Populus trichocarpa (Black Cottonwood) As a Model for Plant Genomic Studies: A Review

Numerous plants have been the subject of recent research in the pharmacological, cosmetic, and agro-alimentary domains due to their chemical composition and multiple therapeutic capabilities. Populus trichocarpa is one of the most common trees found in deciduous forests (Salicaceae family). The current study examines Populus trichocarpa as a model plant for plant genomics research, as well as the most recent findings on phytochemical composition and medicinal potential. More than 45,000 potential protein-coding genes were discovered. In the Populus genome, a whole-genome duplication event was discovered, with approximately 8,000 pairs of duplicated genes surviving. Furthermore, the reproductive biology of Populus provides new opportunities and challenges in the study and analysis of natural genetic and phenotypic variation. In the present review, we endeavour to describe and compile the available knowledge on Populus trichocarpa as a model plant for genomic investigations and to bring that material up to date of Populus trichocarpa's phytochemical and medicinal properties.

Promising introduced Black Cottonwood species for bioenergy and forage production

The winter-hardy introduced North American Populus trichocarpa Torr. & Gray is of particular interest. The results of the study of some clones of poplar on the experimental sites of the Voronezh region are presented. It was found that the rootability of standard stem cuttings of poplar was 98-100%. The survival of plants during the first 3-5 years varied from 75 to 100%. The growing season in different years was 135-146 days. The yield of standard cuttings on root-cutting plantations under favorable conditions and optimal age varied in different clones from 592 000 to 1 380 000 pieces per ha. The wood stock at the age of economical exploitability (~25 years) reached 400 m3/ha, while the stock of local balsam poplar at the same age reached 220 m3/ha. The green mass of leaves contained 0.22-0.28 feed units/kg. In addition, the content of digestible protein, calcium, phosphorus, carotene, crude protein, crude fat, crude fiber, nitrogen-free extractives and ash was determined. In general, studied clones of P. trichocarpa can be used in short rotation coppices for bioenergy and feed production, as well as in reclamation plantings. Clones of the poplar can be used in hybridization with black poplars to increase their winter hardiness.

Using Discrete-Point LiDAR to Classify Tree Species in the Riparian Pacific Northwest, USA

Practical methods for tree species identification are important for both land management and scientific inquiry. LiDAR has been widely used for species mapping due to its ability to characterize 3D structure, but in structurally complex Pacific Northwest forests, additional research is needed. To address this need and to determine the feasibility of species modeling in such forests, we compared six approaches using five algorithms available in R’s lidR package and Trimble’s eCognition software to determine which approach most consistently identified individual trees across a heterogenous riparian landscape. We then classified segments into Douglas fir (Pseudotsuga menziesii), black cottonwood (Populus balsamifera ssp. trichocarpa), and red alder (Alnus rubra). Classification accuracies based on the best-performing segmentation method were 91%, 92%, and 84%, respectively. To our knowledge, this is the first study to investigate tree species modeling from LiDAR in a natural Pacific Northwest forest, and the first to model Pacific Northwest species at the landscape scale. Our results suggest that LiDAR alone may provide enough information on tree species to be useful to land managers in limited applications, even under structurally challenging conditions. With slight changes to the modeling approach, even higher accuracies may be possible.

A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

Benzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

First report of Armillaria cepistipes causing root disease on Populus trichocarpa (black cottonwood) in Oregon, USA.

Populus trichocarpa Torr. and Gray (black cottonwood) is an economically and ecologically important tree species native to western North America. It serves as a model tree species in biology and genetics due to its relatively small genome size, rapid growth, and early reproductive maturity (Jansson and Douglas 2007). Black cottonwood is susceptible to root rot caused by at least one species of Armillaria (Raabe 1962), a globally distributed genus that exhibits diverse ecological behaviors (Klopfenstein et al. 2017) and infects numerous woody plant species (Raabe 1962). However, several Armillaria spp. have been isolated from Populus spp. in North America (Mallet 1990), and the most recent report of Armillaria on P. trichocarpa used the now ambiguated name A. mellea (Vahl.) Quel. (see Raabe 1962). In April 2016, mycelial fans and rhizomorphs of an unknown Armillaria species (isolate WV-ARR-3) were collected from P. trichocarpa in a riparian hardwood stand ca. 5.5 km east of Springfield, Oregon, USA (44°3'21.133"N, 122°49'39.935"W). The host was dominant in the canopy, large in diameter (ca. 90-cm dbh) relative to neighboring trees, and exhibited minimal crown dieback (ca. < 5%). A mycelial fan was observed destroying living cambium beneath the inner bark, indicating pathogenicity. The isolate was cultured on malt extract medium (3% malt extract, 3% dextrose, 1% peptone, and 1.5 % agar) and identified as A.cepistipes on the basis of somatic pairing tests and translation elongation factor 1α (tef1) sequences (GenBank Accession No. MK172784). DNA extraction, PCR, and tef1 sequencing followed protocols of Elías-Román et al. (2018). From nine replications of somatic incompatibility tests (18 tester isolates representing six North American Armillaria spp.), the isolate showed high intraspecific compatibility (colorless antagonism) with three A. cepistipes tester isolates (78%), but low compatibility with the other Armillaria spp. (0 – 33%) that occur in the region. Isolate WV-ARR-3 yielded tef1 sequences with a 99% identity to A. cepistipes (GenBank Accession Nos. JF313115 and JF313121). A second isolate (WV-ARR-1; GenBank Accession No. MK172783) with a nearly identical sequence was collected from a maturing P. trichocarpa in a riparian stand ca. 8 km northeast of Monroe, Oregon (44°21’47.57”N, 123°13’14.415”W) along the Willamette River, downstream from the McKenzie river tributary where WV-ARR-3 was collected. Armillaria cepistipes has been reported on Alnus rubra (red alder) in Washington, USA (Banik et al. 1996) and on broad-leaved trees in British Columbia, Canada (Allen et al. 1996). It is generally considered to be a weak pathogen on broad-leaved trees in the Pacific Northwest, but it is also associated with pathogenicity on both coniferous and deciduous trees in Europe (e.g., Lygis et al. 2005). However, a recent phylogenetic study suggested that North American A. cepistipes is phylogenetically distinct from Eurasian A. cepistipes (Klopfenstein et al. 2017), butadditional studies are needed to determine the formal taxonomic status of North American A. cepistipes. To our knowledge, A. cepistipes has not been previously confirmed on P. trichocarpa in the U.S.A. or formally reported as a pathogen of any Populus species in North America. Continued studies are needed to determine the distribution, host range, and ecological role of A. cepistipes in riparian forests of the Pacific Northwest, while monitoring its populations under changing climates.

Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development

Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.

The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)

SummaryEntering and exiting winter dormancy presents important trade-offs between growth and survival at northern latitudes and many forest trees display local adaptation across latitude. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth.We performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment.We uncovered 629 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa.A comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis that autumn phenology transitions.

Genome-wide identification of poplar malectin/malectin-like domain-containing proteins and in-silico expression analyses find novel candidates for signaling and regulation of wood development

Background: Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF1721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their in-silico expression and co-expression networks.Results: P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways.Conclusion: P. trichocarpa MD genes exhibit a variety of domain organizations, and include genes apparently specific to Populus, as well as genes with potential involvement in signaling pathways regulating secondary wall formation.