Multifaceted analyses disclose the role of fruit size and skin-russeting in the accumulation pattern of phenolic compounds in apple

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

Gene expression is highly impacted by the environment and can be reflective of past events that affected developmental processes. It is therefore expected that gene expression can serve as a signal of a current or future phenotypic traits. In this paper we identify sets of genes, which we call Prognostic Transcriptomic Biomarkers (PTBs), that can predict firmness in Malus domestica (apple) fruits. In apples, all individuals of a cultivar are clones, and differences in fruit quality are due to the environment. The apples transcriptome responds to these differences in environment, which makes PTBs an attractive predictor of future fruit quality. PTBs have the potential to enhance supply chain efficiency, reduce crop loss, and provide higher and more consistent quality for consumers. However, several questions must be addressed. In this paper we answer the question of which of two common modeling approaches, Random Forest or ElasticNet, outperforms the other. We answer if PTBs with few genes are efficient at predicting traits. This is important because we need few genes to perform qPCR, and we answer the question if qPCR is a cost-effective assay as input for PTBs modeled using high-throughput RNA-seq. To do this, we conducted a pilot study using fruit texture in the 'Gala' variety of apples across several postharvest storage regiments. Fruit texture in 'Gala' apples is highly controllable by post-harvest treatments and is therefore a good candidate to explore the use of PTBs. We find that the RandomForest model is more consistent than an ElasticNet model and is predictive of firmness (r2 = 0.78) with as few as 15 genes. We also show that qPCR is reasonably consistent with RNA-seq in a follow up experiment. Results are promising for PTBs, yet more work is needed to ensure that PTBs are robust across various environmental conditions and storage treatments.

De novo transcriptome assembly and functional analysis reveal a dihydrochalcone 3-hydroxylase(DHC3H) of wild Malus species that produces sieboldin in vivo

Sieboldin is a specialised secondary metabolite of the group of dihydrochalcones (DHC), found in high concentrations only in some wild Malus species, closely related to the domesticated apple (Malus × domestica L.). To date, the first committed step towards the biosynthesis of sieboldin remains unknown. In this study, we combined transcriptomic analysis and a de novo transcriptome assembly to identify two putative 3-hydroxylases in two wild Malus species (Malus toringo (K. Koch) Carriere syn. sieboldii Rehder, Malus micromalus Makino) whose DHC profile is dominated by sieboldin. We assessed the in vivo activity of putative candidates to produce 3-hydroxyphloretin and sieboldin by de novo production in Saccharomyces cerevisiae. We found that CYP98A proteins of wild Malus accessions (CYP98A195, M. toringo and CYP98A196, M. micromalus) were able to produce 3-hydroxyphloretin, ultimately leading to sieboldin accumulation by co-expression with PGT2. CYP98A197-198 genes of M. × domestica, however, were unable to hydroxylate phloretin in vivo. CYP98A195-196 proteins exerting 3-hydroxylase activity co-localised with an endoplasmic reticulum marker. CYP98A protein model from wild accessions showed mutations in key residues close to the ligand pocket predicted using phloretin for protein docking modelling. These mutations are located within known substrate recognition sites of cytochrome P450s, which could explain the acceptance of phloretin in CYP98A protein of wild accessions. Screening a Malus germplasm collection by HRM marker analysis for CYP98A genes identified three clusters that correspond to the alleles of domesticated and wild species. Moreover, CYP98A isoforms identified in M. toringo and M. micromalus correlate with the accumulation of sieboldin in other wild and hybrid Malus genotypes. Taken together, we provide the first evidence of an enzyme producing sieboldin in vivo that could be involved in the key hydroxylation step towards the synthesis of sieboldin in Malus species.

Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)

An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada's Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.

Advances in Understanding the Causes, Molecular Mechanism, and Perspectives of Russeting on Tree Fruit

The external quality of fruit is one of its most important qualities; good external quality attracts consumers easily and increases the value of fruit. Fruit russeting is one of the factors that influences the external quality of fruit and has been studied in most horticultural plants. However, the molecular mechanism of russeting has never been discussed so far. In this review, we summarize the research progress on fruit russeting, including causes, microscopic histomorphology, composition, genetics, and regulation and made a series of elaboration on the current research on fruit russeting. This study aims to provide insights into the mechanisms underlying fruit russeting. It also puts forward ideas for research on fruit russeting, which may provide a reference for future research.

Identification of Novel Candidate Genes Involved in Apple Cuticle Integrity and Russeting-Associated Triterpene Synthesis Using Metabolomic, Proteomic, and Transcriptomic Data

Apple russeting develops on the fruit surface when skin integrity has been lost. It induces a modification of fruit wax composition, including its triterpene profile. In the present work, we studied two closely related apple varieties, 'Reinette grise du Canada' and 'Reinette blanche du Canada', which display russeted and non-russeted skin phenotypes, respectively, during fruit development. To better understand the molecular events associated with russeting and the differential triterpene composition, metabolomics data were generated using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) and combined with proteomic and transcriptomic data. Our results indicated lower expression of genes linked to cuticle biosynthesis (cutin and wax) in russet apple throughout fruit development, along with an alteration of the specialized metabolism pathways, including triterpene and phenylpropanoid. We identified a lipid transfer protein (LTP3) as a novel player in cuticle formation, possibly involved in the transport of both cutin and wax components in apple skin. Metabolomic data highlighted for the first time a large diversity of triterpene-hydroxycinnamates in russeted tissues, accumulation of which was highly correlated with suberin-related genes, including some enzymes belonging to the BAHD (HXXXD-motif) acyltransferase family. Overall, this study increases our understanding about the crosstalk between triterpene and suberin pathways.

Differential regulation of triterpene biosynthesis induced by an early failure in cuticle formation in apple

Waxy apple cuticles predominantly accumulate ursane-type triterpenes, but the profile shifts with the induction of skin russeting towards lupane-type triterpenes. We previously characterised several key enzymes in the ursane-type and lupane-type triterpene pathways, but this switch in triterpene metabolism associated with loss of cuticle integrity is not fully understood. To analyse the relationship between triterpene biosynthesis and russeting, we used microscopy, RNA-sequencing and metabolite profiling during apple fruit development. We compared the skin of three genetically-close clones of 'Golden Delicious' (with waxy, partially russeted and fully russeted skin). We identified a unique molecular profile for the russet clone, including low transcript abundance of multiple cuticle-specific metabolic pathways in the early stages of fruit development. Using correlation analyses between gene transcription and metabolite concentration we found MYB transcription factors strongly associated with lupane-type triterpene biosynthesis. We showed how their transcription changed with the onset of cuticle cracking followed by russeting and that one factor, MYB66, was able to bind the promoter of the oxidosqualene cyclase OSC5, to drive the production of lupeol derivatives. These results provide insights into the breakdown of cuticle integrity leading to russet and how this drives MYB-regulated changes to triterpene biosynthesis.

Resource recovery and biorefinery potential of apple orchard waste in the circular bioeconomy

In this review investigate the apple orchard waste (AOW) is potential organic resources to produce multi-product and there sustainable interventions with biorefineries approaches to assesses the apple farm industrial bioeconomy. The thermochemical and biological processes like anaerobic digestion, composting and , etc., that generate distinctive products like bio-chemicals, biofuels, biofertilizers, animal feed and biomaterial, etc can be employed for AOW valorization. Integrating these processes can enhanced the yield and resource recovery sustainably. Thus, employing biorefinery approaches with allied different methods can link to the progression of circular bioeconomy. This review article mainly focused on the different biological processes and thermochemical that can be occupied for the production of waste to-energy and multi-bio-product in a series of reaction based on sustainability. Therefore, the biorefinery for AOW move towards identification of the serious of the reaction with each individual thermochemical and biological processes for the conversion of one-dimensional providences to circular bioeconomy.