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Genetic and Phenotypic Variation in Tree Crops Biodiversity
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Genetic and Phenotypic Variation in Tree Crops Biodiversity

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

Deadline for manuscript submissions: closed (20 September 2020) | Viewed by 53953

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Dr. Gaetano Distefano

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Guest Editor
Dipartimento di Agricoltura, Università degli Studi di Catania, Alimentazione e Ambiente (Di3A), Sez. Arboricoltura e Genetica agraria, Via Valdisavoia 5, 95123 Catania, Italy
Interests: tree crop biotechnology; tree crop genomics; transgenics; biodiversity evaluation and analysis; fruit tree crops breeding; reproductive biology on fruit crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic and Phenotypic Variation in Tree Crop Biodiversity

The last few years have seen a dramatic increase in the use of DNA-derived data and innovative phenotyping to obtain insights into the causative genes underlying traits of agronomical interest, or to characterize the tree genetic resources. The latter, in particular, could represent an important source of genetic diversity that can be readily used to enhance the adaptability to limiting environmental factors and resistance to biotic stresses, or to promote novel genotypes with improved agronomic traits. Studies may focus on different aspects—such as species relationship and evolution, the extent and distribution of diversity in crop and forestry species, accession identity and detection of novel variants—providing valuable information for germplasm management and the prevention of genetic erosion. In particular, the use of molecular markers could have direct positive implications for the genetic characterization of tree germplasm resources, laying a foundation for the use of genetic polymorphisms to make predictions of phenotype changes through marker–trait association analysis. The paucity of the available phenotypic data, with respect to genetic, is still an important limiting factor, and the linking of genotypic and phenotypic information remains one of the greatest challenges in current genetics research.

On the whole, studies on tree crop biodiversity could provide the essential building blocks to ensure future improvements in production and quality, and for innovations in tree crop development and utilization.

Assoc. Prof. Gaetano Distefano
Guest Editor

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Keywords

  • genetic resources
  • molecular markers
  • germplasm
  • agronomic trait
  • conservation

Published Papers (16 papers)

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Editorial

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4 pages, 656 KiB  
Editorial
Research and Application of Molecular and Phenotypic Data for Tree Biodiversity Evaluation
by Gaetano Distefano
Forests 2021, 12(5), 564; https://doi.org/10.3390/f12050564 - 30 Apr 2021
Viewed by 1285
Abstract
The main challenges for tree crop improvement are linked to the sustainable development of agro-ecological habitats, improving the adaptability to limiting environmental factors and resistance to biotic stresses or promoting novel genotypes with improved agronomic traits [...] Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)

Research

Jump to: Editorial, Review

13 pages, 1555 KiB  
Article
Deciphering S-RNase Allele Patterns in Cultivated and Wild Accessions of Italian Pear Germplasm
by Stefania Bennici, Mario Di Guardo, Gaetano Distefano, Giuseppina Las Casas, Filippo Ferlito, Paolo De Franceschi, Luca Dondini, Alessandra Gentile and Stefano La Malfa
Forests 2020, 11(11), 1228; https://doi.org/10.3390/f11111228 - 22 Nov 2020
Cited by 6 | Viewed by 1870
Abstract
The genus Pyrus is characterized by an S-RNase-based gametophytic self-incompatibility (GSI) system, a mechanism that promotes outbreeding and prevents self-fertilization. While the S-genotype of the most widely known pear cultivars was already described, little is known on the S-allele variability [...] Read more.
The genus Pyrus is characterized by an S-RNase-based gametophytic self-incompatibility (GSI) system, a mechanism that promotes outbreeding and prevents self-fertilization. While the S-genotype of the most widely known pear cultivars was already described, little is known on the S-allele variability within local accessions. The study was conducted on 86 accessions encompassing most of the local Sicilian varieties selected for their traits of agronomic interest and complemented with some accessions of related wild species (P. pyrifolia Nakai, P. amygdaliformis Vill.) and some national and international cultivars used as references. The employment of consensus and specific primers enabled the detection of 24 S-alleles combined in 48 S-genotypes. Results shed light on the distribution of the S-alleles among accessions, with wild species and international cultivars characterized by a high diversity and local accessions showing a more heterogeneous distribution of the S-alleles, likely reflecting a more complex history of hybridization. The S-allele distribution was largely in agreement with the genetic structure of the studied collection. In particular, the “wild” genetic background was often characterized by the same S-alleles detected in P. pyrifolia and P. amygdaliformis. The analysis of the S-allele distribution provided novel insight into the contribution of the wild and international cultivars to the genetic background of the local Sicilian or national accessions. Furthermore, these results provide information that can be readily employed by breeders for the set-up of novel mating schemes. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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17 pages, 4470 KiB  
Article
Comparative Survey of Morphological Variations and Plastid Genome Sequencing Reveals Phylogenetic Divergence between Four Endemic Ilex Species
by Tao Su, Mengru Zhang, Zhenyu Shan, Xiaodong Li, Biyao Zhou, Han Wu and Mei Han
Forests 2020, 11(9), 964; https://doi.org/10.3390/f11090964 - 03 Sep 2020
Cited by 19 | Viewed by 2568
Abstract
Holly (Ilex L.), from the monogeneric Aquifoliaceae, is a woody dioecious genus cultivated as pharmaceutical and culinary plants, ornamentals, and industrial materials. With distinctive leaf morphology and growth habitats, but uniform reproductive organs (flowers and fruits), the evolutionary relationships of Ilex remain [...] Read more.
Holly (Ilex L.), from the monogeneric Aquifoliaceae, is a woody dioecious genus cultivated as pharmaceutical and culinary plants, ornamentals, and industrial materials. With distinctive leaf morphology and growth habitats, but uniform reproductive organs (flowers and fruits), the evolutionary relationships of Ilex remain an enigma. To date, few contrast analyses have been conducted on morphology and molecular patterns in Ilex. Here, the different phenotypic traits of four endemic Ilex species (I. latifolia, I. suaveolens, I. viridis, and I. micrococca) on Mount Huangshan, China, were surveyed through an anatomic assay and DNA image cytometry, showing the unspecified link between the examined morphology and the estimated nuclear genome size. Concurrently, the newly-assembled plastid genomes in four Ilex have lengths ranging from 157,601 bp to 157,857 bp, containing a large single-copy (LSC, 87,020–87,255 bp), a small single-copy (SSC, 18,394–18,434 bp), and a pair of inverted repeats (IRs, 26,065–26,102 bp) regions. The plastid genome annotation suggested the presence of numerable protein-encoding genes (89–95), transfer RNA (tRNA) genes (37–40), and ribosomal RNA (rRNA) genes (8). A comprehensive comparison of plastomes within eight Ilex implicated the conserved features in coding regions, but variability in the junctions of IRs/SSC and the divergent hotspot regions potentially used as the DNA marker. The Ilex topology of phylogenies revealed the incongruence with the traditional taxonomy, whereas it informed a strong association between clades and geographic distribution. Our work herein provided novel insight into the variations in the morphology and phylogeography in Aquifoliaceae. These data contribute to the understanding of genetic diversity and conservation in the medicinal Ilex of Mount Huangshan. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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11 pages, 1606 KiB  
Article
Identification of a Natural Hybrid between Castanopsis sclerophylla and Castanopsis tibetana (Fagaceae) Based on Chloroplast and Nuclear DNA Sequences
by Xiaorong Zeng, Risheng Chen, Yunxin Bian, Xinsheng Qin, Zhuoxin Zhang and Ye Sun
Forests 2020, 11(8), 873; https://doi.org/10.3390/f11080873 - 11 Aug 2020
Cited by 2 | Viewed by 2256
Abstract
Castanopsis × kuchugouzhui Huang et Y. T. Chang was recorded in Flora Reipublicae Popularis Sinicae (FRPS) as a hybrid species on Yuelushan mountain, but it is treated as a hybrid between Castanopsis sclerophylla (Lindl.) Schott. and Castanopsis tibetana Hance in Flora of China. [...] Read more.
Castanopsis × kuchugouzhui Huang et Y. T. Chang was recorded in Flora Reipublicae Popularis Sinicae (FRPS) as a hybrid species on Yuelushan mountain, but it is treated as a hybrid between Castanopsis sclerophylla (Lindl.) Schott. and Castanopsis tibetana Hance in Flora of China. After a thorough investigation on Yuelushan mountain, we found a population of C. sclerophylla and one individual of C. × kuchugouzhui, but no living individual of C. tibetana. We collected C. × kuchugouzhui, and we sampled 42 individuals of C. sclerophylla from Yuelushan and Xiushui and 43 individuals of C. tibetana from Liangyeshan and Xiushui. We used chloroplast DNA sequences and 29 nuclear microsatellite markers to investigate if C. × kuchugouzhui is a natural hybrid between C. sclerophylla and C. tibetana. The chloroplast haplotype analysis showed that C. × kuchugouzhui shared haplotype H2 with C. sclerophylla on Yuelushan. The STRUCTURE analysis identified two distinct genetic pools that corresponded well to C. sclerophylla and C. tibetana, revealing the genetic admixture of C. × kuchugouzhui. Furthermore, the NewHybrids analysis suggested that C. × kuchugouzhui is an F2 hybrid between C. sclerophylla and C. tibetana. Our results confirm that C. × kuchugouzhui recorded in FRPS is a rare hybrid between C. sclerophylla and C. tibetana. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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16 pages, 2047 KiB  
Article
Genome Cytosine Methylation May Affect Growth and Wood Property Traits in Populations of Populus tomentosa
by Kaifeng Ma, Yuepeng Song, Dong Ci, Daling Zhou, Min Tian and Deqiang Zhang
Forests 2020, 11(8), 828; https://doi.org/10.3390/f11080828 - 29 Jul 2020
Cited by 2 | Viewed by 1854
Abstract
Growth and wood formation are crucial and complex biological processes during tree development. These biological regulatory processes are presumed to be controlled by DNA methylation. However, there is little direct evidence to show that genes taking part in wood regulation are affected by [...] Read more.
Growth and wood formation are crucial and complex biological processes during tree development. These biological regulatory processes are presumed to be controlled by DNA methylation. However, there is little direct evidence to show that genes taking part in wood regulation are affected by cytosine methylation, resulting in phenotypic variations. Here, we detected epimarkers using a methylation-sensitive amplification polymorphism (MSAP) method and performed epimarker–trait association analysis on the basis of nine growth and wood property traits within populations of 432 genotypes of Populus tomentosa. Tree height was positively correlated with relative full-methylation level, and 1101 out of 2393 polymorphic epimarkers were associated with phenotypic traits, explaining 1.1–7.8% of the phenotypic variation. In total, 116 epimarkers were successfully sequenced, and 96 out of these sequences were linked to putative genes. Among them, 13 candidate genes were randomly selected for verification using quantitative real-time PCR (qRT-PCR), and it also showed the expression of nine putative genes of PtCYP450, PtCpn60, PtPME, PtSCP, PtGH, PtMYB, PtWRKY, PtSTP, and PtABC were negatively correlated with DNA methylation level. Therefore, it suggested that changes in DNA methylation might contribute to regulating tree growth and wood property traits. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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12 pages, 1233 KiB  
Article
Preliminary Evidence for Domestication Effects on the Genetic Diversity of Guazuma crinita in the Peruvian Amazon
by Lady Laura Tuisima-Coral, Petra Hlásná Čepková, John C. Weber and Bohdan Lojka
Forests 2020, 11(8), 795; https://doi.org/10.3390/f11080795 - 23 Jul 2020
Cited by 8 | Viewed by 2023
Abstract
Guazuma crinita, a fast-growing timber tree species, was chosen for domestication in the Peruvian Amazon because it can be harvested at an early age and it contributes to the livelihood of local farmers. Although it is in an early stage of domestication, we [...] Read more.
Guazuma crinita, a fast-growing timber tree species, was chosen for domestication in the Peruvian Amazon because it can be harvested at an early age and it contributes to the livelihood of local farmers. Although it is in an early stage of domestication, we do not know the impact of the domestication process on its genetic resources. Amplified fragment length polymorphic (AFLP) fingerprints were used to estimate the genetic diversity of G. crinita populations in different stages of domestication. Our objectives were (i) to estimate the level of genetic diversity in G. crinita using AFLP markers, (ii) to describe how the genetic diversity is distributed within and among populations and provenances, and (iii) to assess the genetic diversity in naturally regenerated, cultivated and semi-domesticated populations. We generated fingerprints for 58 leaf samples representing eight provenances and the three population types. We used seven selective primer combinations. A total of 171 fragments were amplified with 99.4% polymorphism at the species level. Nei’s genetic diversity and Shannon information index were slightly higher in the naturally regenerated population than in the cultivated and semi-domesticated populations (He = 0.10, 0.09 and 0.09; I = 0.19, 0.15 and 0.16, respectively). The analysis of molecular variation showed higher genetic diversity within rather than among provenances (84% and 4%, respectively). Cluster analysis (unweighted pair group method with arithmetic mean) and principal coordinate analysis did not show correspondence between genetic and geographic distance. There was significant genetic differentiation among population types (Fst = 0.12 at p ˂ 0.001). The sample size was small, so the results are considered as preliminary, pending further research with larger sample sizes. Nevertheless, these results suggest that domestication has a slight but significant effect on the diversity levels of G. crinita and this should be considered when planning a domestication program. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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15 pages, 1246 KiB  
Article
Plus Tree Selection of Quercus salicina Blume and Q. glauca Thunb. and Its Implications in Evergreen Oaks Breeding in Korea
by In Sik Kim, Kyung Mi Lee, Donghwan Shim, Jin Jung Kim and Hye-In Kang
Forests 2020, 11(7), 735; https://doi.org/10.3390/f11070735 - 06 Jul 2020
Cited by 5 | Viewed by 3066
Abstract
This study was conducted to select plus trees of two evergreen oaks, Quercus salicina and Q. glauca, in Korea. Evergreen oaks are distributed in subtropical region in Korea and have recently emerged as one of the alternative tree species against climate change. [...] Read more.
This study was conducted to select plus trees of two evergreen oaks, Quercus salicina and Q. glauca, in Korea. Evergreen oaks are distributed in subtropical region in Korea and have recently emerged as one of the alternative tree species against climate change. Accordingly, a tree breeding program is underway to foster evergreen oaks as a reforestation species for the future. Through intensive survey on the distribution range, 15 stands (8 for Q. salicina, 3 for Q. glauca, and 4 for both species) were selected as base populations. To select candidate trees, we developed a subjective grading system with six characteristics in three categories and introduced a weighted generalized value (GVIw) to compare superiority of candidate trees. The candidate trees were screened using baseline value ‘0’, i.e., if GVIw > 0, then accepted and if GVIw < 0, then rejected. After then, adjustment was conducted to avoid biasing the selection of plus trees for a particular location. Through this process, 44 candidate trees in Q. salicina and 41 candidate trees in Q. glauca were selected as plus trees. Finally, the results and implications were discussed in relation to evergreen oak breeding in Korea. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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24 pages, 3773 KiB  
Article
Genetic Diversity of Paeonia rockii (Flare Tree Peony) Germplasm Accessions Revealed by Phenotypic Traits, EST-SSR Markers and Chloroplast DNA Sequences
by Xin Guo, Fangyun Cheng and Yuan Zhong
Forests 2020, 11(6), 672; https://doi.org/10.3390/f11060672 - 12 Jun 2020
Cited by 11 | Viewed by 3449
Abstract
Research Highlights: This study, based on the first collection of cultivated Paeonia rockii (flare tree peony, FTP) germplasm across the main distribution area by our breeding desires, comprehensively evaluates these accessions by using phenotypic traits, expressed sequence tag (EST)-simple sequence repeat (SSR) markers [...] Read more.
Research Highlights: This study, based on the first collection of cultivated Paeonia rockii (flare tree peony, FTP) germplasm across the main distribution area by our breeding desires, comprehensively evaluates these accessions by using phenotypic traits, expressed sequence tag (EST)-simple sequence repeat (SSR) markers and chloroplast DNA sequences (cpDNA). The results show that these accessions collected selectively by us can represent the genetic background information of FTP as a germplasm of tree crops. Background and Objectives: FTP has high cultural, ornamental and medicinal value traditionally, as well as recently presenting a significance as an emerging edible oil with high α-linolenic acid contents in the seeds. The objectives of this study are to reveal the characteristics of the genetic diversity of FTP, as well as to provide scientific suggestions for the utilization of tree peony breeding and the conservation of germplasm resource. Materials and Methods: Based on the phenotypic traits, EST-SSR markers and chloroplast DNA sequence variation, we studied the diversity of a newly established population of 282 FTP accessions that were collected and propagated by ourselves in our breeding project in recent years. Results: (1) There was an abundant variation in phenotype of the accessions, and the phenotypic variation was evenly distributed within the population, without significant hierarchical structure, (2) the EST-SSR data showed that these 282 accessions had relatively high genetic diversity, in which a total of 185 alleles were detected in 34 pairs of primers. The 282 accessions were divided into three distinct groups, and (3) the chloroplast DNA sequences (cpDNA) data indicated that these accessions had a higher genetic diversity than the population level and a lower genetic diversity than the species level of wild P. rockii, and the existing spatial genetic structure of these accessions can be divided into two branches. Conclusions: From the results of the three analyses, we found that these accessions can fully reflect the genetic background information of FTP germplasm resources, so their protection and utilization will be of great significance for genetic improvement of woody peonies. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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16 pages, 6002 KiB  
Article
Genetic Structure and Pod Morphology of Inga edulis Cultivated vs. Wild Populations from the Peruvian Amazon
by Alexandr Rollo, Maria M. Ribeiro, Rita L. Costa, Carmen Santos, Zoyla M. Clavo P., Bohumil Mandák, Marie Kalousová, Hana Vebrová, Edilberto Chuqulin, Sergio G. Torres, Roel M. V. Aguilar, Tomáš Hlavsa and Bohdan Lojka
Forests 2020, 11(6), 655; https://doi.org/10.3390/f11060655 - 08 Jun 2020
Cited by 5 | Viewed by 3585
Abstract
Research Highlights: This study assesses the genetic diversity and structure of the ice-cream-bean (Inga edulis Mart.; Fabaceae) in wild and cultivated populations from the Peruvian Amazon. This research also highlights the importance of protecting the biodiversity of the forest in the [...] Read more.
Research Highlights: This study assesses the genetic diversity and structure of the ice-cream-bean (Inga edulis Mart.; Fabaceae) in wild and cultivated populations from the Peruvian Amazon. This research also highlights the importance of protecting the biodiversity of the forest in the Peruvian Amazon, to preserve the genetic resources of species and allow further genetic improvement. Background and Objectives: Ice-cream-bean is one of the most commonly used species in the Amazon region for its fruits and for shading protection of other species (e.g., cocoa and coffee plantations). Comprehensive studies about the impact of domestication on this species’ genetic diversity are needed, to find the best conservation and improvement strategies. Materials and Methods: In the current study, the genetic structure and diversity were assessed by genotyping 259 trees, sampled in five wild and 22 cultivated I. edulis populations in the Peruvian Amazon, with microsatellite markers. Pod length was measured in wild and cultivated trees. Results: The average pod length in cultivated trees was significantly higher than that in wild trees. The expected genetic diversity and the average number of alleles was higher in the wild compared to the cultivated populations; thus, a loss of genetic diversity was confirmed in the cultivated populations. The cultivated trees in the Loreto region had the highest pod length and lowest allelic richness; nevertheless, the wild populations’ genetic structure was not clearly differentiated (significantly different) from that of the cultivated populations. Conclusions: A loss of genetic diversity was confirmed in the cultivated populations. The species could have been simultaneously domesticated in multiple locations, usually from local origin. The original I. edulis Amazonian germplasm should be maintained. Cultivated populations’ new germplasm influx from wild populations should be undertaken to increase genetic diversity. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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15 pages, 3443 KiB  
Article
High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China
by Yanwen Deng, Tingting Liu, Yuqing Xie, Yaqing Wei, Zicai Xie, Youhai Shi and Xiaomei Deng
Forests 2020, 11(4), 469; https://doi.org/10.3390/f11040469 - 21 Apr 2020
Cited by 19 | Viewed by 3164
Abstract
Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the [...] Read more.
Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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10 pages, 1648 KiB  
Article
Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea
by Tao Yu, Jian Gao, Bing-Hong Huang, Buddhi Dayananda, Wen-Bao Ma, Yu-Yang Zhang, Pei-Chun Liao and Jun-Qing Li
Forests 2020, 11(4), 462; https://doi.org/10.3390/f11040462 - 19 Apr 2020
Cited by 10 | Viewed by 3067
Abstract
The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient [...] Read more.
The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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16 pages, 5217 KiB  
Article
Complete Chloroplast Genome of Michelia shiluensis and a Comparative Analysis with Four Magnoliaceae Species
by Yanwen Deng, Yiyang Luo, Yu He, Xinsheng Qin, Chonggao Li and Xiaomei Deng
Forests 2020, 11(3), 267; https://doi.org/10.3390/f11030267 - 27 Feb 2020
Cited by 19 | Viewed by 3185
Abstract
Michelia shiluensis is a rare and endangered magnolia species found in South China. This species produces beautiful flowers and is thus widely used in landscape gardening. Additionally, its timber is also used for furniture production. As a result of low rates of natural [...] Read more.
Michelia shiluensis is a rare and endangered magnolia species found in South China. This species produces beautiful flowers and is thus widely used in landscape gardening. Additionally, its timber is also used for furniture production. As a result of low rates of natural reproduction and increasing levels of human impact, wild M. shiluensis populations have become fragmented. This species is now classified as endangered by the IUCN. In the present study, we characterized the complete chloroplast genome of M. shiluensis and found it to be 160,075 bp in length with two inverted repeat regions (26,587 bp each), a large single-copy region (88,105 bp), and a small copy region (18,796 bp). The genome contained 131 genes, including 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The guanine-cytosine content represented 39.26% of the overall genome. Comparative analysis revealed high similarity between the M. shiluensis chloroplast genome and those of four closely related species: Michelia odora, Magnolia laevifolia, Magnolia insignis, and Magnolia cathcartii. Phylogenetic analysis shows that M. shiluensis is most closely related to M. odora. The genomic information presented in this study is valuable for further classification, phylogenetic studies, and to support ongoing conservation efforts. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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20 pages, 6260 KiB  
Article
Constitutive and Cold Acclimation-Regulated Protein Expression Profiles of Scots Pine Seedlings Reveal Potential for Adaptive Capacity of Geographically Distant Populations
by Danas Baniulis, Monika Sirgėdienė, Perttu Haimi, Inga Tamošiūnė and Darius Danusevičius
Forests 2020, 11(1), 89; https://doi.org/10.3390/f11010089 - 10 Jan 2020
Cited by 6 | Viewed by 2201
Abstract
Geographically distant Scots pine (Pinus sylvestris L.) populations are adapted to specific photoperiods and temperature gradients, and markedly vary in the timing of growth patterns and adaptive traits. To understand the variability of adaptive capacity within species, molecular mechanisms that govern the [...] Read more.
Geographically distant Scots pine (Pinus sylvestris L.) populations are adapted to specific photoperiods and temperature gradients, and markedly vary in the timing of growth patterns and adaptive traits. To understand the variability of adaptive capacity within species, molecular mechanisms that govern the physiological aspects of phenotypic plasticity should be addressed. Protein expression analysis is capable of depicting molecular events closely linked to phenotype formation. Therefore, in this study, we used comparative proteomics analysis to differentiate Scots pine genotypes originating from geographically distant populations in Europe, which show distinct growth and cold adaptation phenotypes. Needles were collected from 3-month-old seedlings originating from populations in Spain, Lithuania and Finland. Under active growth-promoting conditions and upon acclimation treatment, 65 and 53 differentially expressed proteins were identified, respectively. Constitutive protein expression differences detected during active growth were associated with cell metabolism and stress response, and conveyed a population-specific adaptation to the distinct climatic conditions. Acclimation-induced protein expression patterns suggested the presence of a similar cold adaptation mechanism among the populations. Variation of adaptive capacity among the genotypes was potentially represented by a constitutive low level of expression of the Ser/Thr-protein phosphatase, the negative regulator of the adaptive response. Also, overall less pronounced acclimation-induced response in seedlings from the Spanish population was observed. Thus, our study demonstrates that comparative proteomic analysis of young conifer seedlings is capable of providing insights into adaptation processes at the cellular level, which could help to infer variability of adaptive capacity within the plant species. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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19 pages, 10001 KiB  
Article
Bark Features for Identifying Resonance Spruce Standing Timber
by Florin Dinulică, Cristian-Teofil Albu, Maria Magdalena Vasilescu and Mariana Domnica Stanciu
Forests 2019, 10(9), 799; https://doi.org/10.3390/f10090799 - 12 Sep 2019
Cited by 14 | Viewed by 2976
Abstract
Measuring the acoustic properties of wood is not feasible for most luthiers, so identifying simple, valid criteria for diagnosis remains an exciting challenge when selecting materials for manufacturing musical instruments. This article aims to verify whether the bark qualities as a marker of [...] Read more.
Measuring the acoustic properties of wood is not feasible for most luthiers, so identifying simple, valid criteria for diagnosis remains an exciting challenge when selecting materials for manufacturing musical instruments. This article aims to verify whether the bark qualities as a marker of resonance wood are indeed useful. The morphometric and colour traits (in CIELab space) of the bark scales were compared with the structural (width and regularity of the growth rings and of the latewood) and acoustic features (transverse sound velocity, radiation ratio, impedance, and wood basic density) of the wood from 145 standing and 10 felled spruce trees, which are considered a resource of the resonance wood in the Romanian Carpathians. It has been emphasized that the spruce trees with acoustic and structural features that match the requirements for the manufacture of violins have a bark phenotype distinguishable by colour (higher redness, lower yellowness and brightness)—as well as by scale shape (higher slenderness and width). The south-facing side of the trunk and the external side of the scale are best for identifying resonance trees by their bark. Additionally, the mature bark phenotypes denote topoclinal variations and do not depend on tree age. Moreover, the differences among bark phenotypes are noticeable to the naked eye. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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12 pages, 2051 KiB  
Article
Assessment of Genetic Diversity of Tea Germplasm for Its Management and Sustainable Use in Korea Genebank
by Kyung Jun Lee, Jung-Ro Lee, Raveendar Sebastin, Myoung-Jae Shin, Seong-Hoon Kim, Gyu-Taek Cho and Do Yoon Hyun
Forests 2019, 10(9), 780; https://doi.org/10.3390/f10090780 - 08 Sep 2019
Cited by 15 | Viewed by 3129
Abstract
Tea (Camellia sinensis (L.) O. Kuntze) is cultivated in many developing Asian, African, and South American countries, and is the most widely consumed beverage in the world. It is of critical importance to understand the genetic diversity and population structure of tea [...] Read more.
Tea (Camellia sinensis (L.) O. Kuntze) is cultivated in many developing Asian, African, and South American countries, and is the most widely consumed beverage in the world. It is of critical importance to understand the genetic diversity and population structure of tea germplasm for effective collection, conservation, and utilization. In this study, 410 tea accessions collected from South Korea were analyzed using 21 simple sequence repeat (SSR) markers. Among 410 tea accessions, 85.4% (350 accessions) were collected from Jeollanam-do. A total of 286 alleles were observed, and the genetic diversity and evenness were estimated to be on average 0.79 and 0.61, respectively, across all the tested samples. Using discriminant analysis of principal components, four clusters were detected in 410 tea accessions. Among them, cluster 1 showed a higher frequency of rare alleles (less than 1%). Using the calculation of the index of association and rbaD value, each cluster showed a clonal mode of reproduction. The result of analysis of molecular variance (AMOVA) showed that most of the variation observed was within populations (99%) rather than among populations (1%). The present study revealed the presence of lower diversity and simpler population structure in Korean tea germplasms. Consequently, more attention should be focused on collecting and conserving the new tea individuals to broaden genetic variation of new cultivars in future breeding of the tea plant. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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Review

Jump to: Editorial, Research

19 pages, 1918 KiB  
Review
Mutation Mechanism of Leaf Color in Plants: A Review
by Ming-Hui Zhao, Xiang Li, Xin-Xin Zhang, Heng Zhang and Xi-Yang Zhao
Forests 2020, 11(8), 851; https://doi.org/10.3390/f11080851 - 06 Aug 2020
Cited by 61 | Viewed by 12731
Abstract
Color mutation is a common, easily identifiable phenomenon in higher plants. Color mutations usually affect the photosynthetic efficiency of plants, resulting in poor growth and economic losses. Therefore, leaf color mutants have been unwittingly eliminated in recent years. Recently, however, with the development [...] Read more.
Color mutation is a common, easily identifiable phenomenon in higher plants. Color mutations usually affect the photosynthetic efficiency of plants, resulting in poor growth and economic losses. Therefore, leaf color mutants have been unwittingly eliminated in recent years. Recently, however, with the development of society, the application of leaf color mutants has become increasingly widespread. Leaf color mutants are ideal materials for studying pigment metabolism, chloroplast development and differentiation, photosynthesis and other pathways that could also provide important information for improving varietal selection. In this review, we summarize the research on leaf color mutants, such as the functions and mechanisms of leaf color mutant-related genes, which affect chlorophyll synthesis, chlorophyll degradation, chloroplast development and anthocyanin metabolism. We also summarize two common methods for mapping and cloning related leaf color mutation genes using Map-based cloning and RNA-seq, and we discuss the existing problems and propose future research directions for leaf color mutants, which provide a reference for the study and application of leaf color mutants in the future. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Variation in Tree Crops Biodiversity)
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