as significant correlations among the quality traits. The GWAS identified 25 significant associations distributed across 14 chromosomes. Allele segregation analysis of the identified loci highlighted favorable alleles associated with desired traits, such as reduced cooking time, increased dry matter content, enhanced hardness, and good moldability. Within the set of 42 putative candidate genes, we identified specific genes differentially expressed in tubers of distinct genotypes with contrasting quality attributes. Furthermore, we conducted a comparative analysis with previously reported quantitative trait loci for dry matter content and showed that multiple genomic regions govern this trait in D. alata. Our study offers valuable insights into the links between these key culinary traits and the underlying genetic basis in D. alata. These findings have practical implications for breeding programs aimed at enhancing the quality attributes of greater yam.

Grape breeding programs are mostly focused on developing new varieties with high production volume, sugar contents, and phenolic compound diversity combined with resistance and tolerance to the main pathogens under culture and adverse environmental conditions. The Niagara variety (Vitis labrusca x Vitis vinifera) is one of the most widely produced and commercialized table grapes in Brazil. In this work, we selected three Niagara somatic variants with contrasting berry phenotypes and performed morphological and transcriptomic analyses of their berries. Histological sections of the berries were also performed to understand anatomical and chemical composition differences of the berry skin between the genotypes. An RNA-Seq pipeline was implemented, followed by global coexpression network modeling. Niagara Steck, an intensified russet mutant with the most extreme phenotype, showed the largest difference in expression and showed selection of coexpressed network modules involved in the development of its russet-like characteristics. Enrichment analysis of differently expressed genes and hub network modules revealed differences in transcription regulation, auxin signaling and cell wall and plasmatic membrane biogenesis. Cutin- and suberin-related genes were also differently expressed, supporting the anatomical differences observed with microscopy.

Strigolactones are ecologically, developmentally, and physiologically important hormones, but much remains unknown about their evolution and role in non-model species. Sorghum is an important C4 cereal for [~]1 billion people globally and exhibits natural variation in root-exuded strigolactones. Differences in sorghum strigolactone stereochemistry are associated with resistance to a parasitic plant, but with evidence for potential trade-offs. In the present study, we studied sorghum mutants of loci in the strigolactone biosynthetic pathway, CAROTENOID CLEAVAGE DIOXYGENASE 8 (CCD8) and LOW GERMINATION STIMULANT 1 (LGS1). We found that CCD8 CRISPR-Cas9 deletions changed the accumulation of low abundance metabolites, reduced net carbon assimilation rate, altered root architecture and anatomy, and reduced the establishment and benefit of mycorrhizal symbionts. For LGS1 CRISPR-Cas9 deletions, we found net carbon assimilation rate to be reduced, the colonization of mycorrhizal symbionts to be delayed, and evidence for regulatory pathways involved in stress response and growth to be impacted. We further tested the impacts of restoring functionality of LGS1 into a normally non-functional background (RTx430). Notably, we did not see consistent impacts of LGS1 loss-of-function across LGS1 deletion and insertion mutants, though root exudates from insertion mutants increased stimulation of Striga germination, suggesting that background specific modifiers may buffer the strigolactone impacts of loss-of-function at LGS1. Our study begins to give context to the trade-offs associated with a host resistance strategy to a parasitic plant and more broadly contributes to understanding the role strigolactones play in sorghum physiological processes, growth, and development.

Durable host plant resistance (HPR) to insect pests is critical for sustainable agriculture. Natural variation exists for aphid HPR in sorghum (Sorghum bicolor) but the genetic architecture and phenotype has not been clarified for most sources. To assess the threat of a sorghum aphid (Melanaphis sorghi) biotype shift, we characterized the phenotype of Resistance to Melanaphis sorghi 1 (RMES1) and contributing HPR architecture in globally-admixed populations selected under severe aphid infestation in Haiti. We found RMES1 reduces sorghum aphid fecundity but not bird cherry-oat aphid (Rhopalosiphum padi) fecundity, suggesting a discriminant HPR response typical of gene-for-gene interaction. A second resistant gene, RMES2, were more frequent than RMES1 resistant alleles in landraces and historic breeding lines. RMES2 contributes early and mid-season aphid resistance in a segregating F2 population, however RMES1 was only significant with mid-season fitness. In a fixed population with high aphid resistance, RMES1 and RMES2 were selected for demonstrating a lack of significant antagonistic pleiotropy. Associations with resistance co-located with cyanogenic glucoside biosynthesis genes support additional HPR sources. Globally, therefore, a vulnerable HPR source (RMES1) is bolstered by a second common source of resistance in breeding programs (RMES2) which may be staving off a biotype shift. HIGHLIGHTThe globally-deployed sorghum aphid resistance gene, RMES1, reduces aphid reproduction and therefore is vulnerable to a biotype shift. A second major gene, RMES2, and cyanogenesis may increase global durability of resistance.

Parasitic plants exhibit unique adaptations, including specialized structures like haustoria and reduced organs. We analyzed genomic and transcriptomic data from nine parasitic species across hemi-, holo-, and endoparasitic lifestyles, uncovering distinct patterns of lncRNA abundance and expression. Holoparasites exhibited the highest lncRNA counts, while endoparasites displayed notable reductions. Expression analyses revealed tissue-specific patterns, with elevated lncRNA activity in haustorial tissues of Cuscuta. Phylogenetic analyses suggested horizontal gene transfer (HGT) of lncRNA sequences, particularly in Sapria. These findings highlight the potential involvement of lncRNAs in parasitic plant adaptation, host interaction, and genomic evolution through HGT.

The mapping and introduction of sustainable plant immunity to pests and diseases in fruit tree is still a major challenge in modern breeding. This study aims at deciphering the genetic architecture underlying resistance or tolerance across environments for major pests and diseases in peach (P. persica) and apricot (P. armeniaca). We set up a multi-environment trial (MET) approach by studying two core collections of 206 peach and 150 apricot accessions deployed under low phytosanitary conditions in respectively three and two environmentally contrasted locations in South-East of France. To capture the complex dynamics of pest and disease spread in naturally infected orchards, visual scoring of symptoms was repeated within and between 3 years, for five and two pests and diseases respectively for peach and apricot, resulting in the maximum of damage score and the AUDPC. These traits were used as phenotypic inputs in our genome-wide association studies (GWAS) strategy, and leading to the identification of: i) non-additive genotype-phenotype associations, ii) environment-shared QTLs iii) environment-specific QTLs, and iv) interactive QTLs which changes in direction ( antagonist) or intensity ( differential) according to the environment. By conducting GWAS with multiple methods, we successfully identified a total of 60 high confidence QTLs, leading to the identification of 87 candidate genes, the majority belonging to the Leucine-rich repeat containing receptors (LRR-CRs) family gene. Finally, we provided a comparative analysis of our results on peach and apricot, two closely related species. The present results contribute to the development of genomics-assisted breeding to improve biotic resilience in Prunus varieties.

Berry and cluster size are pivotal determinants of grapevine productivity and consumer preferences and remain major targets in grapevine breeding. However, given their complexity as quantitative traits under polygenic control, a deeper understanding of their genetic determinants is needed. The gene pool of the Brazilian grapevine has made a significant contribution to enhancing grapevine performance in tropical and subtropical regions. In this study, we conducted a genome-wide association study (GWAS) using a diverse panel of 288 Vitis spp. accessions from the Instituto Agronomico Germplasm Bank, Brazil. This panel was phenotyped for six cluster architecture traits over 12 years and genotyped using the Vitis18kSNP array. Using two different algorithms, the GWAS identified 56 significant SNPs distributed across 17 chromosomes, validating previously identified quantitative trait loci (QTLs) and revealing novel associations. Four closely spaced markers on Chr1 suggest the presence of a QTL influencing five traits simultaneously. A strong association signal, with phenotypic variance explained (PVE) values of approximately 29-35%, indicated a major QTL for berry length (BL) and width (BWi) on Chr14. Additionally, major-effect SNP loci were identified for cluster weight (CW) on Chr1, cluster length (CL) on Chr7 and 14, cluster width (CWi) on Chr6 and 18, and berry weight (BW) on Chr4, with PVE values ranging from 18-27%. Furthermore, 80 genes associated with berry traits and 52 genes associated with cluster traits were identified as putative candidate genes in the genomic regions associated with significant SNPs. These candidate genes are involved in the regulation of growth and development, hormone regulation, protein synthesis, stress response, and other physiological processes essential for cell health and functionality. Our results provide valuable insights into the genetic determinants of grape berry size and cluster architecture, offering critical data to support future functional studies and enhance the efficiency of related breeding programs.

Grapevine cultivation at high altitudes provides a viable option for producing premium quality wines in the context of climate change. This is primarily attributed to cooler temperatures, wider thermal amplitudes, and increased UV-B radiation. Although high UV-B levels can cause oxidative-stress, grape berries acclimate by generating UV-blocking anthocyanins and antioxidant compounds accumulated in the berry skins, thereby enhancing the organoleptic qualities and aging capacity of wine. This UV-B exclusion study examines how Malbec berries respond to solar UV-B at a high-altitude vineyard in Mendoza, Argentina (1350 m a.s.l.). The results showed that high solar UV-B acts both as a photomorphogenic signal and a stressor. The proteomic changes of berries exposed to +UV-B conditions indicate a decrease of photosynthesis and oxidative phosphorylation, coupled with an increase of glycolysis and tricarboxylic acid cycle as compensatory respiration pathways. Furthermore, numerous chaperones and proteins associated with the antioxidant system exhibited increased abundance to maintain cellular homeostasis. Lastly, veraison-stage berries exposed to +UV-B displayed an activation of the UVR8 signaling cascade and the phenylpropanoid pathway, resulting in higher concentration of phenolic compounds and more oxidation-resistant types of anthocyanins. This is the first report of field-grown grape berry proteomic modulation in response to solar UV-B, and it may have significant implications for the cultivation of high-quality wine grapes in both current and future climate scenarios. Significance

Phytoplasmas inhabit phloem sieve elements and cause abnormal growth and altered sugar partitioning. But how they interact with phloem functions is not clearly known. The phloem responses were investigated in tomato infected by Candidatus Phytoplasma solani, at the beginning of the symptomatic stage of infection, both in symptomatic and asymptomatic leaves, the first symptoms appearing in the sink top leaf at the stem apex. Antisense lines impaired in the phloem sucrose transporters SUT1 and SUT2 were included. The infection in source leaves was not associated with symptoms. In the symptomatic, sink leaf, yellowing and leaf curling was associated with higher starch accumulation and expression of defense genes. The transcriptional analysis of symptomatic leaf midribs indicated that transcript levels for genes acting in the glycolysis and peroxisome metabolism in infected plants differed from these in non-infected plants. Phytoplasma multiplied actively in at least three additional lower leaves although they were symptomless, with no sign of activation of defense markers, although the rate of exudation of sucrose from these symptomless, source leaves was lower for infected plants. A few metabolites in phloem-enriched exudate were affected by the infection, such as glycolate and aspartate, and some of them were also affected in the control SUT1- and SUT2- antisense lines, in which sucrose retrieval or release in the sieve elements are impaired. A metabolic switch could explain the delivery of more glycolate into the sieve elements of infected plants. The findings suggest a link between sugar transport and redox homeostasis. One sentence summaryAn impairment of sucrose retrieval and release in the sieve elements occurs during phytoplasma infection, associated with changes in sugar and peroxisome metabolism

Seed coat color is a well described trait in lettuce (Lactuca sativa), varying from black to pale white pigmentation. In this study, we delve into seed coat color variation of several species within the Lactuca genus, encompassing L. sativa and 15 wild varieties, offering broader insights into the diversity of this trait. To capture seed coat color quantitatively, we use grey pixel values from publicly available images, enabling us to measure seed coat color as a continuous trait across the genus. Darker seed coats predominate within the Lactuca genus, with L. sativa displaying a distinctive bimodal distribution of black and white seed coats. Lactuca virosa exhibits the darkest seed coat coloration and less variation, while Lactuca saligna and Lactuca serriola display lighter shades and greater variability. To identify the polymorphic loci underlying the observed variation we performed GWAS on seed coat color in both L. sativa and L. serriola. For L. sativa, we confirmed the one known major QTL linked to black and white seed coat color, which we reproduce in two independent, published genotype collections (n=129, n=138). Within the same locus, we identify additional candidate genes associated with seed coat color. For L. serriola, GWAS yielded several minor QTLs linked to seed coat color, harboring candidate genes predicted to be part of the anthocyanin pathway. These findings highlight the phenotypic diversity present within the broader Lactuca genus and provide insights into the genetic mechanisms governing seed coat coloration in both cultivated lettuce and its wild relatives.

Cassava is a crucial staple crop for smallholder farmers in tropical Asia and Sub-Saharan Africa. Although high yield remains the top priority for farmers, the significance of nutritional values has increased in cassava breeding programs. A notable negative correlation between provitamin A and starch accumulation poses a significant challenge for breeding efforts. The negative correlation between starch and carotenoid levels in conventional and genetically modified cassava plants implies the absence of a direct genomic connection between the two traits. The competition among various carbon pathways seems to account for this relationship. In this study, we conducted a thorough analysis of 49 African cassava genotypes with varying levels of starch and provitamin A. Our goal was to identify factors contributing to differential starch accumulation. With the carotenoid levels of the varieties considered as a confounding effect on starch production, we found that yellow and white-fleshed storage roots did not differ significantly in most measured components of starch or de novo fatty acid biosynthesis. However, genes and metabolites associated with myo-inositol synthesis and cell wall component production were substantially enriched in high provitamin A genotypes. These results indicate that yellow-fleshed cultivars, in comparison to their white-fleshed counterparts, direct more carbon towards the synthesis of raffinose and cell wall components, a finding that is supported by a significant rise in the starch-free residue to total dry yield ratio in yellow storage roots versus white storage roots. Our findings enhance comprehension of the biosynthesis of starch and carotenoids in the storage roots of cassava.

BackgroundPrevious reports in several plant species have shown that thiamin applied on foliage primes plant immunity and is effective in controlling fungal, bacterial, and viral diseases. However, the effectiveness of thiamin against potato (Solanum tuberosum) pathogens has seldom been investigated. Additionally, the transcriptomics and metabolomics of immune priming by thiamin have not previously been investigated. Here, we tested the effect of thiamin application against Alternaria solani, a necrotrophic fungus that causes early blight disease on potato foliage, and identified associated changes in gene expression and metabolite content. ResultsFoliar applications of thiamin reduced lesion size by approximately 33% when applied at an optimal concentration of 10 mM. However, the effect of thiamin on preventing lesion growth was temporally limited, as we observed a reduction of lesion size when leaves were inoculated 4 h, but not 24 h, following thiamin treatment. Additionally, we found that the effect of thiamin on lesion size was restricted to the site of application and was not systemic. Gene expression analysis via RNA-seq showed that thiamin induced the expression of genes involved in the synthesis of salicylic acid (SA) and phenylpropanoids to higher levels than the pathogen alone, as well as fatty acid metabolism genes that may be related to jasmonic acid biosynthesis. Thiamin also delayed the downregulation of photosynthesis-associated genes in plants inoculated with A. solani, which is a typical plant response to pathogens, but could also induce a similar repression of primary metabolic pathways in non-infected leaves. Metabolite analyses revealed that thiamin treatment in the absence of pathogen decreased the amounts of several organic compounds involved in the citric acid cycle as well as sugars, sugar alcohols, and amino acids. ConclusionsOur study indicates that thiamin priming of plant defenses may occur through perturbation of primary metabolic pathways and a re-allocation of energy resources towards defense activities.

Viroids, minimalist plant pathogens, present significant threats to crops by causing severe diseases. The use of high-throughput sequencing technologies for analyzing the transcriptomes of viroid-infected host plants has yielded informative information on gene regulation by these pathogens, however a complete understanding of the transcriptome data suffers from the inclusion of numerous genes of unknown function. Co-expression analysis addresses this by clustering genes into modules based on global gene expression levels. Our previous study emphasized basic helix-loop-helix protein (bHLH) transcriptional reprogramming in tomato in response to different potato spindle tuber viroid (PSTVd) strains. In the current research, we delve into tissue-specific gene modules, particularly in root and leaf tissues, governed by bHLH transcription factors during PSTVd infections. Utilizing public datasets that span Control (C; (mock-inoculated), PSTVd-mild (M), and PSTVd-severe (S23) strains in time-course infections, we uncovered differentially expressed gene modules. These modules were functionally characterized, identifying essential hub genes. We identified the roles of bHLH transcription factors (TFs) in managing processes like photosynthesis and rapid membrane repair in infected roots. In leaves, external layer alterations influenced photosynthesis, linking bHLH TFs to distinct metabolic functions. Expanding on these findings, we explored bipartite networks, discerning both common and unique bHLH TF regulatory roles, notably highlighting the bifan motifs significance in these interactions. Through this holistic approach, we deepen our understanding of viroid-host interactions and the intricate regulatory mechanisms underpinning them.

BackgroundCandidatus Phytoplasma infection is among the most destructive plant diseases, characterized by phyllody, witches broom, virescence etc. Sesame (Sesamum indicum L.), one of the oldest cultivated oilseed crops, valued for its nutritional and medicinal properties, is highly susceptible to phytoplasma infection, causing substantial annual yield losses. The present study aimed to investigate the metabolomic and molecular alterations in sesame plants as a consequence of phytoplasma infection in two distinct tissue types, leaves and flowers, using a multi-omics approach. ResultsThe study revealed that phytoplasma infection significantly alters the expression of floral homeobox and meristem identity genes in an antagonistic manner, resulting in the development of leaf-like traits in floral tissues. Integrated analyses of transcriptomic and metabolomic datasets showed that control leaves, control flowers, infected leaves, and infected flowers each displayed distinct metabolomic and transcriptomic profiles. Metabolomic profiling demonstrated major changes in pathways such as porphyrin metabolism, brassinosteroid metabolism, and phenylpropanoid biosynthesis. Complementary KEGG pathway enrichment analysis of transcriptome data confirmed strong enrichment of secondary metabolite biosynthesis in both tissue types upon infection. Tissue-specific responses were evident. Floral tissues accumulated green pigments due to increased porphyrin biosynthesis and reduced degradation, while leaves showed simultaneous upregulation of both biosynthesis and breakdown pathways of porphyrins. Floral tissues exhibited stronger stress-associated responses, including upregulation of genes related to stress enzymes, phenylpropanoids, and lignification-related metabolites. In contrast, certain compounds such as lignans were specifically accumulated in leaves upon infection. These observations were further supported by biochemical, histological, and qRT-PCR assays. ConclusionThis study provides the first clear evidence of tissue-specific metabolic reprogramming in sesame under Ca. Phytoplasma infection through integrated transcriptomic and metabolomic analyses. These findings improve our understanding of host-pathogen interactions and offer a basis for strategies to reduce phytoplasma-induced yield losses.

MYZUS PERSICAE-INDUCED LIPASE1 (MPL1) encodes a lipase in Arabidopsis thaliana that is required for controlling infestation by the green peach aphid (GPA; Myzus persicae), an important phloem sap-consuming insect pest. Previously, we demonstrated that MPL1 expression was upregulated in response to GPA infestation, and GPA fecundity was higher on the mpl1 mutant, compared to the wild-type (WT), and lower on 35S:MPL1 plants that constitutively expressed MPL1 from the 35S promoter. Here, we show that the MPL1 promoter is active in the phloem and expression of the MPL1 coding sequence from the phloem-specific SUC2 promoter is sufficient to restore resistance to the GPA in the mpl1 mutant. The GPA infestation-associated upregulation of MPL1 requires CYCLOPHILIN 20-3 (CYP20-3), which encodes a 12-oxo- phytodienoic acid (OPDA)-binding protein that is involved in OPDA signaling and is required for controlling GPA infestation. OPDA promotes MPL1 expression to limit GPA fecundity, a process that requires CYP20-3 function. These results along with our observation that constitutive expression of MPL1 from the 35S promoter restores resistance to the GPA in the cyp20-3 mutant, and MPL1 feedbacks to limit OPDA levels in GPA-infested plants, suggest that an interplay between MPL1, OPDA, and CYP20-3 contributes to resistance to the GPA. HighlightInteraction between MYZUS PERSICAE-INDUCED LIPASE 1 function in the phloem, and 12-oxo-phytodienoic acid (OPDA) and CYCLOPHILIN 20-3, which encodes an OPDA-binding protein that is involved in OPDA signaling, is involved in controlling green peach aphid infestation on Arabidopsis thaliana.

- Passion flower extrafloral nectaries (EFNs) protrude from adult leaves and facilitate mutualistic interactions with insects, but how age cues control EFN establishment remains poorly understood. - Here, we combined genetic and molecular studies to investigate how leaf development and EFN patterning are regulated through the age-dependent miR156-SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) module in two EFN-containing Passiflora species with distinct leaf shapes. - Low levels of miR156 correlate with leaf maturation and EFN formation in Passiflora edulis and P. cincinnata. Consistently, overexpression of miR156 (miR156-OE), which leads to low levels of SPLs, affected leaf ontogeny and EFN development in both species. Laminar EFNs were underdeveloped and less abundant in both P. edulis and P. cincinnata miR156-OE leaves. Importantly, the ecological relationships established by EFNs and their sugar profiles were negatively regulated by high levels of miR156. Moreover, transcriptome analysis of young leaf primordia revealed that miR156-targeted SPLs may be required for proper expression of leaf and EFN development- associated genes in P. edulis and P. cincinnata. - Our work provides the first evidence that the highly conserved miR156/SPL module regulates EFN development in an age-dependent manner and that the program responsible for EFN development is closely associated with the heteroblastic developmental program of the EFN-bearing leaves.

The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forward genetics perspective. We explored the relationship between different branches of the phenylpropanoid and isoprenoid pathways while examining an infrequent berry skin color variegation in grapevine. Red and white berry skin sections were compared at the genetic, transcriptomic and metabolomic levels showing that, as in most cultivated white grape varieties, the uncolored skin section convened the non-functional alleles of the anthocyanin regulators MYBA1 and MYBA2, explaining the lack of pigments. In contrast, light-responsive flavonols and monoterpenes increased in anthocyanin-depleted areas. We disclosed an enrichment of the flavonol, terpene and carotenoid pathways among up-regulated genes from white-skin sections, accompanied by increased expressions of flavonol regulators and the still uncharacterized MYB24 gene. We used DAP-seq to examine the in vitro binding of affinity-purified MYB24 protein to genomic DNA and demonstrated its binding in the promoter regions of terpene (22) and carotenoid (6) genes, in addition to more than 30 photosynthesis and light-response genes, including the flavonol-regulator HY5 homologue (HYH). We confirmed the activation of TPS35 and HYH promoter:luciferase reporters in the presence of MYB24 and the grape bHLH MYC2, all of which correlate in their higher expression in white skin variegated sections. The integration of several datasets allowed to define a list of high confidence targets, suggesting MYB24 as a modulator of light responses including the synthesis of flavonoids (flavonols) and isoprenoids (terpenes, and putatively carotenoids). The correspondence between MYB24 and monoterpenes in all conditions surveyed implies that this regulatory network is broadly triggered towards berry ripening, and that the absence of anthocyanin sunscreens accelerates its activation most likely in a dose-dependent manner due to increased radiation exposure.

Withdrawal StatementThe authors have wthdrawn this manuscript (DOI: https://doi.org/10.1101/2025.09.05.674467) because they have identified issues with the data and can no longer stand by the conclusions; the authors agree that the original version remains online labeled as "Withdrawn" to preserve the scholarly record. Therefore, the authors do not wish this work to be cited as reference for the project If you have any questions, please contact the corresponding author."

Anthocyanins are flavonoids responsible for the color of berries in skin-pigmented grapevine (Vitis vinifera L.). Due to the widely adopted vegetative propagation of this species, somatic mutations occurring in meristematic cell layers can be fixed and passed into the rest of the plant when cloned. In this study we focused on the transcriptomic and metabolic differences between two color somatic variants. Using microscopic, metabolic and mRNA profiling analyses we compared the table grape cultivar (cv.) Red Globe (RG, with purplish berry skin) and cv. Chimenti Globe (CG, with a contrasting reddish berry skin color). As expected, significant differences were found in the composition of flavonoids and other phenylpropanoids, but also in their upstream precursors shikimate and phenylalanine. Among primary metabolites, sugar phosphates related with sucrose biosynthesis were less accumulated in cv. CG. The red-skinned cv. CG only contained di-hydroxylated anthocyanins (i.e. peonidin and cyanidin) while the tri-hydroxylated derivatives malvidin, delphinidin and petunidin were absent, in correlation to the reddish cv. CG skin coloration. Transcriptomic analysis showed alteration in flavonoid metabolism and terpenoid pathways and in primary metabolism such as sugar content. Eleven flavonoid 35-hydroxylase gene copies were down-regulated in cv. CG. This family of cytochrome P450 oxidoreductases are key in the biosynthesis of tri-hydroxylated anthocyanins. Many transcription factors appeared down-regulated in cv. CG in correlation to the metabolic and transcriptomic changes observed. The use of molecular markers and its confirmation with our RNA-seq data showed the exclusive presence of the null MYBA2 white allele (i.e. homozygous in both L1 and L2 layers) in the two somatic variants. Therefore, the differences in MYBA1 expression seem sufficient for the skin pigmentation differences and the changes in MYBA target gene expression in cv. Chimenti Globe.