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To satisfy the year-round demand of good quality fruit, apples are stored under controlled atmosphere conditions (CA; reduced O2 and elevated CO2 levels) in combination with low temperature. Such conditions reduce the metabolic activity of the fruit, thus controlling the ripening process. However, internal browning, can be elicited by the CA conditions. Different apple cultivars vary in their susceptibility to internal browning. ‘Braeburn’ apple is particularly susceptible to a storage-related internal browning disorder called ‘Braeburn’ browning disorder (BBD), which is characterised by the development of brown patches which may be accompanied by cavities in the fruit cortex. The combination of brown tissue and off-flavours makes apples unacceptable in the market, thus resulting in large economic losses. BBD depends on several preharvest factors (e.g., calcium and potassium fertilizers, and the use of triazole fungicides), the harvest date and postharvest factors (e.g., time of CA application, 1-MCP use, O2 and CO2 levels in the storage atmosphere, and storage temperature). However, how these factors influence the browning incidence in ‘Braeburn’ apple and the fruit metabolic profile is not well known.The objective of this work was to offer a better understanding of internal browning in rsquo; fruit, and to screen for metabolite biomarkers for predicting the early occurrence of the disorder in storage.In the first part of this work, wenbsp;rsquo; and rsquo;nbsp;with different susceptibilities for internalnbsp;In season 2010-2011, 12 different combinations of preharvest factors (calcium and potassium fertilizers, and triazole fungicides), harvest datesnbsp;postharvest factors (time of CA application, 1-MCP, O2, CO2 and temperature) were used for growing and storage of fruit. These factorsnbsp;selected based on information on literature about their involvement innbsp;in apple. In order to study the incidence of BBD in storage as influenced by the aforementioned factors, the apple fruit were then followed during the course of CA storage (after 3nbsp;6 months) with browning assessments. The results confirmed that rsquo; was resistant to the occurrence of browning, whereaslsquo;Braeburn’ developed browning with thenbsp;increasing with storage time. BBD incidence was reduced with calcium and potassium fertilizers application, while it wasnbsp;when triazolesnbsp;used. Delayed controlled atmosphere application resulted in lessnbsp;while treatment with 1-MCP increased BBD incidence. More BBD wasnbsp;in fruit stored at above-optimal CO2 levels. BBD incidence was increased when O2 concentration in CA was increased from 1 kPa to 3 kPa (optimum CA) or 6 kPa. Finally, the various factors showed anbsp;effect for different growing seasons and storage time.The second part of this work consisted of conducting at-harvest metabolomic analysis onlsquo;Braeburn’ fruit generated from the first part so that the effect ofnbsp;different preharvest factors on the apple metabolites could be studied. Besides, rsquo; fruitnbsp;one specific combination of pre- and postharvest factors were further sampled at various storage time-points (2 and 4 weeks, and 4 and 8 months) for metabolomicnbsp;so that a first glimpse of the metabolic changes during storage and due to BBD could be achieved. The results showed no significant difference in the primary metabolites between the different levels of the applied preharvest applications. Early during storage, fruit developed BBD, with the severity increasingnbsp;storage duration. This was correlated to a group of primary metabolites that showed either an increase (e.g., alanine, galactose) or a decrease (e.g., malate, sucrose) in concentration with time. Radial distribution of the metabolites in the fruit tissuenbsp;also observed;nbsp;metabolites (e.g., galactose, mannitol)nbsp;higher in concentration in the inner cortex, whilenbsp;concentrations of other metabolites (e.g., mannose, sucrose) were higher in the outer cortex.In the third part of this work, we conducted metabolomic analyses on rsquo; fruit grown and stored at different pre- and postharvest factors from the season 2011-2012. The results of the browning analysis from the previous season were used for the selection of the conditions to be used for fruit growing and storage innbsp;season. These fruitnbsp;thennbsp;and sampled throughout the storage period until 6 months with thenbsp;of investigating the effects of thenbsp;and postharvest factors on the metabolic profile of ‘Braeburnnbsp;fruit, and to screen for metabolites as biomarkers for the early prediction ofnbsp;This part of the work resulted in the identification ofnbsp;main metabolic changes (at harvest and after 6 months of storage) associated with the various pre- and postharvest factors, some of which could be correlated to thenbsp;of cellular respiration and the stress state of the tissue. Internal browning was observed during CA storage as early as 2 weeks after harvest. A clear spatial distribution of certain metabolites between the inner and outer cortex was observed which was mainly attributed to at-harvest differences and gas gradients inside the fruit. The screening for potential BBD biomarker metabolites did notnbsp;anynbsp;that could reliably predict the early incidence of thenbsp;fourth part ofnbsp;work consisted of conducting metabolomic analysis on fruit from 5 commercial rsquo;nbsp;from the season 2012-2013. These fruit were harvested and stored at commercial CA conditions. This part of thenbsp;aimed to investigate the development of BBD in fruit from commercial orchards stored under commercial CA conditions, and tonbsp;a comparison between thenbsp;orchards at the level of primary metabolites. Besides, a comparison to multiple batches from an experimental orchard from the previous season was done. Metabolic analyses were performed at harvest and after 3 and 6 months of storage, and 1 week of shelf-life usingnbsp;chromatography – mass spectrometry. The results show that BBD developed in fruit from the commercial orchards after 6 months of storage, the severity increasednbsp;the fruitnbsp;placed in shelf-life, and fruit from the different orchards showed different susceptibilities to the disorder. Fruit from the different commercial orchards didnbsp;differ significantly at the level of the primary metabolitesnbsp;clusterednbsp;fromnbsp;experimental batches.