Transcriptomic profiling of apple seeds
Ontology highlight
ABSTRACT:
ORGANISM(S): Malus domestica
PROVIDER: GSE62415 | GEO | 2014/11/21
SECONDARY ACCESSION(S): PRJNA264060
REPOSITORIES: GEO
Similar Datasets
Project description:Comparison of seed of two different types of developing fruits in apple: central and lateral. Our objective is to find transcriptomic signatures that allow to explain the physiological drop of young lateral fruitlets Apple seeds transcriptomes were generated by deep sequencing by triplicate from seeds collected from central and lateral fruitlets at 20 days after petal fall (DAPF)
2014-11-21 | E-GEOD-62415 | biostudies-arrayexpress
Project description:Experiments were carried out in 2008 on 8-year-old apple trees (cv. Golden Delicious/M9) trained with standard horticultural practices at the experimental farm of the IASMA (Trento, Italy). Populations of fruits with different abscission potentials (abscising fruitlets versus persisting fruitlets), were established as described by Dal Cin et al. (2005, 2007, 2009), Angeli et al. (2002), and other preliminary experiments (unpublished data). Briefly, the abscising population was made up of lateral fruitlets treated with benzylaminopurine (BA) at 200 ppm (commercial name Brancher-Dirado), when fruits had an average size of 13 mm (about 15 days after petal fall, DAPF). The population of central persisting fruitlets was generated by removing all the laterals from each cluster at petal fall, and leaving exclusively the central flower that had been hand-pollinated at full bloom with compatible pollen (cv. Stark Red). Samples of the two populations were collected at defined time points from groups of twenty homogeneous trees randomly distributed in the orchard in four blocks. Fruits were collected and categorised into three classes of size (class 1, smaller fruits; class 2, medium fruits; class 3, bigger fruits), two classes related to the position within the clusters (lateral versus central fruits), and two classes on the base of the treatment (BA-treated versus untreated fruits). Fruits of the intermediate size (class 2 fruits in Figure 1) were not considered for sampling and subsequent molecular analyses, and only fruits of the two more divergent size classes 1 and 3 were kept. This resulted in a combined categorisation of fruits into 4 classes: 1) untreated lateral fruitlets, 2) lateral fruitlets treated with BA, 3) untreated central fruitlets, and 4) central fruitlets treated with BA (Figure 1). Each class was further distinguished into the two size categories 1 (small fruits) and 3 (bigger fruits), for a total of eight experimental theses. Fruitlet shedding and ethylene evolution were monitored throughout the physiological drop from the beginning of the experiments up to 46 DAPF in all fruitlet classes, separately. Seed and cortex (including epidermis) samples were collected from all classes of fruitlets at 0 (T0), 1 (T1), 2 (T2), 4 (T3), 6 (T4), and 8 (T5) days after the BA treatment from control and treated trees, and according to their position within the clusters (central vs lateral) and size (small vs big), as described. The latter parameter was decided at each sampling date based upon the mean cross diameter of the whole population of lateral fruits, calculated over a sample of 100 fruits measured randomly on twenty trees. The small ones had a cross diameter below the mean - s.d. (standard deviation), whereas the big ones had a cross diameter above the mean + s.d. Lateral fruitlets were collected from intact clusters showing a clear hierarchy in terms of fruit size (i.e. with a clearly distinguishable central fruit, bigger than any lateral). Acronyms were ascribed to samples according to the following code: the first letter(s) describes fruitlet position within the cluster and the presence of BA treatment (L=untreated lateral, C=untreated central, LB=treated lateral, CB=treated central), then a digit to describe the size (1=small, 3=big), and finally a digit to described the time point (0=time of the treatment, 1=1 day after treatment, 2=2 days after treatment, 3=4 days after treatment, etc.). For example, LB32 is a lateral fruit, treated with BA, big sized, 2 days after treatment.<br>For microarray hybridizations, only samples of T0, T2, and T3 were used.
2010-12-31 | E-MEXP-2764 | biostudies-arrayexpress
Project description:Apple seeds were subjected to accelerated aging. After 7, 14, and 21 days of aging, embryos were isolated. Part of the embryos were shortly fumigated with nitric oxide (NO). After 48 h of embryos culture (aged embryos or aged embryos treated with NO), embryonic axes were used to extract the total RNA. RT-qPCR were done to analyze the changes in the expression of genes related to seed aging. Short-term (3 h) treatment of embryos isolated from accelerated aged apple seeds (Malus domestica Borkh.) with NO partially reduced the effects of aging. The aim of the study was to investigate the impact of the short-term NO treatment of embryos isolated from apple seeds subjected to accelerated aging on the expression of genes potentially linked to the regulation of seed aging. Apple seeds were artificially aged for 7, 14, or 21 days. Then the embryos were isolated from the seeds, treated with NO, and cultured for 48 h. Progression of seeds aging was associated with the decreased transcript levels of most of the analyzed genes (Lea1, Lea2a, Lea4, Hsp70b, Hsp20a, Hsp20b, ClpB1, ClpB4, Cpn60a, Cpn60b, Raptor, and Saur). The role of NO in the mitigation of seed aging depended on the duration of the aging. After 7 and 14 days of seed aging, a decreased expression of genes potentially associated with the promotion of aging (Tor, Raptor, Saur) was noted. NO-dependent regulation of seed aging was associated with the stimulation of the expression of genes encoding chaperones and proteins involved in the repair of damaged proteins. After NO application, the greatest upregulation of ClpB, Pimt was noted in the embryos isolated from seeds subjected to 7-day long accelerated aging, Hsp70b, Hsp70c, Cpn in the embryos of seeds aged for 14 days, and Lea2a in the embryos of seeds after 21 days of aging.
2022-07-07 | GSE207591 | GEO
Project description:The main objective of this analysis was to sequence the epigenome of the Apple (Malus domestica) doubled haploid 'Golden Delicious' tree. Our secondary objective was to identify differentially methylated regions between DNA purified from leaves and young fruits.
2016-09-17 | GSE87014 | GEO
Project description:The main objective of this analysis was to sequence the epigenome of two apple (Malus domestica) doubled haploid 'Golden Delicious' fruits (GDDH13 and GDDH18). Our secondary objective was to identify differentially methylated regions between DNA purified from the GDDH13 genotype and the GDDH18 genotypes at two developmental stages.
2017-04-27 | GSE93950 | GEO
Project description:Based on sensorial analysis over 4 years, 6 apple genotypes with contrasted fruit texture (mealy or not) were selected among a progeny. Apple samples were collected at 100 days after flowering (100 DAF), harvest (H), after 2 and 4 months of cold storage (60DAH and 120DAH respectively). 6 apple hybrids were analysed in dye-switch. Biological replicates are fruits from 2 to 4 different harvest years. Each mealy hybrid was compared to a non-mealy hybrid from the same harvest year in 12 dye-swap 3 pairs at 4 four time points).
2015-06-25 | E-GEOD-59947 | biostudies-arrayexpress
Project description:Gene expression in feeding larvae reciprocally transplanted into snowberry and apple fruits
2015-10-01 | GSE66975 | GEO
Project description:The self-abscising characteristic of fruit is a prominent trait for labor-saving cultivation in apple (Malus × domestica). Up to 30 days after full bloom, early abscission leaves only central fruit in a cluster, while four lateral fruits are abscised. Since fruit abscission is possibly induced during earlier phases of fruit development, samples were collected at full bloom and 10 days after full bloom. Comparative analysis between central and lateral pedicels in self-abscising apple can be used to identify the genes that trigger the abscission mechanism, as the destinies of the pedicels in a cluster are obvious. Transcriptome analysis was performed using RNA-Seq to compare expression profiles between the surviving central pedicel to be survived and abscised lateral pedicel to be abscised from self-abscising apple. A total of 797,647 ESTs were assembled into 65,876 contigs which were annotated and analyzed with using Blast2GO. A total of 1,585 differentially expressed genes in central and lateral pedicels were identified using the NOISeq software. , and these genes were were characterized using the MapMan ontology software. Transcription factors involved in vascular bundle differentiation functioned in the central pedicel, while the signaling cascade of IAA14/SLR-ARF7, which progressed during lateral root emergence from primary roots, operated in lateral pedicels. Future studies should explore associations between the mechanisms of lateral root emergence and pedicel abscission during early phases of fruit development, as well as the interconnection among hormones.
2017-08-05 | GSE60091 | GEO
Project description:Ontogenic scab resistance in apple leaves and fruits is a horizontal resistance against the plant pathogen VenturiaM- inaequalis and is expressed as decrease of disease symptoms and incidence with the ageing of the leaves. Several studies at biochemical level tried to unveil the nature of this resistance, however without any conclusive results. We decided therefore to investigate the genetic origin of this phenomenon by performing a full quantitative trascriptome sequencing and comparison of young (susceptible) and old (ontogenic resistant) leaves, infected or not with the pathogen. Two time points at 72 and 96 hours post inoculation were chosen for RNA sampling and sequencing. Comparison between the different conditions (young and old leaves, inoculated or not) should allow finding genes differentially expressed which may represent different induced plant defense reaction leading to ontogenic resistance or be the cause for a constitutive (not inoculated with the pathogen) shift toward resistance in old leaves. Differentially expressed genes were then characterized for their function by homology to A.M- thaliana and other plantsM-^R genes, particularly looking for genes involved in pathways already suspected of appertaining to ontogenic resistance in apple or other hosts, or to plant defense mechanisms in general.
2013-11-18 | E-MTAB-1726 | biostudies-arrayexpress
Project description:Fire blight (FB) is a bacterial disease affecting plants from Rosaceae family, including apple and pear. FB develops after the infection of Erwinia amylovora, gram-negative enterobacterium, and results in burnt-like damages and wilting, which can affect all organs of the plant. Although the mechanisms underlying disease response in apples are not elucidated yet, it has been well described that FB resistance depends on the rootstock type. The main objective of this work was to identify miRNAs involved in response to bacterial infection in order to better explain apple defense mechanisms against fire blight disease. We performed deep sequencing of eighteen small RNA libraries obtained from inoculated and non-inoculated Gala apple leaves. 233 novel plant mature miRNAs were identified together with their targets and potential role in response to bacterial infection. We identify three apple miRNAs responding to inoculation (mdm-miR168a,b, mdm-miR194C and mdm-miR1392C) as well as miRNAs reacting to bacterial infection in a rootstock-specific manner (miR395 family). Our results provide insights into the mechanisms of fire blight resistance in apple.
2016-08-28 | GSE72346 | GEO