Research progress of fruit color development in apple (Malus domestica Borkh.)

Genetic factors explaining anthocyanin pigmentation differences

BACKGROUND

Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins.

RESULTS

A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties was performed within numerous plant species covering the taxonomic diversity of flowering plants. The literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from four previous studies were reanalyzed to determine the genes possibly responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the intraspecific pigmentation differences was quantified. Differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are significantly more prone to account for pigmentation differences compared to bHLH or WD40 genes. Among the structural genes, DFR genes are most often associated with anthocyanin loss.

CONCLUSIONS

These findings support previous assumptions about the susceptibility of transcriptional regulation to evolutionary changes and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent prevalent role in the specificity of the MBW complex.

Image analysis and polyphenol profiling unveil red-flesh apple phenotype complexity

BACKGROUND

The genetic basis of colour development in red-flesh apples (Malus domestica Borkh) has been widely characterised; however, current models do not explain the observed variations in red pigmentation intensity and distribution. Available methods to evaluate the red-flesh trait rely on the estimation of an average overall colour using a discrete class notation index. However, colour variations among red-flesh cultivars are continuous while development of red colour is non-homogeneous and genotype-dependent. A robust estimation of red-flesh colour intensity and distribution is essential to fully capture the diversity among genotypes and provide a basis to enable identification of loci influencing the red-flesh trait.

RESULTS

In this study, we developed a multivariable approach to evaluate the red-flesh trait in apple. This method was implemented to study the phenotypic diversity in a segregating hybrid F1 family (91 genotypes). We developed a Python pipeline based on image and colour analysis to quantitatively dissect the red-flesh pigmentation from RGB (Red Green Blue) images and compared the efficiency of RGB and CIEL*a*b* colour spaces in discriminating genotypes previously classified with a visual notation. Chemical destructive methods, including targeted-metabolite analysis using ultra-high performance liquid chromatography with ultraviolet detection (UPLC-UV), were performed to quantify major phenolic compounds in fruits' flesh, as well as pH and water contents. Multivariate analyses were performed to study covariations of biochemical factors in relation to colour expression in CIEL*a*b* colour space. Our results indicate that anthocyanin, flavonol and flavanol concentrations, as well as pH, are closely related to flesh pigmentation in apple.

CONCLUSTION

Extraction of colour descriptors combined to chemical analyses helped in discriminating genotypes in relation to their flesh colour. These results suggest that the red-flesh trait in apple is a complex trait associated with several biochemical factors.

Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species

KEY MESSAGE

Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.

Decoding plant specialized metabolism: new mechanistic insights

Secondary metabolite (SM) production provides biotic and abiotic stress resistance and enables plants to adapt to the environment. Biosynthesis of these metabolites involves a complex interplay between transcription factors (TFs) and regulatory elements, with emerging evidence suggesting an integral role for chromatin dynamics. Here we review key TFs and epigenetic regulators that govern SM biosynthesis in different contexts. We summarize relevant emerging technologies and results from the model species arabidopsis (Arabidopsis thaliana) and outline aspects of regulation that may also function in food, feed, fiber, oil, or industrial crop plants. Finally, we highlight how effective translation of fundamental knowledge from model to non-model species can benefit understanding of SM production in a variety of ecological, agricultural, and pharmaceutical contexts.

The Expression of Key Ethylene and Anthocyanin Biosynthetic Genes of 'Honeycrisp' Apples Subjected to the Combined Use of Reflective Groundcovers and Aminoethoxyvinylglycine in the Mid-Atlantic US

The decreased profitability of important apple cultivars, such as 'Honeycrisp', results from the poor red skin coloration and high fruit drop in the mid-Atlantic US. Apple red skin coloration is determined by the anthocyanin concentration. Reflective groundcovers promote red skin coloration, whereas aminoethoxyvinylglycine (AVG) decreases the ethylene production and fruit drop, thus reducing the coloration. Although our previous study showed that combinations of these practices impact the fruit quality and color, research is lacking regarding their effects at the gene and metabolite levels. In this work, for two years, we compared the differences in the internal ethylene concentration (IEC), red skin coloration, fruit drop, transcript accumulation of key ethylene and anthocyanin biosynthetic pathway-related genes, and total anthocyanin concentration of 'Honeycrisp' apples. The fruit was treated with combinations of reflective groundcover (Extenday) and AVG (130 mg L-1) and was assessed throughout ripening. Extenday-only-treated fruit displayed the highest upregulation of ethylene and anthocyanin biosynthetic-related genes and of total anthocyanins, exceeding 50% blush, while boosting the IEC. In contrast, AVG significantly decreased the expression of key ethylene and anthocyanin biosynthetic-related genes and total anthocyanins, thus preventing apples from reaching 50% blush, while also decreasing the IEC and fruit drop. The combination of Extenday x AVG fine-tuned the transcript accumulation of ethylene and anthocyanin biosynthetic-related genes as well as the total anthocyanins, allowing the 'Honeycrisp' fruit to exceed 50% blush, while increasing the IEC moderately and reducing the fruit drop (as compared to Extenday-only and control), thus enhancing the fruit economic value.

A high-density linkage map construction in guava (Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population

Psidium guajava L. is an important fruit crop in the tropical and subtropical regions of the world. The advanced breeding methods are not employed for important commercial traits like peel and pulp color, seed hardiness, fruit size, etc., due to the scarcity of genome-wide molecular markers and high-density linkage maps. In this study, we employed single-nucleotide polymorphism (SNP) markers and identified quantitative trait loci (QTL) regions that are associated with color traits of leaf, peel, and pulp in the guava intervarietal mapping population. The mapping population was developed from the contrasting genotypes of fruit and leaf color. Variations in color among the segregating hybrids were recorded both visually and using a Color reader. A high-density linkage map of guava was constructed using the SNP markers from genotyping by sequencing (GBS) of 150 hybrid individuals of the cross 'Arka Poorna' (green) x 'Purple Local' (purple). The integrated linkage map consisted of 1426 SNPs mapped on 11 linkage groups (LG), spanning a total distance of around 730 cM with an average of 129.6 markers per LG. Through QTL analysis for color traits, a minor QTL region was identified for visually scored leaf color and peel color on LG1, whereas a major QTL was detected for pulp color in LG4. The Hunter color values (L* and, a*) also had major QTLs with overlapping marker intervals for leaf and peel colors, establishing the association of SNP markers to the trait. The QTLs harbored genes and transcription factors involved in lycopene and anthocyanin pigment biosynthesis. This is the first report of a high-density linkage map based on SNP markers in guava and QTL mapping for color characters in leaf, fruit peel and pulp. The genotyping information generated in this study can aid in genetic engineering and marker-assisted breeding in guava.

Transcriptome Analysis of White- and Red-Fleshed Apple Fruits Uncovered Novel Genes Related to the Regulation of Anthocyanin Biosynthesis

The red flesh coloration of apples is a result of a biochemical pathway involved in the biosynthesis of anthocyanins and anthocyanidins. Based on apple genome analysis, a high number of regulatory genes, mainly transcription factors such as MYB, which are components of regulatory complex MYB-bHLH-WD40, and several structural genes (PAL, 4CL, CHS, CHI, F3H, DFR, ANS, UFGT) involved in anthocyanin biosynthesis, have been identified. In this study, we investigated novel genes related to the red-flesh apple phenotype. These genes could be deemed molecular markers for the early selection of new apple cultivars. Based on a comparative transcriptome analysis of apples with different fruit-flesh coloration, we successfully identified and characterized ten potential genes from the plant hormone transduction pathway of auxin (GH3); cytokinins (B-ARR); gibberellins (DELLA); abscisic acid (SnRK2 and ABF); brassinosteroids (BRI1, BZR1 and TCH4); jasmonic acid (MYC2); and salicylic acid (NPR1). An analysis of expression profiles was performed in immature and ripe fruits of red-fleshed cultivars. We have uncovered genes mediating the regulation of abscisic acid, salicylic acid, cytokinin, and jasmonic acid signaling and described their role in anthocyanin biosynthesis, accumulation, and degradation. The presented results underline the relationship between genes from the hormone signal transduction pathway and UFGT genes, which are directly responsible for anthocyanin color transformation as well as anthocyanin accumulation during apple-fruit ripening.

The role of environmental stress in fruit pigmentation

For many fruit crops, the colour of the fruit outwardly defines its eating quality. Fruit pigments provide reproductive advantage for the plant as well as providing protection against unfavourable environmental conditions and pathogens. For consumers these colours are considered attractive and provide many of the dietary benefits derived from fruits. In the majority of species, the main pigments are either carotenoids and/or anthocyanins. They are produced in the fruit as part of the ripening process, orchestrated by phytohormones and an ensuing transcriptional cascade, culminating in pigment biosynthesis. Whilst this is a controlled developmental process, the production of pigments is also attuned to environmental conditions such as light quantity and quality, availability of water and ambient temperature. If these factors intensify to stress levels, fruit tissues respond by increasing (or ceasing) pigment production. In many cases, if the stress is not severe, this can have a positive outcome for fruit quality. Here, we focus on the principal environmental factors (light, temperature and water) that can influence fruit colour.

Metabolome and Transcriptome Profiling Reveals the Function of MdSYP121 in the Apple Response to Botryosphaeria dothidea

The vesicular transport system is important for substance transport in plants. In recent years, the regulatory relationship between the vesicular transport system and plant disease resistance has received widespread attention; however, the underlying mechanism remains unclear. MdSYP121 is a key protein in the vesicular transport system. The overexpression of MdSYP121 decreased the B. dothidea resistance of apple, while silencing MdSYP121 resulted in the opposite phenotype. A metabolome and transcriptome dataset analysis showed that MdSYP121 regulated apple disease resistance by significantly affecting sugar metabolism. HPLC results showed that the levels of many soluble sugars were significantly higher in the MdSYP121-OE calli. Furthermore, the expression levels of genes related to sugar transport were significantly higher in the MdSYP121-OE calli after B. dothidea inoculation. In addition, the relationships between the MdSYP121 expression level, the soluble sugar content, and apple resistance to B. dothidea were verified in an F1 population derived from a cross between 'Golden Delicious' and 'Fuji Nagafu No. 2'. In conclusion, these results suggested that MdSYP121 negatively regulated apple resistance to B. dothidea by influencing the soluble sugar content. These technologies and methods allow us to investigate the molecular mechanism of the vesicular transport system regulating apple resistance to B. dothidea.

Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit

Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.

Phenotypic, Physiological, and Molecular Response of Loropetalum chinense var. rubrum under Different Light Quality Treatments Based on Leaf Color Changes

Light quality is a vital environmental signal used to trigger growth and to develop structural differentiation in plants, and it influences morphological, physiological, and biochemical metabolites. In previous studies, different light qualities were found to regulate the synthesis of anthocyanin. However, the mechanism of the synthesis and accumulation of anthocyanins in leaves in response to light quality remains unclear. In this study, the Loropetalum chinense var. rubrum "Xiangnong Fendai" plant was treated with white light (WL), blue light (BL), ultraviolet-A light (UL), and blue light plus ultraviolet-A light (BL + UL), respectively. Under BL, the leaves were described as increasing in redness from "olive green" to "reddish-brown". The chlorophyll, carotenoid, anthocyanin, and total flavonoid content were significantly higher at 7 d than at 0 d. In addition, BL treatment also significantly increased the accumulation of soluble sugar and soluble protein. In contrast to BL, ultraviolet-A light increased the malondialdehyde (MDA) content and the activities of three antioxidant enzymes in the leaves, including catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), in varying degrees over time. Moreover, we also found that the CRY-like gene, HY5-like gene, BBX-like gene, MYB-like gene, CHS-like gene, DFR-like gene, ANS-like gene, and UFGT-like gene were significantly upregulated. Furthermore, the SOD-like, POD-like, and CAT-like gene expressions related to antioxidase synthesis were found under ultraviolet-A light conditions. In summary, BL is more conducive to reddening the leaves of "Xiangnong Fendai" and will not lead to excessive photooxidation. This provides an effective ecological strategy for light-induced leaf-color changes, thereby promoting the ornamental and economic value of L. chinense var. rubrum.

MutantPpbbx24-delgene positively regulates light-induced anthocyanin accumulation in the red pear.. [DOI: 10.1101/2023.05.19.541476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Anthocyanins are pigments and nutrients in red pears regulated by BBX family genes. Herein, we characterized a 14-nucleotide deletion mutation in the coding region of thePpBBX24gene from ‘Red Zaosu’ pear (Pyrus pyrifoliaWhite Pear Group), namedPpbbx24-del. Genetic and biochemical approaches were used to compare the roles of PpBBX24 and Ppbbx24-del in anthocyanin accumulation.Ppbbx24-delplayed a positive role in anthocyanin biosynthesis of the ‘Red Zaosu’ pear peel by light treatment. Functional analyses based on overexpression in tobacco and transient overexpression in pear fruit peels showed thatPpbbx24-delpromoted anthocyanin accumulation. Cyanidin and peonidin were major differentially expressed anthocyanins, and transcript levels of some structural genes in the anthocyanin biosynthesis pathway were significantly increased. Protein interaction assays showed that PpBBX24 was located in the nucleus and interacted with PpHY5, whereas Ppbbx24-del was colocalized in the nucleoplasm and did not interact with PpHY5. PpHY5 and Ppbbx24-del had positive regulatory effects on the expression ofPpCHS,PpCHI, andPpMYB10when acting alone, but had cumulative effects on gene activation when acting simultaneously. Alone, PpBBX24 had no significant effect on the expression ofPpCHS,PpCHI, orPpMYB10, whereas it inhibited the activation effects of PpHY5 on downstream genes when it existed with PpHY5. Our study demonstrated that mutant Ppbbx24-del positively regulates the anthocyanin accumulation in pear. The results of this study clarify the mechanism and enrich the regulatory network of anthocyanin biosynthesis, which lays a theoretical foundation forPpbbx24-deluse to create red pear cultivars.

Analyzing the Quality Parameters of Apples by Spectroscopy from Vis/NIR to NIR Region: A Comprehensive Review

Spectroscopic methods deliver a valuable non-destructive analytical tool that provides simultaneous qualitative and quantitative characterization of various samples. Apples belong to the world's most consumed crops and with the current challenges of climate change and human impacts on the environment, maintaining high-quality apple production has become critical. This review comprehensively analyzes the application of spectroscopy in near-infrared (NIR) and visible (Vis) regions, which not only show particular potential in evaluating the quality parameters of apples but also in optimizing their production and supply routines. This includes the assessment of the external and internal characteristics such as color, size, shape, surface defects, soluble solids content (SSC), total titratable acidity (TA), firmness, starch pattern index (SPI), total dry matter concentration (DM), and nutritional value. The review also summarizes various techniques and approaches used in Vis/NIR studies of apples, such as authenticity, origin, identification, adulteration, and quality control. Optical sensors and associated methods offer a wide suite of solutions readily addressing the main needs of the industry in practical routines as well, e.g., efficient sorting and grading of apples based on sweetness and other quality parameters, facilitating quality control throughout the production and supply chain. This review also evaluates ongoing development trends in the application of handheld and portable instruments operating in the Vis/NIR and NIR spectral regions for apple quality control. The use of these technologies can enhance apple crop quality, maintain competitiveness, and meet the demands of consumers, making them a crucial topic in the apple industry. The focal point of this review is placed on the literature published in the last five years, with the exceptions of seminal works that have played a critical role in shaping the field or representative studies that highlight the progress made in specific areas.

Effects of Different Light Wavelengths on Fruit Quality and Gene Expression of Anthocyanin Biosynthesis in Blueberry (Vaccinium corymbosm)

Different light wavelengths display diverse effects on fruit quality formation and anthocyanin biosynthesis. Blueberry is a kind of fruit rich in anthocyanin with important economic and nutritional values. This study explored the effects of different light wavelengths (white (W), red (R), blue (B) and yellow (Y)) on fruit quality and gene expression of anthocyanin biosynthesis in blueberry. We found that the B and W treatments attained the maximum values of fruit width, fruit height and fruit weight in blueberry fruits. The R treatment attained the maximum activities of superoxide dismutase (SOD) and peroxidase (POD), and the Y treatment displayed the maximum contents of ascorbic acid (AsA), glutathione (GSH) and total phenol in fruits, thus improving blueberry-fruit antioxidant capacity. Interestingly, there were differences in the solidity-acid ratio of fruit under different light-wavelength treatments. Moreover, blue light could significantly improve the expression levels of anthocyanin biosynthesis genes and anthocyanin content in fruits. Correlation and principal component analysis showed that total acid content and antioxidant enzymes were significantly negatively correlated with anthocyanin content in blueberry fruits. These results provide new insights for the application of light wavelength to improve blueberry fruit quality and anthocyanin content.

Molecular and Biochemical Characterization of Field Resistant Isolates of Glomerella cingulata to Pyraclostrobin in China

Glomerella leaf spot (GLS) caused by Glomerella cingulata is a destructive disease that results in severe defoliation and fruit spots in apples worldwide. The compound of pyraclostrobin and tebuconazole was registered in 2018 in China to control GLS. In 2020, the high-level resistance of G. cingulata to pyraclostrobin was found in the field in Shandong Province, with a resistance frequency of 4.8%. Except for a significant decrease in virulence, there was no fitness penalty in mycelial growth, sporulation, and stress tolerance of G. cingulata associated with the resistance to pyraclostrobin. No cross-resistance was detected between pyraclostrobin and tebuconazole or bromothalonil. The point mutation GGT (G) → GCT (A) at codon 143 in the Cytochrome b (Cytb) gene was identified in the pyraclostrobin-resistant isolates. Molecular docking analysis suggested that G143A significantly alters the affinity of pyraclostrobin to the Cytb protein. Based on the point mutation (G143A) in the Cytb gene, a cleaved amplified polymorphic sequences method was developed to detect pyraclostrobin resistance in G. cingulata populations. Results of this study will provide valuable information for the scientific management of GLS.

Mdm-miR858 targets MdMYB9 and MdMYBPA1 to participate anthocyanin biosynthesis in red-fleshed apple

Anthocyanins are important secondary metabolites in plants. They are important for human health because of their antioxidant activities and because their dietary intake reduces the incidence of cardiovascular and cerebrovascular diseases and tumors. The biosynthesis of anthocyanins and its regulation in fruits and vegetables is a global research hotspot. Compared with cultivated apples, the red-fleshed apple is a relatively new and popular commodity in the market. Previous studies on red-fleshed apples have focused on the basis for the high anthocyanin content and the transcriptional regulation of anthocyanin synthesis. In the present study, we focused on the mechanism of microRNA-mediated post-transcriptional regulation of anthocyanin synthesis in red-fleshed apples. We identified a microRNA (miRNA), designated mdm-miR858, that is specifically expressed in the flesh of apple fruit. The expression level of miR858 was significantly lower in red-fleshed apples than in white-fleshed apples. The overexpression of mdm-miR858 significantly inhibited anthocyanin accumulation, whereas the silencing of mdm-miR858 promoted anthocyanin synthesis in STTM858 transgenic apple calli. Further analyses showed that mdm-miR858 targets the transcription factor genes MdMYB9 and MdMYBPA1 to participate anthocyanin accumulation in apple. Our results also show that MdHY5, a transcription factor in the light signaling pathway, can bind to the promoter of mdm-miR858 to inhibit its transcription, thereby regulating anthocyanin synthesis. Based on our results, we describe a novel HY5-miR858-MYB loop involved in the modulation of anthocyanin biosynthesis. These findings provide new information about how plant miRNAs regulate anthocyanin anabolism and provide a basis for breeding new anthocyanin-rich, red-fleshed apple varieties.

Biostimulants promote the accumulation of carbohydrates and biosynthesis of anthocyanins in 'Yinhongli' plum

Biostimulants play an important role in promoting crop growth and development and improving fruit yield, but their influence on fruit quality in horticulture plants is still unclear. In this study, four types of biostimulants, Ainuo (AN), Aigefu (AG), Weiguo (WG), and Guanwu Shuang (GS) were applied to the fruit surface of 'Yinhongli' plum at 60 and 75 days after anthesis to investigate their effect on carbohydrates and biosynthesis of anthocyanins, and also analyze the relationship between sugar and anthocyanin accumulation during fruit color change to ripening. Results showed that all biostimulant treatments significantly improved fruit appearance quality, and increased single fruit weight and TSS/TA. Cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside, are the most important anthocyanins in the red skin of the 'Yinhongli' plum, and no anthocyanin was detected in the green skin. In addition, WG and GS treatments significantly increased the expression of structural genes involved in anthocyanin biosynthesis compared with the control, especially chalcone synthase (CHS) and flavonoid 3-O-glucosyltransferase (UFGT) at 95-105 d after anthesis, leading to anthocyanin accumulation 10 days earlier than the control. Correlation analysis showed that there was a significant correlation between total sugar and anthocyanin content during fruit coloring and ripening.

Transcriptome analysis reveals the fruit color variation in Ailanthus altissima

Anthocyanins are responsible for the intensity of color in plants; however, the systematic mechanisms underlying the color differences in the fruit of Ailanthus altissima remain unknown. Therefore, this study aims to analyze the transcriptomes of the white and red fruit of A. altissima by screening and validating the key genes involved in flavonoid and anthocyanin biosynthesis. Samples of A. altissima fruit were collected 30, 45, and 60 days after flowering, and their pigment and sugar content were determined. The anthocyanin content was significantly higher in red than in white fruits. Transcriptome analysis was also performed on the fruit samples, 73,807 unigenes were assembled and annotated to seven databases. Twenty-one co-expressed modules were identified via weighted gene co-expression network analysis, of which two were associated with flavonoids and anthocyanins. Furthermore, in three growth stages, 126, 30, and 124 differentially expressed genes were screened between white and red fruit. Genes involved in flavonoid and anthocyanin metabolism were identified. AaDFR (A. altissima bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase) and AaANS (A. altissima anthocyanidin synthase) were associated with flavonoid and anthocyanin metabolism. Members of the AaDFR and AaANS families were also identified, and their basic physicochemical characteristics, conserved domains, motif compositions, phylogenetics, and expression levels were analyzed. The overexpression of AaDFR and AaANS in transgenic Arabidopsis significantly increased the content of seed and foliar flavonoids and anthocyanins. The study elucidated the different mechanisms underlying fruit color development and provided insight into A. altissima plants breeding with commercially desirable properties.

Endophytic bacterium Pseudomonas protegens suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest fruits

Apple (Malus domestica Borkh.), one of the most economically important fruits widely consumed worldwide, has been suffering from apple ring rot caused by Botryosphaeria dothidea, which dramatically affects its quality and yield. In the present study, we demonstrated that Pseudomonas protegens, isolated from Chinese leek (Allium tuberosum), significantly suppressed the mycelial growth and propagation of B. dothidea, respectively, further displayed a considerably inhibitory effect on the apple ring rot of postharvest fruits. In addition, P. protegens significantly improved the total soluble solid/titrable acidity (TSS/TA) ratio and soluble sugar/titrable acidity (SS/TA) ratio and drastically maintained the fruit firmness. Further analysis manifested that P. protegens substantially induced the defense-related genes such as MdGLU, MdPAL, MdPOD, MdCAL, and transcription factors related to the resistance to B. dothidea, including MdWRKY15, MdPUB29, MdMyb73, and MdERF11 in apple fruits. Meanwhile, P. protegens considerably restrained the expressions of the pathogenicity-related genes in B. dothidea, including the BdCYP450, BdADH, BdGHY, BdATS, Bdα/β-HY, and BdSTR. By inference, P. protegens inhibited the apple ring rot on postharvest fruits by activating the defense system of apple fruit and repressing the pathogenic factor of B. dothidea. The study provided a theoretical basis and a potential alternative to manage the apple ring rot on postharvest fruits.

Transcriptome and Metabolome Analysis Reveals the Effect of Nitrogen-Potassium on Anthocyanin Biosynthesis in "Fuji" Apple

Nitrogen (N) and potassium (K) have significant effects on apple peel color. To further understand the molecular mechanism of N-K regulation of apple color, we analyzed the apple peel under different N and K treatments using isotope labeling, transcriptomics, and metabolomics. Under high N treatments, fruit red color and anthocyanin content decreased significantly. High N decreased the ¹³C distribution rate and increased the Ndff values of fruits, while K increased the expression of MdSUTs and MdSOTs and promoted ¹³C transportation to fruits. Anthocyanin-targeted metabonomics and transcriptome analysis revealed that high N downregulated the expression of structural genes related to the anthocyanin synthesis pathway (MdPAL, Md4CL, MdF3H, MdANS, and MdUFGT) and their regulators (MdMYBs and MdbHLHs), and also decreased some metabolites contents. K alleviated this inhibition and seven anthocyanins were regulated by N-K. Our results improve the understanding of the synergistic regulation of apple fruit coloring by N-K.

Multi-omics analyses reveal MdMYB10 hypermethylation being responsible for a bud sport of apple fruit color

Apple bud sports offer a rich resource for clonal selection of numerous elite cultivars. The accumulation of somatic mutations as plants develop may potentially impact the emergence of bud sports. Previous studies focused on somatic mutation in the essential genes associated with bud sports. However, the rate and function of genome-wide somatic mutations that accumulate when a bud sport arises remain unclear. In this study, we identified a branch from a 10-year-old tree of the apple cultivar 'Oregon Spur II' as a bud sport. The mutant branch showed reduced red coloration on fruit skin. Using this plant material, we assembled a high-quality haplotype reference genome consisting of 649.61 Mb sequences with a contig N50 value of 2.04 Mb. We then estimated the somatic mutation rate of the apple tree to be 4.56 × 10 -8 per base per year, and further identified 253 somatic single-nucleotide polymorphisms (SNPs), including five non-synonymous SNPs, between the original type and mutant samples. Transcriptome analyses showed that 69 differentially expressed genes between the original type and mutant fruit skin were highly correlated with anthocyanin content. DNA methylation in the promoter of five anthocyanin-associated genes was increased in the mutant compared with the original type as determined using DNA methylation profiling. Among the genetic and epigenetic factors that directly and indirectly influence anthocyanin content in the mutant apple fruit skin, the hypermethylated promoter of MdMYB10 is important. This study indicated that numerous somatic mutations accumulated at the emergence of a bud sport from a genome-wide perspective, some of which contribute to the low coloration of the bud sport.

Research Progress on Genetic Basis of Fruit Quality Traits in Apple (Malus × domestica)

Identifying the genetic variation characteristics of phenotypic traits is important for fruit tree breeding. During the long-term evolution of fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity. Apple (Malus × domestica Borkh.) shows strong ecological adaptability and is widely cultivated, and is among the most economically important fruit crops worldwide. However, the high level of heterozygosity and large genome of apple, in combination with its perennial life history and long juvenile phase, complicate investigation of the genetic basis of fruit quality traits. With continuing augmentation in the apple genomic resources available, in recent years important progress has been achieved in research on the genetic variation of fruit quality traits. This review focuses on summarizing recent genetic studies on apple fruit quality traits, including appearance, flavor, nutritional, ripening, and storage qualities. In addition, we discuss the mapping of quantitative trait loci, screening of molecular markers, and mining of major genes associated with fruit quality traits. The overall aim of this review is to provide valuable insights into the mechanisms of genetic variation and molecular breeding of important fruit quality traits in apple.

Analysis of Apple Fruit (Malus × domestica Borkh.) Quality Attributes Obtained from Organic and Integrated Production Systems

The aim of this study was to compare total phenolic content (TPC), radical-scavenging activity (RSA), total anthocyanin content (TAC), sugar and polyphenolic profiles of two apple cultivars (‘Discovery’ and ‘Red Aroma Orelind’) from organic and integrated production systems in climatic conditions of Western Norway. Sixteen sugars and four sugar alcohols and 19 polyphenols were found in the peel, but less polyphenols were detected in the pulp. The peel of both apples and in both production systems had significantly higher TPC and RSA than the pulp. The peel from integrated apples had higher TPC than the peel from organic apples, while organic apples had higher TAC than the integrated. Sucrose and glucose levels were higher in organic apples; fructose was cultivar dependent while minor sugars were higher in integrated fruits. The most abundant polyphenolic compound in the peel of the tested cultivars was quercetin 3-O-galactoside, while chlorogenic acid was most abundant in the pulp. Regarding polyphenols, phloretin, phloridzin, protocatechuic acid, baicalein and naringenin were higher in organic apple, while quercetin 3-O-galactoside, kaempferol 3-O-glucoside, chlorogenic acid and syringic acid was higher in integrated fruits. In conclusion, organic ‘Discovery’ and integrated ‘Red Aroma Orelind’ had higher bioavailability of health related compounds from the peel and the pulp.

Phytochemical Content and Antioxidant Activity of Malus domestica Borkh Peel Extracts

Apple is an important dietary source of carotenoids and phenolic compounds, and its regular consumption is associated with several health benefits. The aim of this study was to evaluate the phytochemical composition of fresh peels of four red-skinned (“Champion”, “Generos”, “Idared”, “Florina”) and two yellow-skinned (“Golden Delicious”, “Reinette Simirenko”) apple varieties. Antioxidant activity of apple peel extracts was determined by ferric reducing antioxidant power (FRAP) and ABTS radical scavenging capacity assays. Total carotenoid and polyphenolic contents were determined spectrophotometrically, while the profile of individual carotenoids and anthocyanins (in red-skinned varieties) was analyzed using high-performance liquid chromatography coupled to a photodiode array detector (HPLC-PDA). Carotenoid composition was specific for each variety, and total carotenoid content was slightly higher in yellow-skinned apple peels compared to red-skinned varieties. In contrast, total phenolic content was higher in the peels of red-skinned cultivars. Anthocyanin profile was predominated by cyanidin-3-O-galactoside. Antioxidant potential followed the trend of the total polyphenolic content, being highest in “Florina”, as measured by both FRAP and ABTS assays. Our results demonstrated apple peels have high phytochemical content with diverse compositions, and their regular consumption can be an excellent source of antioxidants.

Analyses of the photosynthetic characteristics, chloroplast ultrastructure, and transcriptome of apple (Malus domestica) grown under red and blue lights

BACKGROUND

Light quality significantly affects plant growth and development, photosynthesis, and carbon and nitrogen metabolism. Apple (Malus domestica Borkh.) is a widely cultivated and economically important fruit crop worldwide. However, there are still few studies on the effects of different light qualities on the growth and development of apple seedlings.

RESULTS

In this study, we explored the effects of blue and red light treatments on the growth and development, photosynthetic characteristics, leaf chloroplast ultrastructure, and carbon and nitrogen metabolism of apple seedlings. Blue light significantly inhibited apple plant growth and leaf extension, but it promoted the development of leaf tissue structures and chloroplasts and positively affected leaf stomatal conductance, the transpiration rate, and photosynthetic efficiency. The red light treatment promoted apple plant growth and root development, but it resulted in loosely organized leaf palisade tissues and low chlorophyll contents. The blue and red light treatments enhanced the accumulation of ammonium nitrogen in apple seedlings. Moreover, the blue light treatment significantly promoted nitrogen metabolism. Additionally, an RNA-seq analysis revealed that both blue light and red light can significantly up-regulate the expression of genes related to carbon and nitrogen metabolism. Blue light can also promote amino acid synthesis and flavonoid metabolism, whereas red light can induce plant hormone signal transduction. The expression of a gene encoding a bHLH transcription factor (MYC2-like) was significantly up-regulated in response to blue light, implying it may be important for blue light-mediated plant development.

CONCLUSIONS

Considered together, blue and red light have important effects on apple growth, carbon and nitrogen metabolism. These findings may be useful for determining the ideal light conditions for apple cultivation to maximize fruit yield and quality.