Biotechnological approaches for predicting and controlling apple storage disorders

Gapper, Nigel E.; Bowen, Joanna K.; Brummell, David A.

doi:10.1016/j.copbio.2022.102851

Cited by 8 publications

(10 citation statements)

References 41 publications

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“…Apples ( Malus domestica ) are one of the world’s most consumed fruits, with over 4.8 billion kilograms produced annually in the United States [ 1 ]. Advancements in breeding, orchard management, and postharvest storage technologies have made it possible to store apples for up to a year after harvest [ 2 ]. Despite this, producers and packing houses cull millions of kilograms of apples annually due to losses of fruit quality (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…However, there have been recent investigations into developing PTBs for predicting commercially relevant apple disorders; biomarker tests were launched commercially in 2019 for risk assessment of bitter pit and soft scald in ‘Honeycrisp’ apples [ 17 – 19 ]. Although these particular markers have since been discontinued, interest in this area remains [ 2 ]. For example, a recent study sought to develop PTBs to distinguish among harvest times in ‘Royal Gala’ fruit as a method for determining an optimal harvest date [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we seek to answer these questions by developing preliminary PTBs for predicting firmness in ‘Gala’ apples, a variety particularly susceptible to loss of firmness during storage [ 21 ]. We chose firmness as a proof of concept for PTB identification for three reasons: [ 1 ] there already exist several candidate genes within the literature related to firmness identified by genomic means which we can use for model assessment [ 22 ], [ 2 ] firmness can be easily and accurately measured using a penetrometer [ 7 ], and [ 3 ] firmness is strongly impacted by postharvest treatments [ 23 , 24 ] making it controllable within our project’s experimental design. Our experiment was designed to track changes in fruit texture across commercially relevant storage regimes.…”

Section: Introductionmentioning

confidence: 99%

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Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

Hadish,

Hargarten,

Zhang

et al. 2024

PLoS ONE

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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.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

Hadish,

Hargarten,

Zhang

et al. 2024

PLoS ONE

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“…Apples and pears disorders may involve the skin and the sub-epidermal cortex layers of cells (superficial scald) but can also reach the outermost layers of cortical tissues (e.g. soft scald and bitter pit), or involve browning of entire internal portions of the pulp (internal breakdown) or of the fruit core (brown core) ( Gapper et al., 2023 ; Prange and Wright, 2023 ). Among these, superficial scald has received considerable efforts of research activity.…”

Section: Integrated Omics For Studying Chilling Injury Development An...mentioning

confidence: 99%

“…( Sidhu et al., 2023 ). The use of resistant cultivars is the first approach that can be used to avoid CI ( Gapper et al., 2023 ). Apple trees that possess resistance to cold tend to generate apples that can easily be stored at low temperatures without the occurrence of browning syndromes ( Xu et al., 2023 ).…”

Section: Integrated Omics For Studying Chilling Injury Development An...mentioning

confidence: 99%

Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics

Rodrigues,

Ordoñez-Trejo,

Rasori

et al. 2024

Front. Plant Sci.

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Lowering the storage temperature is an effective method to extend the postharvest and shelf life of fruits. Nevertheless, this technique often leads to physiological disorders, commonly known as chilling injuries. Apples and pears are susceptible to chilling injuries, among which superficial scald is the most economically relevant. Superficial scald is due to necrotic lesions of the first layers of hypodermis manifested through skin browning. In peaches and nectarines, chilling injuries are characterized by internal symptoms, such as mealiness. Fruits with these aesthetic or compositional/structural defects are not suitable for fresh consumption. Genetic variation is a key factor in determining fruit susceptibility to chilling injuries; however, physiological, or technical aspects such as harvest maturity and storage conditions also play a role. Multi-omics approaches have been used to provide an integrated explanation of chilling injury development. Metabolomics in pome fruits specifically targets the identification of ethylene, phenols, lipids, and oxidation products. Genomics and transcriptomics have revealed interesting connections with metabolomic datasets, pinpointing specific genes linked to cold stress, wax synthesis, farnesene metabolism, and the metabolic pathways of ascorbate and glutathione. When applied to Prunus species, these cutting-edge approaches have uncovered that the development of mealiness symptoms is linked to ethylene signaling, cell wall synthesis, lipid metabolism, cold stress genes, and increased DNA methylation levels. Emphasizing the findings from multi-omics studies, this review reports how the integration of omics datasets can provide new insights into understanding of chilling injury development. This new information is essential for successfully creating more resilient fruit varieties and developing novel postharvest strategies.

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Transcriptomics of long‐term, low oxygen storage coupled with ethylene signaling interference suggests neofunctionalization of hypoxia response pathways in apple (Malus domestica)

Hadish,

Hargarten,

Zhang

et al. 2024

Plant Direct

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Research on how plants respond to hypoxia has concentrated on model organisms where tissues can only survive hypoxic conditions for a few hours to a few days. In contrast, hypoxic conditions are used commercially as a method to prolong the shelf life of Malus domestica (apple) fruit for up to a year of storage without substantial changes in fruit quality, not to mention a lack of tissue death. This ability of apples to withstand protracted hypoxic conditions is an interesting adaptation that has had limited molecular investigation despite its economic importance. Here, we investigate the long‐term apple hypoxia response using a time‐course RNA‐seq analysis of several postharvest storage conditions. We use phylogenetics, differential expression, and regulatory networks to identify genes that regulate and are regulated by the hypoxia response. We identify potential neofunctionalization of core‐hypoxia response genes in apples, including novel regulation of group VII ethylene response factor (ERF VII) and plant cysteine oxidase (PCO) family members.

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Biotechnological approaches for predicting and controlling apple storage disorders

Cited by 8 publications

References 41 publications

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics

Transcriptomics of long‐term, low oxygen storage coupled with ethylene signaling interference suggests neofunctionalization of hypoxia response pathways in apple (Malus domestica)

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