Dataset Information

Metabolomics study of different tissues of mume 'Longyan' plant grafted on mume rootstock and peach rootstock (Root)

ABSTRACT:

Background: Grafting with the dwarf rootstock is an efficient method to control the plant height in fruit production. However, the molecular mechanism is still unclear. Our previous study showed that the plants with Prunus mume rootstock exhibit a considerable reduction in plant height, internode length and number of nodes compared with Prunus persica rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by ‘P. mume’ rootstocks through transcriptome and metabolomic analysis with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’.

Results: The findings of the study indicate a significant decrease in brassinolide levels in plants that were grafted onto ‘P. mume’ rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased in the research. The present work observed a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto ‘P. mume’ rootstocks. Auxin signaling cues promote PmARF3 transcription, which directly controls this upregulation. Through its binding to PmBAS1 and PmSAUR36 gene promoters, PmLBD3 promotes endogenous brassinolide inactivation and inhibits cell proliferation.

Conclusions: Auxin signaling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and caused dwarf plants in stone fruits.

Root analysis is reported in the current study MTBLS10051.

Leaf analysis is reported in MTBLS10083.

Stem analysis is reported in MTBLS10062.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS10051 | MetaboLights | 2024-08-12

REPOSITORIES: MetaboLights

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Source:

			Action	DRS
	22P11650001_OCTML_NEG.raw	Raw
	22P11650001_OCTML_POS.raw	Raw
	22P11650005_OCTML_NEG.raw	Raw
	22P11650005_OCTML_POS.raw	Raw
	22P11650009_OCTML_NEG.raw	Raw

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Project description:Background: Grafting with the dwarf rootstock is an efficient method to control the plant height in fruit production. However, the molecular mechanism is still unclear. Our previous study showed that the plants with Prunus mume rootstock exhibit a considerable reduction in plant height, internode length and number of nodes compared with Prunus persica rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by ‘P. mume’ rootstocks through transcriptome and metabolomic analysis with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’. Results: The findings of the study indicate a significant decrease in brassinolide levels in plants that were grafted onto ‘P. mume’ rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased in the research. The present work observed a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto ‘P. mume’ rootstocks. Auxin signaling cues promote PmARF3 transcription, which directly controls this upregulation. Through its binding to PmBAS1 and PmSAUR36 gene promoters, PmLBD3 promotes endogenous brassinolide inactivation and inhibits cell proliferation. Conclusions: Auxin signaling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and caused dwarf plants in stone fruits. Leaf analysis is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS10083' rel='noopener noreferrer' target='_blank'>MTBLS10083</a>.Stem analysis is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS10062' rel='noopener noreferrer' target='_blank'>MTBLS10062</a>.Root analysis is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS10051' rel='noopener noreferrer' target='_blank'>MTBLS10051</a>.

Project description:Background: Grafting with the dwarf rootstock is an efficient method to control the plant height in fruit production. However, the molecular mechanism is still unclear. Our previous study showed that the plants with Prunus mume rootstock exhibit a considerable reduction in plant height, internode length and number of nodes compared with Prunus persica rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by ‘P. mume’ rootstocks through transcriptome and metabolomic analysis with two grafting combinations, ‘Longyan/Mume’ and ‘Longyan/Peach’. Results: The findings of the study indicate a significant decrease in brassinolide levels in plants that were grafted onto ‘P. mume’ rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased in the research. The present work observed a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto ‘P. mume’ rootstocks. Auxin signaling cues promote PmARF3 transcription, which directly controls this upregulation. Through its binding to PmBAS1 and PmSAUR36 gene promoters, PmLBD3 promotes endogenous brassinolide inactivation and inhibits cell proliferation. Conclusions: Auxin signaling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and caused dwarf plants in stone fruits. Stem analysis is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS10062' rel='noopener noreferrer' target='_blank'>MTBLS10062</a>.Leaf analysis is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS10083' rel='noopener noreferrer' target='_blank'>MTBLS10083</a>.Root analysis is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS10051' rel='noopener noreferrer' target='_blank'>MTBLS10051</a>.

Project description:Citrus and most other fruit crops are commercially propagated via grafting, which ensures trees have consistent fruit traits combined with favorable traits from the rootstock such as soil adaptability, vigor, and resistance to soil pathogens. Breeding new rootstocks requires careful agronomic evaluations, and widespread use of new rootstocks and scions requires graft compatibility with commercially important scions and rootstocks. Graft incompatibility can occur when the scion and rootstock are not able to form a permanent, healthy union. Understanding and preventing graft incompatibility is therefore of paramount importance in the breeding of new fruit cultivars and in the choice of scion and rootstock by growers. The rootstock US-1283 is a citrandarin generated from a cross of ‘Ninkat’ mandarin (Citrus reticulata) and ‘Gotha Road’ #6 trifoliate orange (Poncirus trifoliata). It was released in 2014 after years of field evaluation because of its superior productivity and good fruit quality on ‘Hamlin’ sweet orange (C. sinensis) under Florida’s growing conditions. Subsequently, it was observed that trees of ‘Bearss’ lemon (C. limon) and ‘Valencia’ sweet orange (C. sinensis) grafted onto US-1283 exhibited apparent incompatible and unhealthy growth near the graft union. The incompatibility manifested as stem grooving and necrosis underneath the bark on the rootstock side of the graft. A genetically similar citrandarin rootstock, US-812 (C. reticulata ‘Sunki’ × P. trifoliata ‘Benecke’), is fully graft compatible with the same scions. Transcriptome analysis was performed on the vascular tissues above and below the graft union of compatible US-812 and incompatible US-1283 graft combinations with ‘Bearss’ and ‘Valencia’ to identify expression networks associated with incompatibility and help understand the processes and potential causes of incompatibility in citrus. Transcriptional reprogramming was stronger in the incompatible rootstock than in the grafted scions. Functional analysis of the transcriptional events below the graft unions of US-1283 incompatible combinations revealed differentially expression genes (DEGs) associated with oxidative stress and plant defense, among other pathways, similar to a pathogen-induced immune response localized to the rootstock, although no known pathogens were detected in the assayed plants. These changes were not observed above the graft unions.Differentially expressed genes (DEGs) in US-1283, but not the scions, were associated with oxidative stress and plant defense, among others, similar to a pathogen-induced immune response localized to the rootstock. No pathogen infection was detected. It is hypothesized this response could have been triggered by signaling miscommunications between rootstock and scion either through 1) unknown molecules from the scion that were perceived as danger signals by the rootstock, 2) missing signals from the scion or missing receptors in the rootstock necessary for the formation of a healthy graft union, 3) the overall perception of the scion by the rootstock as non-self, or 4) a combination of the above.

Project description:Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum. Results: The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which is consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and Pectatelyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation. Conclusions: This comprehensive interaction of the transcriptome and miRNA at tall-culmand dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton.

Project description:Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties.Â In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum. Results: The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which is consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and Pectatelyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation. Conclusions: This comprehensive interaction of the transcriptome and miRNA at tall-culmand dwarf mutant led to the discovery of regulatory mechanisms inÂ plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton. Total RNA was purified from stem apexes of three samples at the fifth true leaf stages and sequenced deeply using Illumina HiSeq 2000 system.

Dataset Information

Metabolomics study of different tissues of mume 'Longyan' plant grafted on mume rootstock and peach rootstock (Root)

Dataset's files

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