Asymmetrical natural hybridization between Populus deltoides and P. balsamifera (Salicaceae)This note is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

Natural hybridization has long been recognized as a means for gene flow between species and has important evolutionary consequences. Although hybridization is generally considered to be symmetrical, with both hybridizing species being equally likely to be the male or female parent, several studies have demonstrated the presence of asymmetrical hybridization and introgression from one species to the other. We investigated the direction of natural hybridization between two sympatric forest tree species in North America ( Populus deltoides Bartr. ex Marsh. and Populus balsamifera L.) using species-specific single nucleotide polymorphism (SNP) markers in both the nuclear and chloroplast genomes. All natural hybrid individuals, identified from morphological traits, had nuclear alleles corresponding to both parental species, while the chloroplast genotypes showed similarity to P. deltoides, indicating asymmetrical hybridization with P. deltoides as the maternal and P. balsamifera as the paternal donor species. This observed asymmetrical hybridization may be attributable to cytonuclear interactions.

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Species-specific single nucleotide polymorphism markers for detecting hybridization and introgression in poplarThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

Canadian Journal of Botany ◽

10.1139/b07-069 ◽

2007 ◽

Vol 85 (11) ◽

pp. 1082-1091 ◽

Cited By ~ 23

Author(s):

Patrick G. Meirmans ◽

Manuel Lamothe ◽

Pierre Périnet ◽

Nathalie Isabel

Keyword(s):

Single Nucleotide Polymorphism ◽

Native Species ◽

Populus Deltoides ◽

Hybrid Poplar ◽

Restriction Enzymes ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Important Species ◽

Species Specific

The increasing use of exotic and hybrid poplar species in forestry and the lack of genetic barriers between most poplar species may present a risk to the genetic integrity of native poplar species. To monitor any spontaneous hybridization and (or) introgression from exotics into native species, it is essential to have a system for the quick and reliable identification of species. We developed a set of single nucleotide polymorphism (SNP) markers that allows the distinction between five commercially important species of poplar ( Populus balsamifera L., Populus deltoides Marsh., Populus trichocarpa Toor. ex Gray, Populus nigra L., and Populus maximowiczii Henry) and their hybrids. Six genomic regions spanning 6.1 kb were screened at the DNA sequence level to search for discriminating SNPs among the five species. A total of 245 SNPs and indels were found, 86 of which were species specific. A subset of 12 species-specific SNPs was chosen for use with high-throughput SNPstream technology. In addition, 32 species-specific SNPs and indels were found that can be assayed using restriction enzymes. Application of the developed markers to a set of hybrid clones showed that the markers are not only useful for monitoring introgression but also for the verification of breeding material.

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Dense Genetic Linkage Maps of Three Populus Species (Populus deltoides, P. nigra and P. trichocarpa) Based on AFLP and Microsatellite Markers

Genetics ◽

10.1093/genetics/158.2.787 ◽

2001 ◽

Vol 158 (2) ◽

pp. 787-809 ◽

Cited By ~ 1

Author(s):

Maria-Teresa Cervera ◽

Véronique Storme ◽

Bart Ivens ◽

Jaqueline Gusmão ◽

Ben H Liu ◽

...

Keyword(s):

Populus Deltoides ◽

Female Parent ◽

Aflp Markers ◽

Linkage Maps ◽

Important Species ◽

Mapping Strategy ◽

Sequence Tagged Sites ◽

Fundamental Research ◽

Populus Species ◽

The Individual

Abstract Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 × P. nigra cv. Ghoy and P. deltoides cv. S9-2 × P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.

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Bark traits, decomposition and flammability of Australian forest trees

Australian Journal of Botany ◽

10.1071/bt16258 ◽

2017 ◽

Vol 65 (4) ◽

pp. 327 ◽

Cited By ~ 4

Author(s):

Saskia Grootemaat ◽

Ian J. Wright ◽

Peter M. van Bodegom ◽

Johannes H. C. Cornelissen ◽

Veronica Shaw

Keyword(s):

Forest Tree ◽

Remarkable Feature ◽

Interspecific Differences ◽

Eucalypt Plantations ◽

Physical Traits ◽

Key Driver ◽

Multiple Species ◽

Species Specific ◽

First Time ◽

Different Tissues

Bark shedding is a remarkable feature of Australian trees, yet relatively little is known about interspecific differences in bark decomposability and flammability, or what chemical or physical traits drive variation in these properties. We measured the decomposition rate and flammability (ignitibility, sustainability and combustibility) of bark from 10 common forest tree species, and quantified correlations with potentially important traits. We compared our findings to those for leaf litter, asking whether the same traits drive flammability and decomposition in different tissues, and whether process rates are correlated across tissue types. Considerable variation in bark decomposability and flammability was found both within and across species. Bark decomposed more slowly than leaves, but in both tissues lignin concentration was a key driver. Bark took longer to ignite than leaves, and had longer mass-specific flame durations. Variation in flammability parameters was driven by different traits in the different tissues. Decomposability and flammability were each unrelated, when comparing between the different tissue types. For example, species with fast-decomposing leaves did not necessarily have fast-decomposing bark. For the first time, we show how patterns of variation in decomposability and flammability of bark diverge across multiple species. By taking species-specific bark traits into consideration there is potential to make better estimates of wildfire risks and carbon loss dynamics. This can lead to better informed management decisions for Australian forests, and eucalypt plantations, worldwide.

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Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

10.21203/rs.3.rs-152687/v1 ◽

2021 ◽

Author(s):

ZHIYONG Chen ◽

Yancen He ◽

Yasir Iqbal ◽

Yanlan Shi ◽

Hongmei Huang ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Genetic Relationships ◽

Female Parent ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Breeding Programs ◽

Sequencing Method ◽

Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

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Species-Specific Marker Discovery in Tilapia

Scientific Reports ◽

10.1038/s41598-019-48339-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 9

Author(s):

Mochamad Syaifudin ◽

Michaël Bekaert ◽

John B. Taggart ◽

Kerry L. Bartie ◽

Stefanie Wehner ◽

...

Keyword(s):

Phylogenetic Trees ◽

Restriction Site ◽

De Novo ◽

Snp Markers ◽

Specific Marker ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Species Analysis ◽

Species Specific ◽

Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

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Evaluation of O3 Effects on Cumulative Photosynthetic CO2 Uptake in Seedlings of Four Japanese Deciduous Broad-Leaved Forest Tree Species Based on Stomatal O3 Uptake

Forests ◽

10.3390/f10070556 ◽

2019 ◽

Vol 10 (7) ◽

pp. 556 ◽

Cited By ~ 2

Author(s):

Masahiro Yamaguchi ◽

Yoshiyuki Kinose ◽

Hideyuki Matsumura ◽

Takeshi Izuta

Keyword(s):

Leaf Area ◽

Tree Species ◽

Net Primary Production ◽

Forest Tree ◽

Co2 Uptake ◽

Growing Seasons ◽

Whole Plant ◽

Broad Leaved Forest ◽

Leaf Level ◽

Species Specific

The current level of tropospheric ozone (O3) is expected to reduce the net primary production of forest trees. Here, we evaluated the negative effects of O3 on the photosynthetic CO2 uptake of Japanese forest trees species based on their cumulative stomatal O3 uptake, defined as the phytotoxic O3 dose (POD). Seedlings of four representative Japanese deciduous broad-leaved forest tree species (Fagus crenata, Quercus serrata, Quercus mongolica var. crispula and Betula platyphylla var. japonica) were exposed to different O3 concentrations in open-top chambers for two growing seasons. The photosynthesis–light response curves (A-light curves) and stomatal conductance were measured to estimate the leaf-level cumulative photosynthetic CO2 uptake (ΣPn_est) and POD, respectively. The whole-plant-level ΣPn_est were highly correlated with the whole-plant dry mass increments over the two growing seasons. Because whole-plant growth is largely determined by the amount of leaf area per plant and net photosynthetic rate per leaf area, this result suggests that leaf-level ΣPn_est, which was estimated from the monthly A-light curves and hourly PPFD, could reflect the cumulative photosynthetic CO2 uptake of the seedlings per unit leaf area. Although the O3-induced reductions in the leaf-level ΣPn_est were well explained by POD in all four tree species, species-specific responses of leaf-level ΣPn_est to POD were observed. In addition, the flux threshold appropriate for the linear regression of the responses of relative leaf-level ΣPn_est to POD was also species-specific. Therefore, species-specific responses of cumulative photosynthetic CO2 uptake to POD could be used to accurately evaluate O3 impact on the net primary production of deciduous broad-leaved trees.

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Extent and patterns of hybridization among the three species of Populus that constitute the riparian forest of southern Alberta, Canada

Canadian Journal of Botany ◽

10.1139/b03-135 ◽

2004 ◽

Vol 82 (2) ◽

pp. 253-264 ◽

Cited By ~ 49

Author(s):

Kevin D Floate

Keyword(s):

Leaf Morphology ◽

Populus Deltoides ◽

Riparian Forest ◽

Elevational Gradient ◽

Future Research ◽

Hybrid Zones ◽

Populus Balsamifera ◽

Balsam Poplar ◽

Southern Alberta ◽

Unique Nature

Three species of Populus (Salicaceae) overlap and hybridize in southern Alberta, Canada. Variation in leaf morphology throughout the region identifies five genetically distinct zones. The drainage of the Oldman River contains a pure zone of balsam poplar (Populus balsamifera L.), a pure zone of plains cottonwood (Populus deltoides Marsh.), plus overlap and hybrid zones of balsam poplar narrowleaf cottonwood (Populus angustifolia James) and balsam poplar narrowleaf cottonwood plains cottonwood. The drainage of the Red Deer River contains a pure zone of balsam poplar, a pure zone of plains cottonwood, plus an overlap and hybrid zone of balsam poplar plains cottonwood. Zones on both drainages coincide with an elevational gradient. Overlap and hybrid zones extend at least 700 river km (the length obtained by measuring distances between sites of hybridization on a river and its tributaries) combined across the two drainages. Principal components analyses on leaf morphology identify a pattern of bidirectional intro gression between sect. Tacamahaca (balsam poplar, narrowleaf cottonwood) species. These analyses also identify a pattern of unidirectional introgression between Tacamahaca and sect. Aigeiros (plains cottonwood) species, with F1 hybrids backcrossing only with the Tacamahaca parent. This pattern of unidirectional introgression subsequently was assessed and supported with data from the drainages of Ashley Creek and the Ogden River, Utah, which contain hybrid and overlap zones between narrowleaf cottonwood (Tacamahaca) and Fremont cottonwood, Populus fremontii S. Watson (Aigeiros). Given its unique nature in terms of extent, health, and composition, and given the effect of plant hybrid zones on the ecology and evolution of their associated organisms, it is hoped that the current study will facilitate future research targeting conservation of this riparian forest in its full genetic complexity.Key words: Populus, hybridization, riparian, cottonwood, introgression.

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Marker allozyme genes and alleles for differentiation of Populus deltoides, P. nigra, P. maximowiczii, and their interspecific hybrids

Canadian Journal of Botany ◽

10.1139/b90-125 ◽

1990 ◽

Vol 68 (5) ◽

pp. 990-998 ◽

Cited By ~ 24

Author(s):

Om P. Rajora

Keyword(s):

Interspecific Hybrids ◽

Populus Deltoides ◽

Single Pair ◽

Enzyme Electrophoresis ◽

Starch Gel Electrophoresis ◽

Root Tips ◽

Controlled Crosses ◽

Populus Species ◽

Species Specific ◽

Allozyme Loci

Horizontal starch gel electrophoresis of enzymes was used to compare the allelic constitution of individuals of Populus deltoides Marsh., P. nigra L., P. maximowiczii Henry, P. ×canadensis Moench, and F1 progeny of controlled crosses. Forty allozyme loci coding for 12 enzyme systems in root tips were observed. Populus deltoides, P. nigra, and P. maximowiczii were genetically distinct from each other. Each of these species had unique alleles at many loci, and one or two of these species also had some species-specific genes. Populus deltoides, P. nigra, and P. maximowiczii could be distinguished by mutually exclusive or unique alleles at any of the four allozyme loci Aco-2, Lap-1, Lap-2, and Pgi-2. Additionally, allozymes of Pgm-1, 6-Pgd-2, 6-Pgd-4, and 6-Pgd-5 could be used as markers to distinguish P. deltoides from P. nigra and P. maximowiczii, allozymes of Mdh-2, Per-3, Pgm-2, and Pgm-3 to distinguish P. nigra from P. deltoïdes and P. maximowiczii, and allozymes of Got-1, Got-4, and Pgi-1 to distinguish P. maximowiczii from P. deltoides and P. nigra. The observed marker allozyme genes and alleles can be effectively used for discriminating among the three Populus species and their interspecific hybrids, and identification and verification of paternity of progeny of single-pair and interspecific pollen-mix controlled crosses. Biochemical and molecular markers have significance in genetics, breeding, and systematics of these Populus species. Key words: Populus, allozymes, diagnostic genes and alleles, species and hybrid differentiation, enzyme electrophoresis.

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The discrimination of cottonwood clones in a mature grove along the Oldman River in southern Alberta

Canadian Journal of Botany ◽

10.1139/b99-123 ◽

1999 ◽

Vol 77 (8) ◽

pp. 1084-1094 ◽

Cited By ~ 1

Author(s):

Lori A Gom ◽

Stewart B Rood

Keyword(s):

Interspecific Hybrids ◽

Clonal Propagation ◽

Populus Deltoides ◽

Leaf Shape ◽

Populus Balsamifera ◽

Balsam Poplar ◽

Populus Angustifolia ◽

Southern Alberta ◽

Gall Mite ◽

Oldman River

In southwestern Alberta, the prairie cottonwood (Populus deltoides Bartr.), balsam poplar (Populus balsamifera L.), narrowleaf cottonwood (Populus angustifolia James), and interspecific hybrids provide the foundation of the biologically rich riparian forests. In addition to seedling-based reproduction, these cottonwoods are capable of clonal propagation, the extent of which is poorly understood. To investigate clonality in mature cottonwoods, a method for clone recognition was investigated. Between 1995 and 1997, the morphology and phenology of each tree in a mature cottonwood grove along the Oldman River were characterized. In decreasing order of utility, the characteristics most effective in revealing clones were sex, leaf shape, floral (inflorescence) phenology, and leaf phenology: flushing, senescence, and abscission. Independent traits of poplar bud gall mite (Aceria parapopuli Keifer) susceptibility and trunk architecture were less useful in clone delineation but validated the clonal determinations. Based on the analysis, the grove's 391 trunks (>10 cm diameter) included 115 genotypes, 48 single-trunked individuals, and 67 multiple-trunked clones. The clones (genets) contained from 2 to 53 trunks (ramets). It was found that 88% of trunks belonged to clonal groups, a proportion that was higher than anticipated. The extensive capacity for clonal recruitment should thus be considered in analyses of cottonwood reproductive ecology and cottonwood conservation and restoration programs.Key words: asexual reproduction, clone delineation, cottonwoods, morphology, phenology, Populus.

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Defining endemism levels for biodiversity conservation: tree species in the Atlantic Forest hotspot

10.1101/2020.02.08.939900 ◽

2020 ◽

Author(s):

Renato A.F. Lima ◽

Vinicius Castro Souza ◽

Marinez Ferreira de Siqueira ◽

Hans ter Steege

Keyword(s):

Biodiversity Conservation ◽

Atlantic Forest ◽

Endemic Species ◽

Forest Tree ◽

Conservation Priorities ◽

Target Area ◽

Multiple Sources ◽

Herbarium Data ◽

Data Driven Approach ◽

Species Specific

AbstractEndemic species are important for biodiversity conservation. Yet, quantifying endemism remains challenging because endemism concepts can be too strict (i.e., pure endemism) or too subjective (i.e., near endemism). We propose a data-driven approach to objectively estimate the proportion of records inside a given the target area (i.e., endemism level) that optimizes the separation of near-endemics from non-endemic species. We apply this approach to the Atlantic Forest tree flora using millions of herbarium records retrieved from multiple sources. We first report an updated checklist of 5044 species for the Atlantic Forest tree flora and then we compare how species-specific endemism levels obtained from herbarium data match species-specific endemism accepted by taxonomists. We show that an endemism level of 90% separates well pure and near-endemic from non-endemic species, which in the Atlantic Forest revealed an overall endemism ratio of 45% for its tree flora. We also found that the diversity of pure and near endemics and of endemics and overall species was congruent in space. Our results for the Atlantic Forest reinforce that pure and near endemic species can be combined to quantify regional endemism and therefore to set conservation priorities taking into account endemic species distribution. We provided general guidelines on how the proposed approach can be used to assess endemism levels of regional biotas in other parts of the world.

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