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Diversity in global gene expression and morphology across a watercress (Nasturtium officinale R. Br.) germplasm collection: first steps to breeding.

Payne AC, Clarkson GJ, Rothwell S, Taylor G - Hortic Res (2015)

Bottom Line: This variation was used to identify three extreme contrasting accessions for further analysis.A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism.In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress.

View Article: PubMed Central - PubMed

Affiliation: Centre for Biological Sciences, Institute for Life Sciences, University of Southampton , Southampton, SO17 1BJ, UK.

ABSTRACT
Watercress (Nasturtium officinale R. Br.) is a nutrient intense, leafy crop that is consumed raw or in soups across the globe, but for which, currently no genomic resources or breeding programme exists. Promising morphological, biochemical and functional genomic variation was identified for the first time in a newly established watercress germplasm collection, consisting of 48 watercress accessions sourced from contrasting global locations. Stem length, stem diameter and anti-oxidant (AO) potential varied across the accessions. This variation was used to identify three extreme contrasting accessions for further analysis. Variation in global gene expression was investigated using an Affymetrix Arabidopsis ATH1 microarray gene chip, using the commercial control (C), an accession selected for dwarf phenotype with a high AO potential (dwarfAO, called 'Boldrewood') and one with high AO potential alone. A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism. In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress. This study provides the first analysis of natural variation across the watercress genome and has identified important underpinning information for future breeding for enhanced anti-carcinogenic properties and morphology traits in this nutrient-intense crop.

No MeSH data available.


Related in: MedlinePlus

(a) Transcriptomic differences between a novel dwarf watercress accession (dwarfAO) and the commercial (C) accession, where an up- or down- regulations, red and blue squares respectively is shown in dwarfAO compared to C. Mapman output illustrating down-regulation of genes in bins relating to plant growth in dwarfAO/C and an up-regulation of genes in the bins relating to plant defence in watercress accession dwarfAO/C. Superscript numbers denote Refs. 43, 54, 45, 34, 31, 3. (b) Overview of significantly different functional categories after microarray analysis. Colour scale represents fold changes, blue down-regulation and red up-regulation. Wilcoxon rank-sum test was applied to all three comparisons performed in PageMan. Clear visual representation of how the functional ontologies differ between the two watercress accessions.
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fig3: (a) Transcriptomic differences between a novel dwarf watercress accession (dwarfAO) and the commercial (C) accession, where an up- or down- regulations, red and blue squares respectively is shown in dwarfAO compared to C. Mapman output illustrating down-regulation of genes in bins relating to plant growth in dwarfAO/C and an up-regulation of genes in the bins relating to plant defence in watercress accession dwarfAO/C. Superscript numbers denote Refs. 43, 54, 45, 34, 31, 3. (b) Overview of significantly different functional categories after microarray analysis. Colour scale represents fold changes, blue down-regulation and red up-regulation. Wilcoxon rank-sum test was applied to all three comparisons performed in PageMan. Clear visual representation of how the functional ontologies differ between the two watercress accessions.

Mentions: Overall there was a clear differentiation in gene expression in the dwarf phenotype in which plant defence was up-regulated whilst plant growth was down-regulated (Figure 3a). This is clearly identified by examining bins in relation to plant growth and defence. dwarfAO exhibited a down-regulation of genes involved in the control of plant growth (brassinosteroids, phenylpropanoids, lignin) and an up-regulation of genes in plant defence (glucosinolates, cyanogenic glycosides, glutathione-S-transferase and ascorbate/glutathione). Gibberellins and brassinosteroids are plant hormones which are required for growth and development. Commonly associated with a dwarf phenotype is a reduction in either of these hormones, plants which are unable to perceive brassinosteroids exhibit typical phenotypes which include the dwarf phenotype.31 The brassinosteroids have been reported to be involved in organ growth, cell expansion, cell division and responses to abiotic and biotic stresses.32 Gene expression analysis from Mapman reveals a down-regulation in the bin representing brassinosteroids for the following genes; Rotundifolia3 (at4g36380), Sterol methyltransferase2 (at1g20330), 7RED (at1g50430) and multiple hits which correspond to brassinosteroid metabolism. For example, ROTUNDIFOLIA3 encodes an enzyme to catalyse C-23 hydroxylation of several brassinosteroids which is in fact two steps shorter than the conventional brassionsteroid pathway,32,33 this gene is down-regulated in dwarfAO.


Diversity in global gene expression and morphology across a watercress (Nasturtium officinale R. Br.) germplasm collection: first steps to breeding.

Payne AC, Clarkson GJ, Rothwell S, Taylor G - Hortic Res (2015)

(a) Transcriptomic differences between a novel dwarf watercress accession (dwarfAO) and the commercial (C) accession, where an up- or down- regulations, red and blue squares respectively is shown in dwarfAO compared to C. Mapman output illustrating down-regulation of genes in bins relating to plant growth in dwarfAO/C and an up-regulation of genes in the bins relating to plant defence in watercress accession dwarfAO/C. Superscript numbers denote Refs. 43, 54, 45, 34, 31, 3. (b) Overview of significantly different functional categories after microarray analysis. Colour scale represents fold changes, blue down-regulation and red up-regulation. Wilcoxon rank-sum test was applied to all three comparisons performed in PageMan. Clear visual representation of how the functional ontologies differ between the two watercress accessions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591680&req=5

fig3: (a) Transcriptomic differences between a novel dwarf watercress accession (dwarfAO) and the commercial (C) accession, where an up- or down- regulations, red and blue squares respectively is shown in dwarfAO compared to C. Mapman output illustrating down-regulation of genes in bins relating to plant growth in dwarfAO/C and an up-regulation of genes in the bins relating to plant defence in watercress accession dwarfAO/C. Superscript numbers denote Refs. 43, 54, 45, 34, 31, 3. (b) Overview of significantly different functional categories after microarray analysis. Colour scale represents fold changes, blue down-regulation and red up-regulation. Wilcoxon rank-sum test was applied to all three comparisons performed in PageMan. Clear visual representation of how the functional ontologies differ between the two watercress accessions.
Mentions: Overall there was a clear differentiation in gene expression in the dwarf phenotype in which plant defence was up-regulated whilst plant growth was down-regulated (Figure 3a). This is clearly identified by examining bins in relation to plant growth and defence. dwarfAO exhibited a down-regulation of genes involved in the control of plant growth (brassinosteroids, phenylpropanoids, lignin) and an up-regulation of genes in plant defence (glucosinolates, cyanogenic glycosides, glutathione-S-transferase and ascorbate/glutathione). Gibberellins and brassinosteroids are plant hormones which are required for growth and development. Commonly associated with a dwarf phenotype is a reduction in either of these hormones, plants which are unable to perceive brassinosteroids exhibit typical phenotypes which include the dwarf phenotype.31 The brassinosteroids have been reported to be involved in organ growth, cell expansion, cell division and responses to abiotic and biotic stresses.32 Gene expression analysis from Mapman reveals a down-regulation in the bin representing brassinosteroids for the following genes; Rotundifolia3 (at4g36380), Sterol methyltransferase2 (at1g20330), 7RED (at1g50430) and multiple hits which correspond to brassinosteroid metabolism. For example, ROTUNDIFOLIA3 encodes an enzyme to catalyse C-23 hydroxylation of several brassinosteroids which is in fact two steps shorter than the conventional brassionsteroid pathway,32,33 this gene is down-regulated in dwarfAO.

Bottom Line: This variation was used to identify three extreme contrasting accessions for further analysis.A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism.In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress.

View Article: PubMed Central - PubMed

Affiliation: Centre for Biological Sciences, Institute for Life Sciences, University of Southampton , Southampton, SO17 1BJ, UK.

ABSTRACT
Watercress (Nasturtium officinale R. Br.) is a nutrient intense, leafy crop that is consumed raw or in soups across the globe, but for which, currently no genomic resources or breeding programme exists. Promising morphological, biochemical and functional genomic variation was identified for the first time in a newly established watercress germplasm collection, consisting of 48 watercress accessions sourced from contrasting global locations. Stem length, stem diameter and anti-oxidant (AO) potential varied across the accessions. This variation was used to identify three extreme contrasting accessions for further analysis. Variation in global gene expression was investigated using an Affymetrix Arabidopsis ATH1 microarray gene chip, using the commercial control (C), an accession selected for dwarf phenotype with a high AO potential (dwarfAO, called 'Boldrewood') and one with high AO potential alone. A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism. In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress. This study provides the first analysis of natural variation across the watercress genome and has identified important underpinning information for future breeding for enhanced anti-carcinogenic properties and morphology traits in this nutrient-intense crop.

No MeSH data available.


Related in: MedlinePlus