Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi
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Date
Authors
Reeksting, Bianca J.
Olivier, Nicholas Abraham
Van den Berg, Noelani
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
BACKGROUND : Avocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation
to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree
death. The decline of orchards infected with P. cinnamomi occurs much faster when exposed to flooding, even if
flooding is only transient. Flooding is a multifactorial stress compromised of several individual stresses, making
breeding and selection for tolerant varieties challenging. With more plantations occurring in marginal areas, with
imperfect irrigation and drainage, understanding the response of avocado to these stresses will be important for
the industry.
RESULTS : Maintenance of energy production was found to be central in the response to flooding, as seen by
up-regulation of transcripts related to glycolysis and induction of transcripts related to ethanolic fermentation.
Energy-intensive processes were generally down-regulated, as evidenced by repression of transcripts related to
processes such as secondary cell-wall biosynthesis as well as defence-related transcripts. Aquaporins were found to
be down-regulated in avocado roots exposed to flooding, indicating reduced water-uptake under these conditions.
CONCLUSIONS : The transcriptomic response of avocado to flooding and P. cinnamomi was investigated utilizing
microarray analysis. Differences in the transcriptome caused by the presence of the pathogen were minor
compared to transcriptomic perturbations caused by flooding. The transcriptomic response of avocado to flooding
reveals a response to flooding that is conserved in several species. This data could provide key information that
could be used to improve selection of stress tolerant rootstocks in the avocado industry.
Description
Additional file 1: Table S1. Primers used in the RT-qPCR validation of
the microarray data. The putative identities assigned to each transcript
are listed in the ‘Gene’ column.
Additional file 2: Table S2. RT-qPCR validation of microarray data. Representative arrays chosen for microarray validation. Five transcripts were selected to ensure the microarray data was comparable with other expression profiling methods. Values indicate fold-changes in gene expression.‹
Additional file 3: Table S3. Avocado transcripts found to be up-regulated in the infected treatment (I) compared to the control treatment (C) at 48 h-post flooding (8 days post-infection).
Additional file 4: Figure S1. Comparison of the repressed avocado transcripts in flooded to non-flooded treatments at 22 h post-flooding (A) and 48 h post-flooding (B). Values for transcripts with more than one probe present on the array were first averaged and then subjected to the thresholds to determine differential expression.
Additional file 5: Figure S2. Differential GO-term distribution after enrichment analysis for sequences up-regulated in the 22HF vs. 22HI comparison. The percentages of sequences associated with GO terms showing over-representation in the 22HF vs. 22HI comparison compared to the reference set consisting of all sequences on the array (FDR < 0.05). Only transcripts showing significant differential expression (log2FC > 1, adj. P-value < 0.05) were included in the analysis.
Additional file 6: Figure S3. Differential GO-term distribution after enrichment analysis for sequences up-regulated in the 48HFI vs. 48HC comparison. The percentages of sequences associated with GO terms showing over-representation in the 48HFI vs. 48HC comparison compared to the reference set consisting of all sequences on the array (FDR < 0.05). Only transcripts showing significant differential expression (log2FC > 1, adj. P-value < 0.05) were included in the analysis.};})()
Additional file 2: Table S2. RT-qPCR validation of microarray data. Representative arrays chosen for microarray validation. Five transcripts were selected to ensure the microarray data was comparable with other expression profiling methods. Values indicate fold-changes in gene expression.‹
Additional file 3: Table S3. Avocado transcripts found to be up-regulated in the infected treatment (I) compared to the control treatment (C) at 48 h-post flooding (8 days post-infection).
Additional file 4: Figure S1. Comparison of the repressed avocado transcripts in flooded to non-flooded treatments at 22 h post-flooding (A) and 48 h post-flooding (B). Values for transcripts with more than one probe present on the array were first averaged and then subjected to the thresholds to determine differential expression.
Additional file 5: Figure S2. Differential GO-term distribution after enrichment analysis for sequences up-regulated in the 22HF vs. 22HI comparison. The percentages of sequences associated with GO terms showing over-representation in the 22HF vs. 22HI comparison compared to the reference set consisting of all sequences on the array (FDR < 0.05). Only transcripts showing significant differential expression (log2FC > 1, adj. P-value < 0.05) were included in the analysis.
Additional file 6: Figure S3. Differential GO-term distribution after enrichment analysis for sequences up-regulated in the 48HFI vs. 48HC comparison. The percentages of sequences associated with GO terms showing over-representation in the 48HFI vs. 48HC comparison compared to the reference set consisting of all sequences on the array (FDR < 0.05). Only transcripts showing significant differential expression (log2FC > 1, adj. P-value < 0.05) were included in the analysis.};})()
Keywords
Microarray, Hypoxia, Aquaporins, Glycolysis, Avocado (Persea americana), Phytophthora cinnamomi, Root rot, Flooding
Sustainable Development Goals
Citation
Reeksting, BJ, Olivier, NA & Van den Berg, N 2016, 'Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi', BMC Plant Biology, vol. 16, art. #205, pp. 1-19.