Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality (original) (raw)
Related papers
Comparative transcript profiling of a peach and its nectarine
Gene expression at harvest was compared for two stone fruit cultivars, a peach and its near-isogenic nectarine mutant, using two microarray platforms, μPEACH1.0 and ChillPeach. Together, both platforms covered over 6,000 genes out of which 417 were differentially expressed between the fruits of the two cultivars at a p value of 0.05. A total of 47 genes in nectarine and 60 genes in peach were at least twofold higher relative to each other. Nectarine had much better storage characteristics than peach and could be stored for over 5 weeks at 5 °C without storage disorders. In an attempt to determine whether gene expression at harvest could give an indication of storage potential, the expression analysis of the two cultivars was compared to that of two genotypes with different sensitivities to chilling injury. Principal component analysis of gene expression results across four fruit types differing in chilling sensitivity resulted in 41 genes whose expression levels separated the fruits according to sensitivity to storage disorders, suggesting that the genes have a role in cold response adaptation.
Journal of Agricultural and Food Chemistry, 2019
Cold storage of fruit is one of the methods most commonly employed to extend the postharvest lifespan of peaches (Prunus persica (L.) Batsch). However, fruit quality in this species is affected negatively by mealiness, a physiological disorder triggered by chilling injury after long periods of exposure to low temperature during storage and manifested mainly as a lack of juiciness, which ultimately modifies the organoleptic properties of peach fruit. The aim of this study was to identify molecular components and metabolic processes underlying mealiness in susceptible and nonsusceptible segregants. Transcriptome and qRT-PCR profiling were applied to individuals with contrasting juiciness phenotypes in a segregating F 2 population. Our results suggest that mealiness is a multiscale phenomenon, since juicy and mealy fruit display distinctive reprogramming processes affecting translational machinery and lipid, sugar and oxidative metabolism. The candidate genes identified may be useful tools for further crop improvement.
Frontiers in Plant Science
IntroductionPeach (Prunus persica (L.) Batsch,) and nectarine fruits (Prunus persica (L.) Batsch, var nectarine), are characterized by a rapid deterioration at room temperature. Therefore, cold storage is widely used to delay fruit post-harvest ripening and extend fruit commercial life. Physiological disorders, collectively known as chilling injury, can develop typically after 3 weeks of low-temperature storage and affect fruit quality.MethodsA comparative transcriptomic analysis was performed to identify regulatory pathways that develop before chilling injury symptoms are detectable using next generation sequencing on the fruits of two contrasting cultivars, one peach (Sagittaria) and one nectarine, (Big Top), over 14 days of postharvest cold storage.ResultsThere was a progressive increase in the number of differentially expressed genes between time points (DEGs) in both cultivars. More (1264) time point DEGs were identified in ‘Big Top’ compared to ‘Sagittaria’ (746 DEGs). Both cu...
Tree Genetics & Genomes, 2013
Gene expression at harvest was compared for two stone fruit cultivars, a peach and its near-isogenic nectarine mutant, using two microarray platforms, μPEACH1.0 and ChillPeach. Together, both platforms covered over 6,000 genes out of which 417 were differentially expressed between the fruits of the two cultivars at a p value of 0.05. A total of 47 genes in nectarine and 60 genes in peach were at least twofold higher relative to each other. Nectarine had much better storage characteristics than peach and could be stored for over 5 weeks at 5°C without storage disorders. In an attempt to determine whether gene expression at harvest could give an indication of storage potential, the expression analysis of the two cultivars was compared to that of two genotypes with different sensitivities to chilling injury. Principal component analysis of gene expression results across four fruit types differing in chilling sensitivity resulted in 41 genes whose expression levels separated the fruits according to sensitivity to storage disorders, suggesting that the genes have a role in cold response adaptation.
Transcriptome Analyses and Postharvest Physiology of Peaches and Nectarines
2009
Genomics approaches and transcriptome analyses are increasingly being used to elucidate mechanisms that regulate complex developmental processes such as fruit ripening and the evolution of quality-related biochemical changes during the postharvest phase. In peach (Prunus persica L.), projects aimed at isolating ESTs corresponding to genes expressed in different fruit tissues and the construction and use of tools such as microarrays has resulted in identification of basic information concerning hormonal regulation, in particular on the role of ethylene and auxin and their interplay and cross-talk during ripening. Functional genomics approaches have been undertaken for studies specifically targeted to identify and characterize genes involved in the peculiar response of peaches and nectarines to applications of 1-MCP and in the development of storage disorders. INTRODUCTION Climacteric fruit exhibit an increase of ethylene biosynthesis during ripening and the hormone regulates many of the changes in the transcriptional profile of genes during this period (Giovannoni, 2004; Cara and Giovannoni, 2008). Such coordinated and programmed modulation of gene expression leads to changes in fruit texture, colour, taste, and aroma, the most important quality parameters considered by consumers together with the increasing interest in nutritive value and safety for human health. These quality attributes are the result of many chemical and structural modifications that are genetically programmed during ripening, when fruit become edible and attractive for consumption, as well as during the postharvest phase. Specific aspects of fruit biochemistry have received great attention due to their importance in fruit quality: elucidation of biosynthetic pathways of pigments, cell wall architecture and composition, sugar and organic acid metabolism. The application of genome-scale gene expression profiling tools allows better elucidation of the basic mechanisms and interactions occurring during ripening and the postharvest phase in different fruit species including peach (Bonghi and Trainotti, 2006; Tonutti and Bonghi, 2009). TRANSCRIPTOME CHANGES DURING THE TRANSITION FROM PRE-CLIMACTERIC TO CLIMACTERIC STAGE IN PEACH FRUIT The Italian Consortium for Genomics studies in Rosaceae species (ESTree Consortium) has developed the first microarray (named µPEACH1.0) containing about 4,800 oligonucleotide (70mer) probes corresponding to genes expressed in fruit throughout development (ESTree Consortium, 2005). Microarray hybridizations indicate 69
Genomics Approaches for Better Understanding the Biological Basis of Fruit Ripening and Quality
Acta Horticulturae, 2006
Genomics tools are nowadays commonly used in many plant science labs and are rapidly spreading for studying transcriptome profiles throughout fruit development and discovering new genes involved in processes modulating quality traits. In fact, transcript profiling (TP) has the potential to reveal transcriptional hierarchy during development for thousands of genes, as well as providing expression data for many genes of unknown or putative function. By using both direct and indirect TP methods, a body of new information is now available concerning ripening regulation in both climacteric and non-climacteric fruits, and a number of genes differentially expressed during the transition from unripe to ripe fruit and related to the evolution of quality parameters have been identified. Concerning direct TP methods, isolated ESTs have been used for digital expression analysis throughout fruit development in several fruit species and for comparative genomics investigations. The comparative approach has allowed to identify genes putatively encoding transcription factors induced at ripening in both grapes and peaches indicating that some regulatory elements are in common in non-climacteric and climacteric fruits. Among direct TP analyses, cDNA-AFLP has been widely used in several fruit types including grape berry: using this technique, we have identified 92 and 82 genes differentially regulated in skins of grape berries during extended ripening off-(detachment) and on-(late harvest) plant, respectively. Some of these genes are in common but others are specifically induced or repressed by each treatment and may be responsible for some quality traits characterizing late-harvest or partially dehydrated grape berries. Considering the indirect analyses, the first peach microarray (µPEACH 1.0) containing oligo-probes corresponding to 4806 unigenes has been constructed and used for comparing transcriptome of pre-climacteric and climacteric peach fruit: 267 and 109 genes appear up-and down-regulated, respectively, during this transition. Among these, genes responsible for typical peach fruit traits (pulp pigmentation) and others, already associated to ripening in other species, but never studied in peach have been identified.
PLoS ONE, 2014
Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding strategies to better cope with chilling injury. Citation: Pons C, Martí C, Forment J, Crisosto CH, Dandekar AM, et al. (2014) A Bulk Segregant Gene Expression Analysis of a Peach Population Reveals Components of the Underlying Mechanism of the Fruit Cold Response. PLoS ONE 9(3): e90706.
Background: Cold storage induces chilling injury (CI) disorders in peach fruit (woolliness/mealiness, flesh browning and reddening/bleeding) manifested when ripened at shelf life. To gain insight into the mechanisms underlying CI, we analyzed the transcriptome of ‘Oded’ (high tolerant) and ‘Hermoza’ (relatively tolerant to woolliness, but sensitive to browning and bleeding) peach cultivars at pre-symptomatic stages. The expression profiles were compared and validated with two previously analyzed pools (high and low sensitive to woolliness) from the Pop-DG population. The four fruit types cover a wide range of sensitivity to CI. The four fruit types were also investigated with the ROSMETER that provides information on the specificity of the transcriptomic response to oxidative stress. Results: We identified quantitative differences in a subset of core cold responsive genes that correlated with sensitivity or tolerance to CI at harvest and during cold storage, and also subsets of genes correlating specifically with high sensitivity to woolliness and browning. Functional analysis indicated that elevated levels, at harvest and during cold storage, of genes related to antioxidant systems and the biosynthesis of metabolites with antioxidant activity correlates with tolerance. Consistent with these results, ROSMETER analysis revealed oxidative stress in ‘Hermoza’ and the progeny pools, but not in the cold resistant ‘Oded’. By contrast, cold storage induced, in sensitivity to woolliness dependant manner, a gene expression program involving the biosynthesis of secondary cell wall and pectins. Furthermore, our results indicated that while ethylene is related to CI tolerance, differential auxin subcellular accumulation and signaling may play a role in determining chilling sensitivity/tolerance. In addition, sugar partitioning and demand during cold storage may also play a role in the tolerance/sensitive mechanism. The analysis also indicates that vesicle trafficking, membrane dynamics and cytoskeleton organization could have a role in the tolerance/sensitive mechanism. In the case of browning, our results suggest that elevated acetaldehyde related genes together with the core cold responses may increase sensitivity to browning in shelf life. Conclusions: Our data suggest that in sensitive fruit a cold response program is activated and regulated by auxin distribution and ethylene and these hormones have a role in sensitivity to CI even before fruit are cold stored.
PLoS ONE, 2012
Cold storage is extensively used to slow the rapid deterioration of peach (Prunus persica L. Batsch) fruit after harvest. However, peach fruit subjected to long periods of cold storage develop chilling injury (CI) symptoms. Post-harvest heat treatment (HT) of peach fruit prior to cold storage is effective in reducing some CI symptoms, maintaining fruit quality, preventing softening and controlling post-harvest diseases. To identify the molecular changes induced by HT, which may be associated to CI protection, the differential transcriptome of peach fruit subjected to HT was characterized by the differential display technique. A total of 127 differentially expressed unigenes (DEUs), with a presence-absence pattern, were identified comparing peach fruit ripening at 20uC with those exposed to a 39uC-HT for 3 days. The 127 DEUs were divided into four expression profile clusters, among which the heat-induced (47%) and heat-repressed (36%) groups resulted the most represented, including genes with unknown function, or involved in protein modification, transcription or RNA metabolism. Considering the CI-protection induced by HT, 23-heat-responsive genes were selected and analyzed during and after short-term cold storage of peach fruit. More than 90% of the genes selected resulted modified by cold, from which nearly 60% followed the same and nearly 40% opposite response to heat and cold. Moreover, by using available Arabidopsis microarray data, it was found that nearly 70% of the peach-heat responsive genes also respond to cold in Arabidopsis, either following the same trend or showing an opposite response. Overall, the high number of common responsive genes to heat and cold identified in the present work indicates that HT of peach fruit after harvest induces a cold response involving complex cellular processes; identifying genes that are involved in the better preparation of peach fruit for cold-storage and unraveling the basis for the CI protection induced by HT. Citation: Lauxmann MA, Brun B, Borsani J, Bustamante CA, Budde CO, et al. (2012) Transcriptomic Profiling during the Post-Harvest of Heat-Treated Dixiland Prunus persica Fruits: Common and Distinct Response to Heat and Cold. PLoS ONE 7(12): e51052.
BMC Genomics, 2015
Background: Cold storage induces chilling injury (CI) disorders in peach fruit (woolliness/mealiness, flesh browning and reddening/bleeding) manifested when ripened at shelf life. To gain insight into the mechanisms underlying CI, we analyzed the transcriptome of 'Oded' (high tolerant) and 'Hermoza' (relatively tolerant to woolliness, but sensitive to browning and bleeding) peach cultivars at pre-symptomatic stages. The expression profiles were compared and validated with two previously analyzed pools (high and low sensitive to woolliness) from the Pop-DG population. The four fruit types cover a wide range of sensitivity to CI. The four fruit types were also investigated with the ROSMETER that provides information on the specificity of the transcriptomic response to oxidative stress.