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Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayval?k.

ABSTRACT: BACKGROUND: Olive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed. For this purpose, cDNA libraries from the leaves of trees in "on year" and in "off year" in July (when fruits start to appear) and in November (harvest time) were constructed. Randomly selected 100 positive clones from each library were analyzed with respect to sequence and size. A fruit-flesh cDNA library was also constructed and characterized to confirm the reliability of each library's temporal and spatial properties. RESULTS: Quantitative real-time RT-PCR (qRT-PCR) analyses of the cDNA libraries confirmed cDNA molecules that are associated with different developmental stages (e. g. "on year" leaves in July, "off year" leaves in July, leaves in November) and fruits. Hence, a number of candidate cDNAs associated with "on year" and "off year" were isolated. Comparison of the detected cDNAs to the current EST database of GenBank along with other non - redundant databases of NCBI revealed homologs of previously described genes along with several unknown cDNAs. Of around 500 screened cDNAs, 48 cDNA elements were obtained after eliminating ribosomal RNA sequences. These independent transcripts were analyzed using BLAST searches (cutoff E-value of 1.0E-5) against the KEGG and GenBank nucleotide databases and 37 putative transcripts corresponding to known gene functions were annotated with gene names and Gene Ontology (GO) terms. Transcripts in the biological process were found to be related with metabolic process (27%), cellular process (23%), response to stimulus (17%), localization process (8.5%), multicellular organismal process (6.25%), developmental process (6.25%) and reproduction (4.2%). CONCLUSIONS: A putative P450 monooxigenase expressed fivefold more in the "on year" than that of "off year" leaves in July. Two putative dehydrins expressed significantly more in "on year" leaves than that of "off year" leaves in November. Homologs of UDP - glucose epimerase, acyl - CoA binding protein, triose phosphate isomerase and a putative nuclear core anchor protein were significant in fruits only, while a homolog of an embryo binding protein / small GTPase regulator was detected in "on year" leaves only. One of the two unknown cDNAs was specific to leaves in July while the other was detected in all of the libraries except fruits. KEGG pathway analyses for the obtained sequences correlated with essential metabolisms such as galactose metabolism, amino sugar and nucleotide sugar metabolisms and photosynthesis. Detailed analysis of the results presents candidate cDNAs that can be used to dissect further the genetic basis of fruit production and / or alternate bearing which causes significant economical loss for olive growers.

SUBMITTER: Dundar E

PROVIDER: S-EPMC3637518 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayvalık.

Dündar Ekrem E Suakar Oznur O Unver Turgay T Dagdelen Ayhan A

BMC genomics 20130403

<h4>Background</h4>Olive cDNA libraries to isolate candidate genes that can help enlightening the molecular mechanism of periodicity and / or fruit production were constructed and analyzed. For this purpose, cDNA libraries from the leaves of trees in "on year" and in "off year" in July (when fruits start to appear) and in November (harvest time) were constructed. Randomly selected 100 positive clones from each library were analyzed with respect to sequence and size. A fruit-flesh cDNA library wa ...[more]

PMID: 23552171

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Project description:BACKGROUND: Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the following year ("off-year"). Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA), being gene-expression regulators that have been found to be involved as key determinants in several physiological processes. RESULTS: Six olive (Olea europaea L. cv. Ayvalik variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on year" and "off year" leaves in July and in November, respectively) and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways. CONCLUSION: A comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also provide significant data on the miRNA-fruit development interaction and advance perspectives in the miRNA profile of the olive tree.

Project description:BACKGROUND:Olive (Olea europaea L.) is an emblematic oil tree crop in the Mediterranean basin. Currently, despite olive features as a moderately thermophilic species, its cultivation is worldwide spreading due to the health-related impact of olive products on human nutrition. A point of concern for the expanding olive cultivation is related to the influence that, in addition to genotype, environmental factors exerts on drupe development and metabolism with consequent impact on fruit key traits. In this context, the aim of the present work was to gain further information on the genetic networks controlling drupe maturation phase and, mainly, on their modulation in response to environmental cues. RESULTS:To achieve this goal, a comparative transcriptome-wide investigation was carried out on drupes of Olea europaea cultivar Carolea, collected from plants growing in areas at different altitude level and therefore experiencing different climatic conditions. Two maturation stages of drupe were analysed: green mature and turning-purple. Metabolic characterization of drupe was also performed. At both transcriptomic and metabolic level differences were detected in the pathway of fatty acids (FAs) and phenol compounds, in relation to both drupe maturation stage and cultivation area. Among the most relevant differences detected during the transition from GM to TP stages there were: the upregulation of FADs genes in the drupes of population growing at 700 masl, the upregulation of phenol biosynthesis-related genes in drupes growing at 10 and 200 masl and very interestingly the downregulation of specific genes involved in secoiridoids production in drupes growing at 700 masl. Globally, these results suggested that stability of FAs and phenols, mainly of secoiridoids group, is promoted at high altitude, while at lower altitude phenol biosynthesis is prolonged. CONCLUSION:The obtained results showed a differential modulation of genetic pathways related to olive compound quality in relation to the cultivation area, likely imposed by the different temperature impending at each altitude. The derived molecular information appears of interest for both breeding and biotechnological programs of olive species, especially with respect to the modulation of antioxidant secoiridoid compounds which play a key role in conferring both sensorial and healthy characteristic to olive products.

Dataset Information

Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayval?k.

Publications

Isolation and expression analysis of cDNAs that are associated with alternate bearing in Olea europaea L. cv. Ayvalık.

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