The Experts below are selected from a list of 4038 Experts worldwide ranked by ideXlab platform
Turgay Unver - One of the best experts on this subject based on the ideXlab platform.
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nutrition metabolism plays an important role in the Alternate Bearing of the olive tree olea europaea l
PLOS ONE, 2013Co-Authors: Mine Turktas, Ekrem Dundar, Pilar Hernandez, Gabriel Dorado, Behcet Inal, Sezer Okay, Emine Gulden Erkilic, Turgay UnverAbstract:The olive tree (Olea europaea L.) is widely known for its strong tendency for Alternate Bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the Alternate Bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between ”on year” and “off year” leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree Alternate Bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the Alternate Bearing in olive tree.
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genome wide identification of Alternate Bearing associated micrornas mirnas in olive olea europaea l
BMC Plant Biology, 2013Co-Authors: Huriye Yanik, Mine Turktas, Ekrem Dundar, Pilar Hernandez, Gabriel Dorado, Turgay UnverAbstract: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.
Nagendra K. Singh - One of the best experts on this subject based on the ideXlab platform.
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Comparative RNA sequencing based transcriptome profiling of regular Bearing and Alternate Bearing mango ( Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying Alternate Bearing
Biotechnology Letters, 2020Co-Authors: Nimisha Sharma, Anand Kumar Singh, Sanjay Singh, Ajay Kumar Mahato, Manish Srivastav, Nagendra K. SinghAbstract:This study is to understand a comprehensive perspective on the molecular mechanisms underlying Alternate Bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, Alternate Bearing etc. showed significant differences between these two different Bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 Alternate Bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; Alternate Bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with Alternate Bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the Bearing tendencies in mango.
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Comparative RNA sequencing based transcriptome profiling of regular Bearing and Alternate Bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying Alternate Bearing
Biotechnology Letters, 2020Co-Authors: Nimisha Sharma, Anand Kumar Singh, Ajay Kumar Mahato, Manish Srivastav, Sanjay Kumar Singh, Nagendra K. SinghAbstract:Objective This study is to understand a comprehensive perspective on the molecular mechanisms underlying Alternate Bearing in mango ( Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Results Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, Alternate Bearing etc. showed significant differences between these two different Bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 Alternate Bearing genes were identified and principally three genes viz; SPL -like gene ( GBVX01015803.1 ), Rumani GA-20 -oxidase-like gene ( GBVX01019650.1 ) and LOC 103420644 ( GBVX01016070.1 ) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene ( gbGBVW01004309.1 ) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; Alternate Bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Conclusions Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with Alternate Bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the Bearing tendencies in mango.
Nimisha Sharma - One of the best experts on this subject based on the ideXlab platform.
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Comparative RNA sequencing based transcriptome profiling of regular Bearing and Alternate Bearing mango ( Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying Alternate Bearing
Biotechnology Letters, 2020Co-Authors: Nimisha Sharma, Anand Kumar Singh, Sanjay Singh, Ajay Kumar Mahato, Manish Srivastav, Nagendra K. SinghAbstract:This study is to understand a comprehensive perspective on the molecular mechanisms underlying Alternate Bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, Alternate Bearing etc. showed significant differences between these two different Bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 Alternate Bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; Alternate Bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with Alternate Bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the Bearing tendencies in mango.
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Comparative RNA sequencing based transcriptome profiling of regular Bearing and Alternate Bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying Alternate Bearing
Biotechnology Letters, 2020Co-Authors: Nimisha Sharma, Anand Kumar Singh, Ajay Kumar Mahato, Manish Srivastav, Sanjay Kumar Singh, Nagendra K. SinghAbstract:Objective This study is to understand a comprehensive perspective on the molecular mechanisms underlying Alternate Bearing in mango ( Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Results Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, Alternate Bearing etc. showed significant differences between these two different Bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 Alternate Bearing genes were identified and principally three genes viz; SPL -like gene ( GBVX01015803.1 ), Rumani GA-20 -oxidase-like gene ( GBVX01019650.1 ) and LOC 103420644 ( GBVX01016070.1 ) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene ( gbGBVW01004309.1 ) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; Alternate Bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Conclusions Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with Alternate Bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the Bearing tendencies in mango.
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Physiological and molecular basis of Alternate Bearing in perennial fruit crops
Scientia Horticulturae, 2019Co-Authors: Nimisha Sharma, Sanjay Singh, Ajay Kumar Mahato, Hutchappa Ravishankar, A.k. Dubey, Nagendra K. SinghAbstract:Abstract In perennial fruit crops, reproductive success and productivity are principally governed by the core event, regular flowering. However, this feature Bearing can be influenced by different factors viz. environmental conditions, germplasm, rootstocks, and cultural operations. The phenomenon of irregular Bearing is more dominant in perennial fruit crops. In order to ensure regular and quality fruit production it is therefore, imperative to regulate the flowering phenology. The comparative studies conducted by the researchers for understanding the physiological and molecular aspects associated with regular and irregular Bearing phenomenon in perennial fruit crops are helpful to understand the crux of flowering, discover the regulatory factors for regularity in Bearing. Further, differential gene expression studies allow the identification of key genes related with the regular Bearing feature. The identified candidate genes in this regard could be harnessed for selection of desirable parents, hybrids in early nursery stage, thus facilitating the plant breeders through precision breeding approaches. This paper reviews the current understanding of the physiological and molecular basis associated with the flowering phenology along with the impact of different factors on Alternate Bearing in perennial fruit crops.
Ajay Kumar Mahato - One of the best experts on this subject based on the ideXlab platform.
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Comparative RNA sequencing based transcriptome profiling of regular Bearing and Alternate Bearing mango ( Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying Alternate Bearing
Biotechnology Letters, 2020Co-Authors: Nimisha Sharma, Anand Kumar Singh, Sanjay Singh, Ajay Kumar Mahato, Manish Srivastav, Nagendra K. SinghAbstract:This study is to understand a comprehensive perspective on the molecular mechanisms underlying Alternate Bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, Alternate Bearing etc. showed significant differences between these two different Bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 Alternate Bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; Alternate Bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with Alternate Bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the Bearing tendencies in mango.
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Comparative RNA sequencing based transcriptome profiling of regular Bearing and Alternate Bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying Alternate Bearing
Biotechnology Letters, 2020Co-Authors: Nimisha Sharma, Anand Kumar Singh, Ajay Kumar Mahato, Manish Srivastav, Sanjay Kumar Singh, Nagendra K. SinghAbstract:Objective This study is to understand a comprehensive perspective on the molecular mechanisms underlying Alternate Bearing in mango ( Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. Results Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, Alternate Bearing etc. showed significant differences between these two different Bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 Alternate Bearing genes were identified and principally three genes viz; SPL -like gene ( GBVX01015803.1 ), Rumani GA-20 -oxidase-like gene ( GBVX01019650.1 ) and LOC 103420644 ( GBVX01016070.1 ) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene ( gbGBVW01004309.1 ) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; Alternate Bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. Conclusions Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with Alternate Bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the Bearing tendencies in mango.
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Physiological and molecular basis of Alternate Bearing in perennial fruit crops
Scientia Horticulturae, 2019Co-Authors: Nimisha Sharma, Sanjay Singh, Ajay Kumar Mahato, Hutchappa Ravishankar, A.k. Dubey, Nagendra K. SinghAbstract:Abstract In perennial fruit crops, reproductive success and productivity are principally governed by the core event, regular flowering. However, this feature Bearing can be influenced by different factors viz. environmental conditions, germplasm, rootstocks, and cultural operations. The phenomenon of irregular Bearing is more dominant in perennial fruit crops. In order to ensure regular and quality fruit production it is therefore, imperative to regulate the flowering phenology. The comparative studies conducted by the researchers for understanding the physiological and molecular aspects associated with regular and irregular Bearing phenomenon in perennial fruit crops are helpful to understand the crux of flowering, discover the regulatory factors for regularity in Bearing. Further, differential gene expression studies allow the identification of key genes related with the regular Bearing feature. The identified candidate genes in this regard could be harnessed for selection of desirable parents, hybrids in early nursery stage, thus facilitating the plant breeders through precision breeding approaches. This paper reviews the current understanding of the physiological and molecular basis associated with the flowering phenology along with the impact of different factors on Alternate Bearing in perennial fruit crops.
Mine Turktas - One of the best experts on this subject based on the ideXlab platform.
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nutrition metabolism plays an important role in the Alternate Bearing of the olive tree olea europaea l
PLOS ONE, 2013Co-Authors: Mine Turktas, Ekrem Dundar, Pilar Hernandez, Gabriel Dorado, Behcet Inal, Sezer Okay, Emine Gulden Erkilic, Turgay UnverAbstract:The olive tree (Olea europaea L.) is widely known for its strong tendency for Alternate Bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the Alternate Bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between ”on year” and “off year” leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree Alternate Bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the Alternate Bearing in olive tree.
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genome wide identification of Alternate Bearing associated micrornas mirnas in olive olea europaea l
BMC Plant Biology, 2013Co-Authors: Huriye Yanik, Mine Turktas, Ekrem Dundar, Pilar Hernandez, Gabriel Dorado, Turgay UnverAbstract: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.
