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Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection.

Thumma BR, Sharma N, Southerton SG - BMC Genomics (2012)

Bottom Line: Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments.Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants.Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Plant Industry, Clunies Ross Street, Acton, ACT, Australia. reddy.thumma@csiro.au

ABSTRACT

Background: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection.

Results: We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments.

Conclusions: Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study.

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Leaf water relations and stomatal conductance in response to water deficit. a). Readings taken 30 days after stress treatment (sampling 1); b). Readings taken 52 days after stress treatment (sampling 2). Stomatal conductance was measured 10 days after stress treatment. Error bars are standard errors of mean (SEM).K–Katherine; M-Mt Isa; P-Petford.
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Figure 1: Leaf water relations and stomatal conductance in response to water deficit. a). Readings taken 30 days after stress treatment (sampling 1); b). Readings taken 52 days after stress treatment (sampling 2). Stomatal conductance was measured 10 days after stress treatment. Error bars are standard errors of mean (SEM).K–Katherine; M-Mt Isa; P-Petford.

Mentions: Leaf water relations were measured on samples collected 30 days (sampling 1) and 52 days (sampling 2) after the imposition of stress treatment. Between the two sampling periods, measurements of water relations (pre-dawn water potential, osmotic potential and turgor pressure) were very similar in control seedlings (Figure 1a, b). However, in stressed seedlings highly significant differences were observed for these traits between the two sampling periods. Within a treatment at both sampling periods, no significant differences were observed between the populations for any of the water relation traits measured (Figure 1a, b). The differences between control and stressed seedlings were much more pronounced 52 days after the imposition of the stress treatment (sampling 2). After 30 days pre-dawn water potentials had decreased to −0.67 MPa in stressed seedlings compared to −0.47 MPa in controls. By 52 days pre-dawn water potentials had fallen to −2.89 MPa and negative turgor pressures were observed in stressed seedlings while in controls these traits were similar to those in sampling 1.


Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection.

Thumma BR, Sharma N, Southerton SG - BMC Genomics (2012)

Leaf water relations and stomatal conductance in response to water deficit. a). Readings taken 30 days after stress treatment (sampling 1); b). Readings taken 52 days after stress treatment (sampling 2). Stomatal conductance was measured 10 days after stress treatment. Error bars are standard errors of mean (SEM).K–Katherine; M-Mt Isa; P-Petford.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472208&req=5

Figure 1: Leaf water relations and stomatal conductance in response to water deficit. a). Readings taken 30 days after stress treatment (sampling 1); b). Readings taken 52 days after stress treatment (sampling 2). Stomatal conductance was measured 10 days after stress treatment. Error bars are standard errors of mean (SEM).K–Katherine; M-Mt Isa; P-Petford.
Mentions: Leaf water relations were measured on samples collected 30 days (sampling 1) and 52 days (sampling 2) after the imposition of stress treatment. Between the two sampling periods, measurements of water relations (pre-dawn water potential, osmotic potential and turgor pressure) were very similar in control seedlings (Figure 1a, b). However, in stressed seedlings highly significant differences were observed for these traits between the two sampling periods. Within a treatment at both sampling periods, no significant differences were observed between the populations for any of the water relation traits measured (Figure 1a, b). The differences between control and stressed seedlings were much more pronounced 52 days after the imposition of the stress treatment (sampling 2). After 30 days pre-dawn water potentials had decreased to −0.67 MPa in stressed seedlings compared to −0.47 MPa in controls. By 52 days pre-dawn water potentials had fallen to −2.89 MPa and negative turgor pressures were observed in stressed seedlings while in controls these traits were similar to those in sampling 1.

Bottom Line: Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments.Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants.Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Plant Industry, Clunies Ross Street, Acton, ACT, Australia. reddy.thumma@csiro.au

ABSTRACT

Background: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq) to identify the candidate genes and alleles and to explore the evolutionary signatures of selection.

Results: We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO) enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs) were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks). The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5) apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments.

Conclusions: Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene categories among the positively selected genes reveals the past selection pressures experienced by the populations used in this study.

Show MeSH
Related in: MedlinePlus