Poplar genome sequence: functional genomics in an ecologically dominant plant species

Brunner, Amy M.; Busov, Victor; Strauss, Steven H.

doi:10.1016/j.tplants.2003.11.006

Cited by 284 publications

(170 citation statements)

References 53 publications

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“…Previous studies revealed that Populus genome had undergone at least three rounds of genome-wide duplications followed by multiple segmental duplication, tandem duplication, and transposition events such as retroposition and replicative transposition [5,68]. Among them, the segmental duplication associated with the salicoid duplication event that occurred 65 million years (Ma) ago significantly contribute to the amplification of many multi-gene families [61,69-71].…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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“…More recently it has joined the league of model organisms (Brunner et al, 2004;Taylor, 2002;Wullschleger et al, 2002) and is the first tree to have a fully sequenced genome (Tuskan et al, 2006). Microarrays constructed from Populus EST collections provide the opportunity to probe the transcriptional response to ozone in Populus, a perennial deciduous tree.…”

Section: Introductionmentioning

confidence: 99%

The physiological, transcriptional and genetic responses of an ozone- sensitive and an ozone tolerant poplar and selected extremes of their F 2 progeny

Street

Tallis

James

et al. 2011

Environmental Pollution

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Ozone-responsive transcriptional changes and genetic control were studied in Populus plants with contrasting ozone sensitivity. a r t i c l e i n f o a b s t r a c tRelatively little is known about the transcriptional response or genetic control of response and adaptation of trees to tropospheric ozone exposure. Such understanding is needed as up to 50% of forests, globally, may be subjected to phytotoxic concentrations of ozone. The physiological, transcriptional and genetic response to ozone was examined in Populus trichocarpa and P. deltoides, which show extreme sensitivity and tolerance to ozone, respectively. Using an inbred F 2 mapping population derived from these two species, we mapped quantitative trait loci (QTL) for traits associated with ozone response, examined segregation of the transcriptional response to ozone and co-located genes showing divergent responses between tolerant and sensitive genotypes with QTL. QTL were identified linking detrimental effects of ozone with leaf and biomass traits and differential responses were found for key genes involved in ethylene production and response.

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“…However, functional dissection of adaptive traits through the development of segregating mapping populations is hampered by the long generation times of trees (e.g., Brunner et al 2004;Neale and Savolainen 2004). An alternative approach is to investigate patterns of genetic variation in natural populations to detect possible statistical associations between phenotypic traits and genetic markers segregating in a population, so-called association mapping (Gaut and Long 2003;Neale and Savolainen 2004).…”

mentioning

confidence: 99%

Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula)

Ingvarsson¹,

García²,

Hall³

et al. 2006

Genetics

165

162

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The initiation of growth cessation and dormancy represents a critical ecological and evolutionary tradeoff between survival and growth in most forest trees. The most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset of these trees in a growth chamber experiment. Buds set showed significant clinal variation with latitude, explaining 90% of the population variation in bud set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of an adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions with excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation can be useful for identifying sites putatively involved in local adaptation.

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Poplar genome sequence: functional genomics in an ecologically dominant plant species

Cited by 284 publications

References 53 publications

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

The physiological, transcriptional and genetic responses of an ozone- sensitive and an ozone tolerant poplar and selected extremes of their F 2 progeny

Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula)

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