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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) Up‐ and down‐regulated gene expression for control (C), high anti‐oxidant (AO) and dwarf, high AO accession (dwarfAO). (b) Mean expression ratio for total gene expression of C, AO and dwarfAO, where green represents down‐regulation, pink represents an up‐regulation of genes in accession C when RMA normalisation to the median was performed. This provides clear visualisation of differing expression of specific genes between three watercress accessions. For example, a gene which is down‐regulated in C will have a green line despite being up‐ or down‐regulated in AO and dwarfAO due to the colour of the line being dependent on expression in C. This aids the visualisation of the change in expression without having to trace the accession back to C. (c) Hierarchical clustering of changes in transcript abundance for C and AO and dwarfAO, performed using TMeV software from normalised expression ratio data. Lilac triangles represent seven different clusters, colour scale indicates signal normalised ratios (red = up‐regulated genes, blue = down‐regulated genes). Only genes with ANOVA significance p ≤ 0.05 are shown.
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fig2: (a) Up‐ and down‐regulated gene expression for control (C), high anti‐oxidant (AO) and dwarf, high AO accession (dwarfAO). (b) Mean expression ratio for total gene expression of C, AO and dwarfAO, where green represents down‐regulation, pink represents an up‐regulation of genes in accession C when RMA normalisation to the median was performed. This provides clear visualisation of differing expression of specific genes between three watercress accessions. For example, a gene which is down‐regulated in C will have a green line despite being up‐ or down‐regulated in AO and dwarfAO due to the colour of the line being dependent on expression in C. This aids the visualisation of the change in expression without having to trace the accession back to C. (c) Hierarchical clustering of changes in transcript abundance for C and AO and dwarfAO, performed using TMeV software from normalised expression ratio data. Lilac triangles represent seven different clusters, colour scale indicates signal normalised ratios (red = up‐regulated genes, blue = down‐regulated genes). Only genes with ANOVA significance p ≤ 0.05 are shown.

Mentions: Figure 2a explores the commonalities between gene lists of significantly different expression between the three accessions of interest, i.e. how many genes in common were up- or down-regulated between these three accessions. This would give an indication of the similarity of these three accessions to each other (control C; high AO; AO and dwarf high AO; dwarfAO). The up-regulation of genes was filtered on expression above 0 and the down-regulation of genes filtered on expression below 0 after log2 had been applied. The examination of up- and down-regulated genes was conducted on lines C, AO and dwarfAO. Accession C and AO had an up-regulation of 80 genes in common whilst only 36 genes were up-regulated in common between accession C and dwarfAO, between accession AO and dwarfAO 63 genes were in common. dwarfAO had the highest number of genes up-regulated with 189 genes in total whilst AO and C had 177 genes. Interestingly there were 0 genes in common for all three accessions (Figure 2a). It is evident that the accessions C, AO and dwarfAO differ at the level of the transcriptome as illustrated in the gene expression output from microarray analysis in Figure 2b, dwarfAO demonstrating the most distinct difference.


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) Up‐ and down‐regulated gene expression for control (C), high anti‐oxidant (AO) and dwarf, high AO accession (dwarfAO). (b) Mean expression ratio for total gene expression of C, AO and dwarfAO, where green represents down‐regulation, pink represents an up‐regulation of genes in accession C when RMA normalisation to the median was performed. This provides clear visualisation of differing expression of specific genes between three watercress accessions. For example, a gene which is down‐regulated in C will have a green line despite being up‐ or down‐regulated in AO and dwarfAO due to the colour of the line being dependent on expression in C. This aids the visualisation of the change in expression without having to trace the accession back to C. (c) Hierarchical clustering of changes in transcript abundance for C and AO and dwarfAO, performed using TMeV software from normalised expression ratio data. Lilac triangles represent seven different clusters, colour scale indicates signal normalised ratios (red = up‐regulated genes, blue = down‐regulated genes). Only genes with ANOVA significance p ≤ 0.05 are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: (a) Up‐ and down‐regulated gene expression for control (C), high anti‐oxidant (AO) and dwarf, high AO accession (dwarfAO). (b) Mean expression ratio for total gene expression of C, AO and dwarfAO, where green represents down‐regulation, pink represents an up‐regulation of genes in accession C when RMA normalisation to the median was performed. This provides clear visualisation of differing expression of specific genes between three watercress accessions. For example, a gene which is down‐regulated in C will have a green line despite being up‐ or down‐regulated in AO and dwarfAO due to the colour of the line being dependent on expression in C. This aids the visualisation of the change in expression without having to trace the accession back to C. (c) Hierarchical clustering of changes in transcript abundance for C and AO and dwarfAO, performed using TMeV software from normalised expression ratio data. Lilac triangles represent seven different clusters, colour scale indicates signal normalised ratios (red = up‐regulated genes, blue = down‐regulated genes). Only genes with ANOVA significance p ≤ 0.05 are shown.
Mentions: Figure 2a explores the commonalities between gene lists of significantly different expression between the three accessions of interest, i.e. how many genes in common were up- or down-regulated between these three accessions. This would give an indication of the similarity of these three accessions to each other (control C; high AO; AO and dwarf high AO; dwarfAO). The up-regulation of genes was filtered on expression above 0 and the down-regulation of genes filtered on expression below 0 after log2 had been applied. The examination of up- and down-regulated genes was conducted on lines C, AO and dwarfAO. Accession C and AO had an up-regulation of 80 genes in common whilst only 36 genes were up-regulated in common between accession C and dwarfAO, between accession AO and dwarfAO 63 genes were in common. dwarfAO had the highest number of genes up-regulated with 189 genes in total whilst AO and C had 177 genes. Interestingly there were 0 genes in common for all three accessions (Figure 2a). It is evident that the accessions C, AO and dwarfAO differ at the level of the transcriptome as illustrated in the gene expression output from microarray analysis in Figure 2b, dwarfAO demonstrating the most distinct difference.

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