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Population Genetic and Morphological Diversity of Woody Plants

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A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (1 April 2023) | Viewed by 21122

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Special Issue Editors

Dr. Igor Poljak

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Guest Editor

Faculty of Forestry and Wood Technology, University of Zagreb, 10000 Zagreb, Croatia
Interests: population genetics; molecular ecology; microsatellites; morphological variability; conservation genetics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Marilena Idžojtić

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Guest Editor

Institute of Forest Genetics, Dendrology and Botany, Department of Forestry, Faculty of Forestry and Wood Technology, University of Zagreb, HR-10000 Zagreb, Croatia
Interests: dendrology; population genetics; morphological analysis

Special Issue Information

Dear Colleagues,

One of the fundamental questions of evolutionary biology is how basic evolutionary processes affect population diversity. In general, population diversity is the result of several evolutionary processes, including gene flow, mutations, genetic drift, and natural selection. These processes usually do not act individually but rather in combination and thus affect the recent diversity and structure of populations.

Generally speaking, the variability of a species reflects their adaptive evolutionary potential and enables them to better adapt to various environmental conditions and survival in unfavorable environments. Greater diversity makes a species more resilient and better adjusted for survival under changing conditions of stress, which is particularly evident with regard to climate change. Insights into the diversity of populations are one of the basic preconditions for the preservation of biological diversity of an area and of individual species and subspecies.

Over the last few decades, research quantifying population diversity has been intensifying, using various genetic and morphological methods. Genetics is a rapidly progressing area of biological sciences with increasing economic and ecologic relevance in forestry and biodiversity conservation over recent years. Although morphological methods were more utilized in the past, they are still often applied today in studies quantifying population diversity, especially in combination with genetic analyses.

The aim of this Special Issue of Forests is to cover research that includes the application of genetic and morphological analyses in forestry and related plant sciences and pertains to the population diversity of woody plants.

Dr. Igor Poljak
Prof. Dr. Marilena Idžojtić
Guest Editors

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Keywords

woody plants
trees and shrubs
population diversity
population structure
biodiversity
genetic analysis
morphometric analysis

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Published Papers (9 papers)

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30 pages, 5693 KiB

Open AccessArticle

Evolutionary Processes Shaping Postglacial Gene Pools of High-Altitude Forests: Evidence from the Endemic Eucalypts of Tasmania

by Rebecca C. Jones, Peter A. Harrison, Corey J. Hudson, Cate A. Hirst, Alexander T. Matthews, Romuald Rouger, Sascha L. Wise, Julianne M. O’Reilly-Wapstra, Robert J. E. Wiltshire, Gregory J. Jordan, René E. Vaillancourt and Brad M. Potts

Forests 2023, 14(6), 1072; https://doi.org/10.3390/f14061072 - 23 May 2023

Viewed by 1765

Abstract

Climatic changes during the Pleistocene were responsible for dramatic redistributions of plant species worldwide. On the rugged southern hemisphere island of Tasmania, temperature increases following the last glaciation saw upslope migration of climatically suitable species from lowland refugia and the expansion of eucalypt-dominated forests and woodlands in the Central Highlands. We integrate multiple lines of evidence (chloroplast and nuclear DNA markers, seedling morphology, and survival in common garden experiments) from a group of closely related endemic eucalypts (the alpine white gums) to argue that (i) the Central Highlands of the island were colonised by multiple glacial refugia with hybridisation among species and previously separated populations, and (ii) natural selection has filtered the admixed populations, resulting in local adaptation to the harsh sub-alpine environment. Chloroplast haplotype diversity decreased and nuclear microsatellite diversity increased with altitude, chloroplast sharing among taxa was common, and nuclear DNA differentiation of morphologically distinct taxa was lower in the Central Highlands compared with lowland regions. Local adaptation in the highlands was signalled by evidence from (i) a glasshouse trial in which directional selection (Q_ST > F_ST) had shaped seedling morphological trait variation and (ii) population survival differences in 35-year-old reciprocal plantings along the major environmental gradients. We conclude that the evolutionary response of these island endemic trees to past climate change has involved the interplay of both hybridisation and natural selection, highlighting the importance of maintaining species interactions under future climate change. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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13 pages, 2744 KiB

Open AccessArticle

Variation Pattern and Genome-Wide Association Study of Leaf Phenotypic Traits among Ancient Ginkgo biloba L. Populations

by Qi Zhou, Xin Shen and Yingang Li

Forests 2022, 13(11), 1764; https://doi.org/10.3390/f13111764 - 26 Oct 2022

Cited by 1 | Viewed by 1652

Abstract

Ginkgo biloba L., as one of the oldest tree species, is a very important medicinal plant due to the metabolites in its leaves. To explore the variations and genetic regulation of leaf phenotypic traits, 321 samples from 12 ancient populations in the major distribution areas in China were collected for the leaf morphometric analysis, and 126 samples from 9 ancient populations were used for the genome-wide association study (GWAS) of leaf traits. The results showed that the leaf weight (fresh weight and dry weight) and size (areas) varied greatly, while the length:width ratio (LWR) was stable. There were significant differences in leaf traits among different ancient populations (p < 0.01), and population ZJ from eastern China—with a greater leaf weight and size—was ideal for leaf production. Leaf thickness (LT) showed correlations with altitude, longitude and frost-free period, while LWR had a correlation with altitude (p < 0.05). However, the correlations between environmental factors and leaf traits were weak, which may be related to the origin of populations and human activities. A GWAS revealed that 29 single nucleotide polymorphism (SNP) loci and 112 candidate genes related to leaf traits, and Gb_04106, which is related to auxin, may be involved in the genetic regulation of LT. It is speculated that environmental factors may induce leaf morphology of G. biloba by affecting the accumulation of secondary metabolites. The results of this study may provide a theoretical basis for studying the variation pattern and genetic regulation of leaf phenotypes. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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13 pages, 16756 KiB

Open AccessArticle

Chloroplast Genome Variation and Phylogenetic Analyses of Seven Dwarf Ornamental Bamboo Species

by Binao Zhou, Wenjing Yao, Chunce Guo, Lili Bian, Yulong Ding and Shuyan Lin

Forests 2022, 13(10), 1671; https://doi.org/10.3390/f13101671 - 12 Oct 2022

Cited by 3 | Viewed by 1784

Abstract

Dwarf ornamental bamboos are a class of low shrub plants with minor interspecific morphological differences and are difficult to distinguish by traditional classification. In order to identify this type of bamboo species at the molecular level, we sequenced the genomes of the chloroplasts in seven species of dwarf ornamental bamboo: Pleioblastus argenteostriatus (Regel) Nakai, Pleioblastus fortunei (Van Houtte) Nakai, Pleioblastus pygmaeus (Miq.) Nakai, Pleioblastus pygmaeus ‘Disticha’, Sasaella glabra (Nakai) Koidz., Sasaella glabra ‘Albostriata’ and Sasaella kongosanensis ‘Aureostriatus’ using high-throughput sequencing. The quadripartite structure of the chloroplast genomes is typical, with sizes ranging from 139,031 bp (P. argenteostriatus) to 139,759 bp (S. kongosanensis ‘Aureostriatus’). The genomes contain 116 genes, including four rRNA genes, 30 tRNA genes and 82 protein-coding genes. Four hotspots, including ndhI-ndhA, trnC-rpoB, petB and ccsA, and a total of 46 simple sequence repeats (SSRs) were identified as potential variable markers for species delimitation and population structure analysis. The phylogenetic analyses of chloroplast genomes of seven dwarf ornamental bamboos indicates that these bamboo species can be classified into three categories: Sasaella I, Pleioblastus II and Pleioblastus III. Except S. kongosanensis ‘Aureostriatus’, the other six species were distributed into two branches, indicating that both S.glabra and S. glabra ‘Albostriata’ belong to Pleioblastus Nakai genus. There are four mutations on the chloroplast genomes of S. glabra and S. glabra ‘Albostriata’, suggesting that the mutations may contribute to their obvious different leaf morphologies. Our study reveals the chloroplast structural variations and their phylogenetic relationship and mutation dynamics in seven dwarf ornamental bamboos and also facilitates studies on population genetics, taxonomy and interspecific identification in dwarf bamboo plants. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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11 pages, 2784 KiB

Open AccessFeature PaperArticle

Morphometric Analyses of Leaf Shapes in Four Sympatric Mediterranean Oaks and Hybrids in the Algerian Kabylie Forest

by Amel Akli, Zaida Lorenzo, Ricardo Alía, Khellaf Rabhi and Enrique Torres

Forests 2022, 13(4), 508; https://doi.org/10.3390/f13040508 - 25 Mar 2022

Cited by 7 | Viewed by 2604

Abstract

(1) Background: local morphological variation can provide useful information to clarify the role of hybridization in Mediterranean oaks. Accordingly, we have characterized putative hybrids and oak species coexisting in a highly diversified oak forest in Algeria with four native oak species (Quercus suber L., Q. ilex L., Q. canariensis Willd., and Q. afares Pomel). (2) Methods: sixteen plots, including 89 trees from the four native species and their putative hybrids were sampled. Leaves were scanned and their geometric morphometry analyzed by using 11 landmarks on the right side on their abaxial surface. Variation within and among species, and the relationship among oak species and their hybrids were analyzed, utilizing an ANOVA and a canonical analysis using morphoJ software. (3) Results: using the geometric morphometry analysis, we observed that Q. afares shape is intermediate between Q. suber and Q. canariensis, being Q. ilex very different from the others, and that there is no overlap among them. Putative hybrids are morphologically close to Q. afares and, to a lesser extent, to Q. suber and, finally, to Q. ilex and Q. canariensis. (4) Conclusions: the study opens the field for future molecular characterization of hybrids, and for determining their role in terms of adaptation to actual and predicted future climatic conditions. The morphological proximity of hybrids to Q. afares demonstrate this species advantage in the area of study and its importance for the future evolution of the species in the Mediterranean. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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13 pages, 2366 KiB

Open AccessArticle

Genetic Evaluation of Juniperus sabina L. (Cupressaceae) in Arid and Semi-Arid Regions of China Based on SSR Markers

by Dongye Lu, Haiguang Huang, Aijun Wang and Guosheng Zhang

Forests 2022, 13(2), 231; https://doi.org/10.3390/f13020231 - 3 Feb 2022

Cited by 8 | Viewed by 2082

Abstract

Juniperus sabina L., a shrub distributed in patches in arid and semi-arid areas of the northern hemisphere, plays an important role in preventing land desertification and maintaining ecosystems. However, few studies have reported genetic diversity and genetic structure of widely distributed populations of J. sabina in northwest China. Here, we evaluated the genetic diversity and genetic structure and predicted the isolation barriers among 11 populations based on 20 simple sequence repeats (SSRs). A total of 134 alleles were generated and the average number of alleles per locus was 6.70. The Shannon diversity index ranged from 0.659 to 0.951, with an average of 0.825. Population structure analysis revealed that the populations were assigned into two genetic groups. The analysis of molecular variance (AMOVA) indicated that 88% of genetic variation existed within populations. Moderate population differentiation was occurred with F_ST value of 0.090. Finally, we concluded that geographic isolation is the main factor affecting the genetic structure of J. sabina populations. The results of this study provide a foundation for the strategies for J. sabina genetic conservation and management. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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12 pages, 2203 KiB

Open AccessArticle

The Genetic Differences and Structure of Selected Important Populations of the Endangered Taxus baccata in the Czech Republic

by Martina Komárková, Petr Novotný, Helena Cvrčková and Pavlína Máchová

Forests 2022, 13(2), 137; https://doi.org/10.3390/f13020137 - 18 Jan 2022

Cited by 4 | Viewed by 1923

Abstract

Taxus baccata L. (common yew) is an endangered tree species in the Czech Republic. However, its natural occurrence has not been adequately protected in all areas of the country. The aim of this study is to determine whether the yew population in the newly established Mařeničky seed orchard (TS_L) enables mixing with other Czech yew populations. Using a set of nuclear microsatellites, the genetic diversity in the Lužické Mountains (TS_L) and in selected wild-provenance populations from the Czech Republic (Jílovské yews, TS_J; Březinské yews, TS_B, and yews from Moravský Karst, TS_M) was studied, as they could be donor sources for potential translocation activities. We observed that the level of genetic diversity within the four Czech yew units that were investigated was high. An analysis of the molecular variance (AMOVA) showed 7% variation among populations, and the genetic differentiation values were low to moderate (F_ST = 0.042–0.108). According to a STRUCTURE analysis, high genetic similarity was observed between the TS_L and TS_B units. Our results provide important genetic suggestions on how conservation management can be designed to maximize its success. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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13 pages, 1952 KiB

Open AccessArticle

High Level of Phenotypic Differentiation of Common Yew (Taxus baccata L.) Populations in the North-Western Part of the Balkan Peninsula

by Katarina Tumpa, Zlatko Liber, Zlatko Šatović, Jasnica Medak, Marilena Idžojtić, Antonio Vidaković, Joso Vukelić, Irena Šapić, Patricija Nikl and Igor Poljak

Forests 2022, 13(1), 78; https://doi.org/10.3390/f13010078 - 7 Jan 2022

Cited by 4 | Viewed by 2293

Abstract

Common or English yew (Taxus baccata L., Taxaceae) is a conifer species, native to Europe, northern Africa, Asia Minor and Caucasus. It is a dioecious, wind-pollinated and animal-dispersed tree, known for its high-quality wood and medicinal properties, albeit poisonous. The species is rare and has been legally protected at the European and national levels. In addition, its low population density and disjunct character of distribution have reinforced the need for its protection as regeneration is mostly lacking. The aim of this study was to phenotypically characterise the north-western Balkan yew populations. Phenotypic diversity was examined for seven populations, using morphometric analysis of nine phenotypic traits of needles. Descriptive and multivariate statistical analyses were conducted to evaluate the inter- and intrapopulation variability. In addition, to test correlations between geographic, climatic and phenotypic data, Mantel test was used. We identified a geographic structure across studied populations that exhibited high levels of variability on intra- and interpopulation levels. Two groups of populations have been defined and are consistent with previously described genetic divergent lineages from separate refugia. In addition, a significant correlation between phenotypic and geographic data were revealed, i.e., isolation by distance (IBD). However, the Mantel test revealed no significant correlation between morphometric and environmental data. In conclusion, our data reveal that the historical events and persistent IBD acted in combination to produce the morphological patterns observed in common yew populations in the north-western part of the Balkan Peninsula. Finally, we suggested conservation measures to be implemented on a stand level, with habitat preservation as the main goal. In addition, ex situ conservation should be considered, both in the form of collections and urban planting, as both provide additional gene pool reserves. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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15 pages, 2609 KiB

Open AccessArticle

Phenotypic Diversity of Almond-Leaved Pear (Pyrus spinosa Forssk.) along Eastern Adriatic Coast

by Antonio Vidaković, Zlatko Liber, Zlatko Šatović, Marilena Idžojtić, Ida Volenec, Ivana Zegnal, Valentino Pintar, Mira Radunić and Igor Poljak

Forests 2021, 12(12), 1630; https://doi.org/10.3390/f12121630 - 25 Nov 2021

Cited by 14 | Viewed by 2818

Abstract

Almond-leaved pear (Pyrus spinosa Forssk., Rosaceae) is a scientifically poorly researched and often overlooked Mediterranean species. It is an insect-pollinated and animal-dispersed spiny, deciduous shrub or a small tree, with high-quality wood and edible fruits. The aim of the study was to assess the phenotypic diversity of almond-leaved pear in the eastern Adriatic region. The examination of phenotypic diversity was based on a morphometric analysis of 17 populations using ten phenotypic traits of leaves. Varieties of multivariate statistical analyses were conducted to evaluate the within- and among-population diversity. In addition, the Mantel tests were used to test the correlations between geographic, environmental, and phenotypic differences among populations. High phenotypic variability was determined both among and within the studied populations. Leaf-size-related traits proved to be the most variable ones, in contrast to more uniform leaf shape traits. Furthermore, three groups of populations were detected using multivariate statistical analyses. The first group included trees from northern- and southernmost populations characterized by high annual precipitation. However, the trees from the second and third group were highly overlapped without a clear geographical pattern. In addition, we revealed that both environmental and geographical interactions proved to be responsible for the patterns of phenotypic variation between almond-leaved pear populations, indicating significant isolation by environment (IBE) and isolation by distance (IBD) patterns. Overall, our results provide useful information about phenotypic diversity of almond-leaved pear populations for further conservation, breeding, and afforestation programs. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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Review

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14 pages, 1427 KiB

Open AccessReview

The Formation of Shapes: Interplay of Genes during Leaf Development Processes

by Jikai Ma and Huogen Li

Forests 2022, 13(10), 1726; https://doi.org/10.3390/f13101726 - 20 Oct 2022

Cited by 1 | Viewed by 3021

Abstract

Leaf shape, as one of the clearest manifestations of plant morphology, shows considerable variation owing to genetics and the environment. Leaf initiation occurs in the peripheral zone of the SAM and goes through the three overlapping phases of leaf primordium initiation, leaf dorsiventral development, and leaf marginal meristem establishment. Transcription factors, such as KNOX, WOX, and CUC; hormone-regulating genes, such as GA2ox, GA20ox, and PIN1; and miRNAs such as miR164/165 are tightly involved in leaf shaping through the generation of intricate cooperative networks in different temporal phases and specific tissue zones. Here, we briefly discuss the critical interplay occurring between certain genes and the pivotal role these play in the leaf developmental network and phytohormone regulation, including AS1/AS2–KNOX–GA20ox–GA, miR164–NAM/CUC–PIN1–auxin, and CUC–BAS1/CYP734A–BR, and we attempt to summarize several basic insights into the mechanisms of leaf shape regulation. Full article

(This article belongs to the Special Issue Population Genetic and Morphological Diversity of Woody Plants)

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