FaMYB9 is involved in the regulation of C6 volatile biosynthesis in strawberry

Substrate cultivation system improved the quality of 'Hongyan' strawberry fruits compared with the soil cultivation system

This study explored the influence of substrate cultivation system on the quality of 'Hongyan' strawberry through physicochemical and sensory evaluation, E-nose, GC-MS, and GC-IMS. Results revealed that substrate cultivation system significantly enhanced the formation of total acids, vitamin C, total phenols, and volatile esters, alcohols, and acids in strawberries. Additionally, it improved the hardness, acidity, aroma intensity, and color of the fruit. ROAV analysis of VOCs demonstrated that substrate cultivation system promoted green, floral, citrus, and wood aromatic notes, while introducing unique caramel and mint flavors. Through VIP values, three key physicochemical parameters and several vital volatile esters, alcohols, and aldehydes were identified as essential biomarkers for distinguishing strawberries grown under substrate cultivation system versus soil cultivation system. Correlation analysis underscored significant relationships between VOCs, particularly esters, aldehydes, and alcohols, and a notable positive correlation between ambient temperature, substrate temperature, fertilization frequency, and the physicochemical properties and characteristic VOCs.

The CsDof1.8-CsLIPOXYGENASE09 module regulates C9 aroma production in cucumber

Nine-carbon aldehydes and their relative alcohols (C9 aromas) are the main aroma compounds of cucumber (Cucumis sativus L.) fruits and provide a unique cucumber-like note. However, the key regulators of C9 aroma accumulation in cucumber fruit are poorly characterized. Based on C9 aroma dynamic analysis and transcriptome analysis during fruit development of two different cucumber inbred lines, Q16 and Q24, Lipoxygenase09 (CsLOX09) was identified as a candidate gene for C9 aroma accumulation. Additionally, Q24 with higher CsLOX09 expression accumulated more C9 aromas than Q16. To verify the function of CsLOX09, Cslox09 homozygote knockout lines were created. C9 aroma content decreased by 80.79% to 99.16% in these mutants compared to the wild type. To further explore the reasons for the difference in CsLOX09 expression between Q16 and Q24 fruits, a co-expression network was constructed by integrating the C9 aroma-associated metabolism and transcriptomic data. Eighteen candidate transcription factors were highly correlated with the expression of CsLOX09. DNA binding with One Finger 1.8 (CsDof1.8) was confirmed to bind directly to the A/TAAAG motif of the CsLOX09 promoter through dual-luciferase, yeast one-hybrid, chromatin immunoprecipitation-qPCR and electrophoretic mobility shift assays. Furthermore, C9 aroma content and CsLOX09 expression were significantly increased in the CsDof1.8 overexpression lines. Overall, these data elucidate the metabolic regulation of C9 aromas in cucumber and provide a foundation for facilitating the regulation of flavor in cucumber breeding.

Identification, characterization, and expression of lipoxygenase genes in sweet cherry (Prunus avium L.) cv. Regina and their relationship with the development of an herbaceous off-flavor during fruit ripening

Flavor is an essential characteristic of fruit quality and is significant for consumers. Off-flavors have been reported in several fruits, including sweet cherry. This fruit has been reported to show an herbaceous/grassy-like flavor. The herbaceous off-flavor in sweet cherries detected in cultivar Regina has been related to the differential development of aroma compounds such as short-chain aldehydes and esters. One of the main biosynthesis pathways for these compounds is the fatty acid oxidation mediated by lipoxygenases (LOX). In order to have a better understanding of the biological basis of the differences in the volatile profile, the LOX gene expression profile was characterized during fruit development with and without herbaceous off-flavor. A genome-wide analysis of LOX in sweet cherry was carried out and compared to other species such as Arabidopsis, tomato, apple, prunus and strawberry. The structural features of 9-LOX and 13-LOX genes, encoded protein domains and their synteny were examined. Moreover, we analyzed the LOX expression at four developmental stages along ripening by RT-qPCR. Thirteen LOX gene candidates (six 9-LOX and seven 13-LOX) were identified. The 13-LOXs, PaLOX10, PaLOX11, and PaLOX12 were differentially expressed in herbaceous sweet cherries. Furthermore, their expression profile positively correlated with key volatile compounds linked to the herbaceous off-flavor. Overall, this study involves the genome-wide characterization of the LOX family in Prunus avium cv. Regina and provides information that can aid in studying LOX-related fruit deterioration in sweet cherries and associated species.

Integrative analysis of non-targeted metabolome and transcriptome reveals the mechanism of volatile formation in pepper fruit

Introduction: Aroma is a key inherent quality attributes of pepper fruit, yet the underlying mechanisms of aroma compound biosynthesis remain unclear. Methods: In this study, the volatile profile of the QH (cultivated Capsicum chinense) and WH (cultivated Capsicum annuum) pepper varieties were putatively identified during fruit development using gas chromatography-mass spectrometry (GC-MS). Results and discussion: The results identified 203 volatiles in pepper, and most of the esters, terpenes, aldehydes and alcohols were significantly down-regulated with fruit ripening. The comparison of volatile components between varieties revealed that aldehydes and alcohols were highly expressed in the WH fruit, while esters and terpenes with fruity or floral aroma were generally highly accumulated in the QH fruit, providing QH with a fruity odor. Transcriptome analysis demonstrated the close relationship between the synthesis of volatiles and the fatty acid and terpene metabolic pathways, and the high expression of the ADH, AAT and TPS genes was key in determining the accumulation of volatiles in pepper fruit. Furthermore, integrative metabolome and transcriptome analysis revealed that 208 differentially expressed genes were highly correlated with 114 volatiles, and the transcription factors of bHLH, MYB, ARF and IAA were identified as fundamental for the regulation of volatile synthesis in pepper fruit. Our results extend the understanding of the synthesis and accumulation of volatiles in pepper fruit.

Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities

The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.

Analysis of Volatile Aroma Components and Regulatory Genes in Different Kinds and Development Stages of Pepper Fruits Based on Non-Targeted Metabolome Combined with Transcriptome

Aroma is a crucial attribute affecting the quality of pepper and its processed products, which has significant commercial value. However, little is known about the composition of volatile aroma compounds (VACs) in pepper fruits and their potential molecular regulatory mechanisms. In this study, HS-SPME-GC-MS combined with transcriptome sequencing is used to analyze the composition and formation mechanism of VACs in different kinds and development stages of pepper fruits. The results showed that 149 VACs, such as esters, alcohols, aldehydes, and terpenoids, were identified from 4 varieties and 3 development stages, and there were significant quantitative differences among different samples. Volatile esters were the most important aroma components in pepper fruits. PCA analysis showed that pepper fruits of different developmental stages had significantly different marker aroma compounds, which may be an important provider of pepper's characteristic aroma. Transcriptome analysis showed that many differential genes (DEGs) were enriched in the metabolic pathways related to the synthesis of VACs, such as fatty acids, amino acids, MVA, and MEP in pepper fruits. In addition, we identified a large number of differential transcription factors (TFs) that may regulate the synthesis of VACs. Combined analysis of differential aroma metabolites and DEGs identified two co-expression network modules highly correlated with the relative content of VACs in pepper fruit. This study confirmed the basic information on the changes of VACs in the fruits of several Chinese spicy peppers at different stages of development, screened out the characteristic aroma components of different varieties, and revealed the molecular mechanism of aroma formation, providing a valuable reference for the quality breeding of pepper.

Effect of drainage ratio during strawberry cultivation:The volatilomics-based shelf-life indicators for strawberry fruit

The metabolome of strawberries at harvest determines their storage capacity. Therefore, dynamics of volatile production during storage of strawberry cultivated under diverse drainage ratios, T1 (12.0%), T2 (25.3%), T3 (36.4%), and T4 (56.5%), were evaluated. Among the various non-target VOCs analysis, there were some groups including aldehydes, esters, and furans occupied over 5% with exhibiting high coefficient of determination (R² ) following the days after storage (DAS). Aldehydes content decreased over the storage period, while the esters (methyl butanoate, methyl hexanoate, ethyl hexanoate, and benzyl acetate) and furanones (furaneol and mesifuran) were increased as representing aroma compounds in strawberry ripening. Even on the same day, it was investigated that the release of VOCs linked to fruit decay was delayed in the groups (T1 and T2) that were given relatively little water compared to T3 and T4. The hexanal and ethyl hexanoate as an over-ripened signal showed a rapid increase from 4 DAS to 5 DAS in T3 and T4, respectively, while T1 and T2 showed significant increase from 5 DAS to 6 DAS. Relatively slower over-ripening tendency of T1 and T2 was supported by changes of firmness, total soluble solid content, anthocyanin content, and antioxidant activity during storage. T1 and T2 showed higher antioxidant activity at the harvest time and lower anthocyanin accumulation than T3 and T4. The present study elucidated that the preharvest drainage changes during cultivation was involved in fruit quality during strawberry storage. Besides, volatilomics analysis depicted that T2 as an optimal ratio, could delay the occurrence of stress and senescence, and guaranteed the strawberry yield. In conclusion, this study provided evidence that the practical application of drainage ratios could improve horticultural product quality even with low water use and VOCs might be considered an early indicator for strawberry fruit shelf-life.

Identification of MYB Transcription Factors Involving in Fruit Quality Regulation of Fragaria × ananassa Duch

The cultivated strawberry (Fragaria × ananassa Duch.) is an important horticultural crop. The economic values of strawberry cultivars are decided by their fruit qualities including taste, color and aroma. The important role of MYB transcription factors in fruit quality regulation is recognized increasingly with the identification of MYB genes involved in metabolism. A total of 407 MYB genes of F. × ananassa (FaMYBs) were identified in the genome-wide scale and named according to subgenome locations. The 407 FaMYBs were clustered into 36 groups based on phylogenetic analysis. According to synteny analysis, whole genome duplication and segmental duplication contributed over 90% of the expansion of the FaMYBs family. A total of 101 FaMYB loci with 1-6 alleles were identified by the homologous gene groups on homologous chromosomes. The differentially expressed FaMYB profiles of three cultivars with different fruit quality and fruit ripe processes provided the 8 candidate loci involved in fruit quality regulation. In this experiment, 7, 5, and 4 FaMYBs were screeded as candidate genes involved in the regulation of metabolism/transportation of anthocyanins, sugars or organic acids and 4-hydroxy-2, 5-dimethyl-3(2H)-furanone, respectively. These results pointed out the key FaMYBs for further functional analysis of gene regulation of strawberry fruit quality and would be helpful in the clarification on ofe roles of MYBs in the metabolism of fruit crops.

Insights into transcription factors controlling strawberry fruit development and ripening

Fruit ripening is a highly regulated and complex process involving a series of physiological and biochemical changes aiming to maximize fruit organoleptic traits to attract herbivores, maximizing therefore seed dispersal. Furthermore, this process is of key importance for fruit quality and therefore consumer acceptance. In fleshy fruits, ripening involves an alteration in color, in the content of sugars, organic acids and secondary metabolites, such as volatile compounds, which influence flavor and aroma, and the remodeling of cell walls, resulting in the softening of the fruit. The mechanisms underlying these processes rely on the action of phytohormones, transcription factors and epigenetic modifications. Strawberry fruit is considered a model of non-climacteric species, as its ripening is mainly controlled by abscisic acid. Besides the role of phytohormones in the regulation of strawberry fruit ripening, a number of transcription factors have been identified as important regulators of these processes to date. In this review, we present a comprehensive overview of the current knowledge on the role of transcription factors in the regulation of strawberry fruit ripening, as well as in compiling candidate regulators that might play an important role but that have not been functionally studied to date.

Application of quantitative proteomics to investigate fruit ripening and eating quality

The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.

Transcriptomic and Metabolomic Analyses Provide Insights into the Formation of the Peach-like Aroma of Fragaria nilgerrensis Schlecht. Fruits

Fragaria nilgerrensis Schlecht. is a wild diploid strawberry species. The intense peach-like aroma of its fruits makes F. nilgerrensis an excellent resource for strawberry breeding programs aimed at enhancing flavors. However, the formation of the peach-like aroma of strawberry fruits has not been comprehensively characterized. In this study, fruit metabolome and transcriptome datasets for F. nilgerrensis (HA; peach-like aroma) and its interspecific hybrids PA (peach-like aroma) and NA (no peach-like aroma; control) were compared. In total, 150 differentially accumulated metabolites were detected. The K-means analysis revealed that esters/lactones, including acetic acid, octyl ester, δ-octalactone, and δ-decalactone, were more abundant in HA and PA than in NA. These metabolites may be important for the formation of the peach-like aroma of F. nilgerrensis fruits. The significantly enriched gene ontology terms assigned to the differentially expressed genes (DEGs) were fatty acid metabolic process and fatty acid biosynthetic process. Twenty-seven DEGs were predicted to be associated with ester and lactone biosynthesis, including AAT, LOX, AOS, FAD, AIM1, EH, FAH, ADH, and cytochrome P450 subfamily genes. Thirty-five transcription factor genes were predicted to be associated with aroma formation, including bHLH, MYB, bZIP, NAC, AP2, GATA, and TCPfamily members. Moreover, we identified differentially expressed FAD, AOS, and cytochrome P450 family genes and NAC, MYB, and AP2 transcription factor genes that were correlated with δ-octalactone and δ-decalactone. These findings provide key insights into the formation of the peach-like aroma of F. nilgerrensis fruits, with implications for the increased use of wild strawberry resources.

GC-MS Metabolite and Transcriptome Analyses Reveal the Differences of Volatile Synthesis and Gene Expression Profiling between Two Apple Varieties

Aroma is a key quality attribute of apples, making major contributions to commercial value and consumer choice. However, the mechanism underlying molecular regulation of aroma formation genes and transcription factors remains poorly understood in apples. Here, we investigated the aroma volatile profiles of two apple varieties with distinctive flavors using headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS). A total of 35 volatile compounds were identified in Granny Smith and Jonagold apples. Aldehydes were the most abundant volatiles contributing to the aroma in Granny Smith apple while esters were the dominant volatile compounds in Jonagold apple. In order to know more about the expression levels of aroma-related genes involved in the metabolic pathways, transcriptome sequencing of these two different apple varieties was conducted utilizing the Illumina platform. In total, 94 differentially expressed genes (DEGs) were found in the fatty acid metabolism, amino acid metabolism, the mevalonate pathway and phenylpropanoid pathway. Furthermore, compared to the Granny Smith apple, the expression of multiple genes and transcription factors were upregulated in the Jonagold apple, which might play important roles in the synthesis of aroma volatile compounds. Our study contributes toward better understanding on the molecular mechanism of aroma synthesis in apples and provides a valuable reference for metabolic engineering and flavor improvement in the future.