Blumea balsamifera
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA728381 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14477926_1.fastq.gz | Fastqsanger.gz | |||
| SRR14477926_2.fastq.gz | Fastqsanger.gz |
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Project description:Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses.
2010-12-31 | GSE21171 | GEO
Project description:Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses. 72 arrays total. 6 genotypes, 2 time points. 2 water regimes. 3 biological replicates per treatment
2010-12-31 | E-GEOD-21171 | biostudies-arrayexpress
Project description:Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genome-wide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intra-provenance cross (north-north cross, 58th parallel) and an inter-provenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a wide-spread North American forest tree. Results: A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar’s 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the inter-provenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar’s distribution, and higher photosynthetic assimilation rates and water-use efficiency at high-latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs, may in fact represent efficient adaptive variations against fast-evolving pathogens.
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