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Forests
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Molecular Markers in Forest Management and Tree Breeding
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Molecular Markers in Forest Management and Tree Breeding

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

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 7579

Special Issue Editor

Dr. Yurry Um

E-Mail Website
Guest Editor
Forest Medicinal Resources Research Center, National Institute of Forest Science, Yongju 36040, Republic of Korea
Interests: forest biotechnology; bioinformatics; genetics; molecular biology

Special Issue Information

Dear Colleagues,

This Special Issue, “Molecular Markers in Forest Management and Tree Breeding”, refers to the use of genetic techniques, specifically the use of molecular markers, to improve the management and breeding of forest tree populations. This Issue aims to identify specific genetic traits that are associated with important characteristics, such as disease resistance, growth rate, and wood quality, as well as the use of marker-assisted selection to improve the efficiency of tree breeding programs. This Special Issue will likely include articles discussing the latest research and advances in this field, as well as case studies and practical applications of molecular markers in forest management and tree breeding.

Dr. Yurry Um
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular markers
  • forest management
  • tree breeding
  • genetics
  • genomics
  • conservation
  • breeding programs
  • marker-assisted selection
  • DNA markers
  • genetic diversity
  • population genetics
  • genetic improvement
  • phenotypic variation
  • forest biotechnology

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Published Papers (5 papers)

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Research

15 pages, 5420 KiB  
Article
Screening and Expression Analysis of POD Gene in POD-H2O2 Pathway on Bud Dormancy of Pear (Pyrus pyrifolia)
by Xuwen Xiang, Keke Song, Yinyin Li, Chenyu Zhang, Ruiqi Zhou, Yu Feng, Jingnan You, Jingdong Wu, Yanhui Zhang, Cuicui Jiang and Yongyu Li
Forests 2024, 15(3), 434; https://doi.org/10.3390/f15030434 - 24 Feb 2024
Cited by 1 | Viewed by 1707
Abstract
Bud endodormancy represents a pivotal and intricate biological process influenced by both genetic and epigenetic factors, the exact mechanism of which remains elusive. Hydrogen peroxide (H2O2) functions as a signalling molecule in the regulation of dormancy, with peroxidase (POD) [...] Read more.
Bud endodormancy represents a pivotal and intricate biological process influenced by both genetic and epigenetic factors, the exact mechanism of which remains elusive. Hydrogen peroxide (H2O2) functions as a signalling molecule in the regulation of dormancy, with peroxidase (POD) playing a crucial role in governing H2O2 levels. Our prior transcriptomic and metabolomic investigations into diverse pear dormancy phases posited that POD predominantly oversees pear bud dormancy. In this study, we utilised qRT-PCR to screen the most significantly expressed gene, Pyrus pyrifolia POD4-like (PpPOD4-like), from seven POD genes. Subsequently, H2O2 test kits, overexpression methods, and subcellular localisation techniques were employed to assess changes in H2O2 content, POD activity, PpPOD4-like expression, and its cellular positioning during pear bud dormancy. Subcellular localisation experiments revealed that PpPOD4-like is situated on the cell membranes. Notably, H2O2 content exhibited a rapid increase during endodormancy and decreased swiftly after ecodormancy. The fluctuation pattern of POD activity aligned with that of H2O2 content. Additionally, PpPOD4-like expression was markedly upregulated, displaying an overall upward trajectory. Our findings indicate that PpPOD4-like modulates H2O2 levels by regulating POD activity, thereby actively participating in the intricate regulation of pear dormancy processes. Full article
(This article belongs to the Special Issue Molecular Markers in Forest Management and Tree Breeding)
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13 pages, 8684 KiB  
Article
Fertility Variation and Effective Population Size across Varying Acorn Yields in Turkey Oak (Quercus cerris L.): Implications for Seed Source Management
by Nebi Bilir, Koeun Jeon, Ye-Ji Kim and Kyu-Suk Kang
Forests 2023, 14(11), 2222; https://doi.org/10.3390/f14112222 - 10 Nov 2023
Viewed by 1027
Abstract
This research examines the impact of varied acorn yields on the effective population size of Turkey oak (Quercus cerris L.) as assessed through the fertility averages of zygotic parents. We selected two distinct populations from the species’ natural habitats based on their [...] Read more.
This research examines the impact of varied acorn yields on the effective population size of Turkey oak (Quercus cerris L.) as assessed through the fertility averages of zygotic parents. We selected two distinct populations from the species’ natural habitats based on their good and poor acorn production rates to investigate acorn production, growth attributes, and their interrelationships over three years of production and two years of growth data. Results showed that the population with good acorn production exhibited greater growth attributes and acorn yields compared to the poor acorn production population. Acorn production had lower coefficients of variation compared to growth attributes. Fertility variation in both populations was moderate, with a decrease in the effective number of parents from the population with abundant acorn production to the one with limited acorn production. The presence of mixed seeds from diverse populations had a detrimental impact on fertility variation and related metrics. Nonetheless, this study suggests that regions with limited acorn production still have the potential for natural regeneration due to their larger effective population size when coupled with appropriate forestry practices such as selective acorn harvesting to enhance genetic diversity. These findings emphasize the importance of accounting for fertility variation in the selection and management of seed sources, even within the context of a limited area and three years of data. Further research should be conducted in larger populations and over longer periods to draw more comprehensive conclusions. Full article
(This article belongs to the Special Issue Molecular Markers in Forest Management and Tree Breeding)
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18 pages, 3662 KiB  
Article
Optimizing a Regional White Spruce Tree Improvement Program: SNP Genotyping for Enhanced Breeding Values, Genetic Diversity Assessment, and Estimation of Pollen Contamination
by Esteban Galeano, Eduardo Pablo Cappa, Jean Bousquet and Barb R. Thomas
Forests 2023, 14(11), 2212; https://doi.org/10.3390/f14112212 - 8 Nov 2023
Cited by 1 | Viewed by 1386
Abstract
The utilization of genotyping has gained significant popularity in tree improvement programs, aiding in enhancing the precision of breeding values, removing pedigree errors, the assessment of genetic diversity, and evaluating pollen contamination. Our study explores the impact of utilizing 5308 SNP markers to [...] Read more.
The utilization of genotyping has gained significant popularity in tree improvement programs, aiding in enhancing the precision of breeding values, removing pedigree errors, the assessment of genetic diversity, and evaluating pollen contamination. Our study explores the impact of utilizing 5308 SNP markers to genotype seed orchard parents (166), progeny in progeny trials (667), and seedlot orchard seedlings (780), to simultaneously enhance variance components, breeding values, genetic diversity estimates, and pollen flow in the Region I white spruce (Picea glauca) breeding program in central Alberta (Canada). We compared different individual tree mixed models, including pedigree-based (ABLUP), genomic-based (GBLUP), and single-step pedigree-genomic-based (ssGBLUP) models, to estimate variance components and predict breeding values for the height and diameter at breast height traits. The highest heritability estimates were achieved using the ssGBLUP approach, resulting in improved breeding value accuracy compared to the ABLUP and GBLUP models for the studied growth traits. In the six orchard seedlots tested, the genetic diversity of the seedlings remained stable, characterized by an average of approximately 2.00 alleles per SNP, a Shannon Index of approximately 0.44, and an expected and observed heterozygosity of approximately 0.29. The pedigree reconstruction of seed orchard seedlings successfully identified consistent parental contributions and equal genotype contributions in different years. Pollen contamination levels varied between 11% and 70% using SNP markers and 8% to 81% using pollen traps, with traps both over- and under-estimating contamination. Overall, integrating genomic information from parents and offspring empowers forest geneticists and breeders in the Region I white spruce breeding program to correct errors, conduct backward and forward selections with greater precision, gain a deeper understanding of the orchard’s genetic structure, select superior seedlots, and accurately estimate the genetic worth of each orchard lot, which can ultimately result in increased and more precise estimates of genetic gain in the studied growth traits. Full article
(This article belongs to the Special Issue Molecular Markers in Forest Management and Tree Breeding)
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13 pages, 9541 KiB  
Article
Transcriptome Analysis and Novel EST-SSR Marker Development for Pinus tabuliformis Seedlings from Four Provenances
by Ju Wang, Shuai Guo, Yongxin Zhang, Feng Zhang, Yufei Yun and Guosheng Zhang
Forests 2023, 14(9), 1810; https://doi.org/10.3390/f14091810 - 5 Sep 2023
Cited by 1 | Viewed by 1217
Abstract
Chinese pine (Pinus tabuliformis) is a conifer species endemic to the temperate, warm temperate, and semi-arid regions of China. It has important ecological and economic values, but lacks suitable molecular markers for genetic studies. In this study, we collected open-pollinated progeny [...] Read more.
Chinese pine (Pinus tabuliformis) is a conifer species endemic to the temperate, warm temperate, and semi-arid regions of China. It has important ecological and economic values, but lacks suitable molecular markers for genetic studies. In this study, we collected open-pollinated progeny seeds from four provenances: Ningcheng (Nc), Qinyuan (Qy), Weichang (Wc), and Pingquan (Pq). We sequenced the transcriptomes of open-pollinated progeny seedlings from four provenances and annotated 18,244 unigenes. We analyzed the expression of genes involved in the auxin indole-3-acetic acid (IAA), cytokinin (CTK), and gibberellin (GA) signaling pathways among the provenances. Additionally, we detected 2811 expressed sequence tag simple sequence repeat (EST-SSR) loci in 2360 unigenes, with a frequency of 14.83% and an average of one locus per 14,556 base pairs (bp). We developed 10 polymorphic primers from 67 pairs and tested them on 56 samples from the four provenances. These primers exhibited moderate to high polymorphism and distinguished all samples clearly. Our study reveals variation in growth and development among open-pollinated progeny seedlings from different provenances of Chinese pine and provides novel markers for its genetic diversity study and marker-assisted breeding. Full article
(This article belongs to the Special Issue Molecular Markers in Forest Management and Tree Breeding)
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19 pages, 2108 KiB  
Article
Construction of Core Collection and Phenotypic Evaluation of Toona sinensis
by Jianhua Dai, Yanru Fan, Shu Diao, Hengfu Yin, Xiaojiao Han and Jun Liu
Forests 2023, 14(6), 1269; https://doi.org/10.3390/f14061269 - 19 Jun 2023
Cited by 3 | Viewed by 1716
Abstract
Toona sinensis is an important “vegetable and timber” tree species that is widely distributed in eastern and southeastern Asia. An efficient mechanism for preserving and utilizing germplasm resources is crucial for speeding up the process of genetic improvement of T. sinensis. We [...] Read more.
Toona sinensis is an important “vegetable and timber” tree species that is widely distributed in eastern and southeastern Asia. An efficient mechanism for preserving and utilizing germplasm resources is crucial for speeding up the process of genetic improvement of T. sinensis. We collected a total of 1040 germplasm resources of T. sinensis from China, Britain, and New Zealand. Using a total of 27,040 markers, we analyzed the genetic diversity, genetic structure, and core collection of these resources. Additionally, a comprehensive evaluation method for phenotypes of T. sinensis was established by principal component analysis (PCA) and the technique for order preference by similarity to ideal solution (TOPSIS). Our analysis included three main results: Firstly, the breeding population, consisting of a total of 1040 individuals, contains a diverse genetic pool and can be divided into two genetic clusters. Secondly, the best core collection was obtained from the alternative population, consisting of a total of 208 individuals and comprising 20% of the breeding population. It was screened out based on Core Hunter 3 software with the average entry-to-nearest-entry (E-NE) algorithm. Finally, a comprehensive evaluation method was established based on eight selected agronomic traits of the core collection. This method allowed us to screen the best individual plants of the core collection, including N0237, N0972, and N0409. Overall, our research findings will enable better preservation and utilization of T. sinensis germplasm resources and result in faster improvement of T. sinensis varieties. Full article
(This article belongs to the Special Issue Molecular Markers in Forest Management and Tree Breeding)
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