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Galaxy in Research: Exploring Genetic Variability in Almond Blooming

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Galaxy in Research: Exploring Genetic Variability in Almond Blooming

Explore how genetic variations influence the blooming periods of almond cultivars, revealing key insights into their molecular regulation.

Almonds (Prunus dulcis) are one of the oldest and most cherished tree nut crops, consumed worldwide for their nutritious kernels. Beyond their culinary and economic significance, almonds also hold cultural importance in various regions. One of the key agronomic traits of almond cultivars is their flowering time, which significantly influences yield and quality. Early or late blooming can affect the crop's exposure to frost, pollination dynamics, and market availability. Understanding the genetic factors underlying flowering time is crucial for breeding programs aimed at developing cultivars adapted to diverse climatic conditions. The latest study by Javed Iqbal Mir, Susheel Kumar Raina, Om Chand Sharma, Wasim Hassan Raja, Sajad-Un-Nabi, Salwee Yasmeen, and Sheikh M. Sultan investigates the transcriptomic differences between two almond cultivars, Waris and Ferralise, which exhibit distinct blooming periods. By leveraging cutting-edge sequencing technologies, the study provides new insights into the molecular mechanisms that regulate this essential trait.

Research Overview

In the study "Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time," Javed Iqbal Mir and colleagues conducted a comparative transcriptomic analysis on two almond cultivars, Waris and Ferralise. These cultivars differ in their blooming periods, providing a unique opportunity to explore the genetic basis of this variation.

Key Findings

· Differential Gene Expression: 3707 differentially expressed genes were identified, with 1558 up-regulated and 2149 down-regulated in Waris compared to Ferralise.

· Auxin Signaling Pathway: Differential regulation of genes involved in the auxin signaling pathway was observed, suggesting its role in flowering time control.

· Protein Degradation and Synthesis: Changes in the expression of ubiquitin ligases, serine/threonine-protein phosphatases, and proteasomes were noted, indicating their involvement in protein turnover during blooming.

· Metabolic Pathways: Differential expression was also found in genes associated with the phosphatidylinositol signaling and pentose phosphate pathways, highlighting their potential roles in almond flowering.

· Gene Annotation and Analysis: A thorough gene annotation against the Prunus dulcis_v2.0 protein database provided insights into the functional aspects of the differentially expressed genes.

Galaxy’s Role

The research team leveraged the Galaxy Europe platform for RNAseq analysis, processing FASTQC files and utilizing BlastX for gene annotation. The platform facilitated creating and analyzing BED files for genes with MSTRG tags using the "BEDtools get fasta" tool.

Significant of Study

This study offers valuable insights into the molecular mechanisms regulating flowering time in almonds. These findings could guide the breeding of late-blooming almond cultivars, which are crucial for adapting to changing climate conditions and extending the growing season.

Acknowledgements

We thank Javed Iqbal Mir and the entire research team for using Galaxy in their study. Their work exemplifies the platform's versatility in advancing plant genomic research.

---

Mir, J. I. ., Raina, S. K. ., Sharma, O. C. ., Neelam, S., Un-Nabi, S.-., Yasmeen, S. ., \& Sultan, S. M. S. (2024). Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time. INDIAN JOURNAL OF GENETICS AND PLANT BREEDING, 84(01), 114–120. https://doi.org/10.31742/ISGPB.84.1.11

https://galaxyproject.org/news/2024-07-30-galaxy-in-research-mir/

linkedin-galaxyproject

📝 New blog post Released!

Galaxy in Research: Exploring Genetic Variability in Almond Blooming (1/18)

Explore how genetic variations influence the blooming periods of almond cultivars, revealing key insights into their molecular regulation. (2/18)

Almonds (Prunus dulcis) are one of the oldest and most cherished tree nut crops, consumed worldwide for their nutritious kernels. Beyond their culinary and economic significance, almonds also hold cultural importance in various regions. One of the key agronomic traits of almond cultivars is their flowering time, which significantly influences yield and quality. Early or late blooming can affect the crop's exposure to frost, pollination dynamics, and market availability. Understanding the genetic factors underlying flowering time is crucial for breeding programs aimed at developing cultivars adapted to diverse climatic conditions. The latest study by Javed Iqbal Mir, Susheel Kumar Raina, Om Chand Sharma, Wasim Hassan Raja, Sajad-Un-Nabi, Salwee Yasmeen, and Sheikh M. Sultan investigates the transcriptomic differences between two almond cultivars, Waris and Ferralise, which exhibit distinct blooming periods. By leveraging cutting-edge sequencing technologies, the study provides new insights into the molecular mechanisms that regulate this essential trait. (3/18)

Research Overview (4/18)

In the study "Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time," Javed Iqbal Mir and colleagues conducted a comparative transcriptomic analysis on two almond cultivars, Waris and Ferralise. These cultivars differ in their blooming periods, providing a unique opportunity to explore the genetic basis of this variation. (5/18)

Key Findings (6/18)

· Differential Gene Expression: 3707 differentially expressed genes were identified, with 1558 up-regulated and 2149 down-regulated in Waris compared to Ferralise. (7/18)

· Auxin Signaling Pathway: Differential regulation of genes involved in the auxin signaling pathway was observed, suggesting its role in flowering time control. (8/18)

· Protein Degradation and Synthesis: Changes in the expression of ubiquitin ligases, serine/threonine-protein phosphatases, and proteasomes were noted, indicating their involvement in protein turnover during blooming. (9/18)

· Metabolic Pathways: Differential expression was also found in genes associated with the phosphatidylinositol signaling and pentose phosphate pathways, highlighting their potential roles in almond flowering. (10/18)

· Gene Annotation and Analysis: A thorough gene annotation against the Prunus dulcis_v2.0 protein database provided insights into the functional aspects of the differentially expressed genes. (11/18)

Galaxy’s Role (12/18)

The research team leveraged the Galaxy Europe platform for RNAseq analysis, processing FASTQC files and utilizing BlastX for gene annotation. The platform facilitated creating and analyzing BED files for genes with MSTRG tags using the "BEDtools get fasta" tool. (13/18)

Significant of Study (14/18)

This study offers valuable insights into the molecular mechanisms regulating flowering time in almonds. These findings could guide the breeding of late-blooming almond cultivars, which are crucial for adapting to changing climate conditions and extending the growing season. (15/18)

Acknowledgements (16/18)

We thank Javed Iqbal Mir and the entire research team for using Galaxy in their study. Their work exemplifies the platform's versatility in advancing plant genomic research. (17/18)

Mir, J. I. ., Raina, S. K. ., Sharma, O. C. ., Neelam, S., Un-Nabi, S.-., Yasmeen, S. ., & Sultan, S. M. S. (2024). Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time. INDIAN JOURNAL OF GENETICS AND PLANT BREEDING, 84(01), 114–120. https://doi.org/10.31742/ISGPB.84.1.11: https://doi.org/10.31742/ISGPB.84.1.11

https://galaxyproject.org/news/2024-07-30-galaxy-in-research-mir/

#UseGalaxy #GalaxyProject #UniFreiburg #usegalaxy #EOSC #EuroScienceGateway (18/18)

mastodon-eu-freiburg

📝 New blog post Released!

Galaxy in Research: Exploring Genetic Variability in Almond Blooming (1/20)

Explore how genetic variations influence the blooming periods of almond cultivars, revealing key insights into their molecular regulation. (2/20)

Almonds (Prunus dulcis) are one of the oldest and most cherished tree nut crops, consumed worldwide for their nutritious kernels. Beyond their culinary and economic significance, almonds also hold cultural importance in various regions. One of the key agronomic traits of almond cultivars is their flowering time, which significantly influences yield and quality. Early or late blooming can affect the crop's exposure to frost, pollination dynamics, and market availability. Understanding the (3/20)

genetic factors underlying flowering time is crucial for breeding programs aimed at developing cultivars adapted to diverse climatic conditions. The latest study by Javed Iqbal Mir, Susheel Kumar Raina, Om Chand Sharma, Wasim Hassan Raja, Sajad-Un-Nabi, Salwee Yasmeen, and Sheikh M. Sultan investigates the transcriptomic differences between two almond cultivars, Waris and Ferralise, which exhibit distinct blooming periods. By leveraging cutting-edge sequencing technologies, the study (4/20)

provides new insights into the molecular mechanisms that regulate this essential trait. (5/20)

Research Overview (6/20)

In the study "Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time," Javed Iqbal Mir and colleagues conducted a comparative transcriptomic analysis on two almond cultivars, Waris and Ferralise. These cultivars differ in their blooming periods, providing a unique opportunity to explore the genetic basis of this variation. (7/20)

Key Findings (8/20)

· Differential Gene Expression: 3707 differentially expressed genes were identified, with 1558 up-regulated and 2149 down-regulated in Waris compared to Ferralise. (9/20)

· Auxin Signaling Pathway: Differential regulation of genes involved in the auxin signaling pathway was observed, suggesting its role in flowering time control. (10/20)

· Protein Degradation and Synthesis: Changes in the expression of ubiquitin ligases, serine/threonine-protein phosphatases, and proteasomes were noted, indicating their involvement in protein turnover during blooming. (11/20)

· Metabolic Pathways: Differential expression was also found in genes associated with the phosphatidylinositol signaling and pentose phosphate pathways, highlighting their potential roles in almond flowering. (12/20)

· Gene Annotation and Analysis: A thorough gene annotation against the Prunus dulcis_v2.0 protein database provided insights into the functional aspects of the differentially expressed genes. (13/20)

Galaxy’s Role (14/20)

The research team leveraged the Galaxy Europe platform for RNAseq analysis, processing FASTQC files and utilizing BlastX for gene annotation. The platform facilitated creating and analyzing BED files for genes with MSTRG tags using the "BEDtools get fasta" tool. (15/20)

Significant of Study (16/20)

This study offers valuable insights into the molecular mechanisms regulating flowering time in almonds. These findings could guide the breeding of late-blooming almond cultivars, which are crucial for adapting to changing climate conditions and extending the growing season. (17/20)

Acknowledgements (18/20)

We thank Javed Iqbal Mir and the entire research team for using Galaxy in their study. Their work exemplifies the platform's versatility in advancing plant genomic research. (19/20)

Mir, J. I. ., Raina, S. K. ., Sharma, O. C. ., Neelam, S., Un-Nabi, S.-., Yasmeen, S. ., & Sultan, S. M. S. (2024). Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time. INDIAN JOURNAL OF GENETICS AND PLANT BREEDING, 84(01), 114–120. https://doi.org/10.31742/ISGPB.84.1.11: https://doi.org/10.31742/ISGPB.84.1.11

https://galaxyproject.org/news/2024-07-30-galaxy-in-research-mir/

@galaxyproject@mstdn.science
#UseGalaxy #GalaxyProject #UniFreiburg #usegalaxy #EOSC #EuroScienceGateway (20/20)

bluesky-galaxyproject

📝 New blog post Released!

Galaxy in Research: Exploring Genetic Variability in Almond Blooming (1/23)

Explore how genetic variations influence the blooming periods of almond cultivars, revealing key insights into their molecular regulation. (2/23)

Almonds (Prunus dulcis) are one of the oldest and most cherished tree nut crops, consumed worldwide for their nutritious kernels. Beyond their culinary and economic significance, almonds also hold cultural importance in various regions. One of the key agronomic traits of almond cultivars is (3/23)

their flowering time, which significantly influences yield and quality. Early or late blooming can affect the crop's exposure to frost, pollination dynamics, and market availability. Understanding the genetic factors underlying flowering time is crucial for breeding programs aimed at (4/23)

developing cultivars adapted to diverse climatic conditions. The latest study by Javed Iqbal Mir, Susheel Kumar Raina, Om Chand Sharma, Wasim Hassan Raja, Sajad-Un-Nabi, Salwee Yasmeen, and Sheikh M. Sultan investigates the transcriptomic differences between two almond cultivars, Waris and (5/23)

Ferralise, which exhibit distinct blooming periods. By leveraging cutting-edge sequencing technologies, the study provides new insights into the molecular mechanisms that regulate this essential trait. (6/23)

Research Overview (7/23)

In the study "Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time," Javed Iqbal Mir and colleagues conducted a comparative transcriptomic analysis on two almond cultivars, Waris and Ferralise. These cultivars differ in their blooming periods, (8/23)

providing a unique opportunity to explore the genetic basis of this variation. (9/23)

Key Findings (10/23)

· Differential Gene Expression: 3707 differentially expressed genes were identified, with 1558 up-regulated and 2149 down-regulated in Waris compared to Ferralise. (11/23)

· Auxin Signaling Pathway: Differential regulation of genes involved in the auxin signaling pathway was observed, suggesting its role in flowering time control. (12/23)

· Protein Degradation and Synthesis: Changes in the expression of ubiquitin ligases, serine/threonine-protein phosphatases, and proteasomes were noted, indicating their involvement in protein turnover during blooming. (13/23)

· Metabolic Pathways: Differential expression was also found in genes associated with the phosphatidylinositol signaling and pentose phosphate pathways, highlighting their potential roles in almond flowering. (14/23)

· Gene Annotation and Analysis: A thorough gene annotation against the Prunus dulcis_v2.0 protein database provided insights into the functional aspects of the differentially expressed genes. (15/23)

Galaxy’s Role (16/23)

The research team leveraged the Galaxy Europe platform for RNAseq analysis, processing FASTQC files and utilizing BlastX for gene annotation. The platform facilitated creating and analyzing BED files for genes with MSTRG tags using the "BEDtools get fasta" tool. (17/23)

Significant of Study (18/23)

This study offers valuable insights into the molecular mechanisms regulating flowering time in almonds. These findings could guide the breeding of late-blooming almond cultivars, which are crucial for adapting to changing climate conditions and extending the growing season. (19/23)

Acknowledgements (20/23)

We thank Javed Iqbal Mir and the entire research team for using Galaxy in their study. Their work exemplifies the platform's versatility in advancing plant genomic research. (21/23)

Mir, J. I. ., Raina, S. K. ., Sharma, O. C. ., Neelam, S., Un-Nabi, S.-., Yasmeen, S. ., & Sultan, S. M. S. (2024). Transcriptomic analysis of almond (Prunus dulcis) cultivars with differential flowering time. INDIAN JOURNAL OF GENETICS AND PLANT BREEDING, 84(01), 114–120. (22/23)

https://doi.org/10.31742/ISGPB.84.1.11: https://doi.org/10.31742/ISGPB.84.1.11

https://galaxyproject.org/news/2024-07-30-galaxy-in-research-mir/

@galaxyproject.bsky.social
#UseGalaxy #GalaxyProject #UniFreiburg #usegalaxy #EOSC #EuroScienceGateway (23/23)

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