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Advances in Forest Tree Genetics and Breeding
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Advances in Forest Tree Genetics and Breeding

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 7694

Special Issue Editors

Prof. Dr. Xiaohua Su

E-Mail Website
Guest Editor
State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
Interests: common research fields in forest trees; conventional breeding; breeding strategy; genetic engineering/genome editing and marker-assisted breeding
Dr. Yanguang Chu

E-Mail Website
Guest Editor
State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
Interests: genomics; genetic regulation; natural variation; marker-assisted breeding in forest trees

Special Issue Information

Dear Colleagues,

Forest trees are important resources that possess multiple values in ecological balance and economic development. They provide raw materials and products for various industries, such as timber, paper and furniture, to support local communities. The long-term health of forests needs to be enhanced by research outputs on forest tree genetics and breeding aiming to understand the genetic basis of complex traits. This field involves the study of genetic variation, identification/manipulation of genes or markers and the development of breeding strategies to improve important traits. The achievements of such studies are often attributed to the use of modern technologies such as high-throughput sequencing, genome editing and genome-wide association studies. This Special Issue will present the latest progress in the field of forest tree genetics and breeding, highlighting the potential of these studies in enhancing forest diversity, productivity and adaptability to changing environments.

Prof. Dr. Xiaohua Su
Dr. Yanguang Chu
Guest Editors

Manuscript Submission Information

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Keywords

  • forest tree genetics and breeding
  • complex traits
  • genetic variation
  • genome editing
  • molecular markers
  • breeding strategy

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Published Papers (8 papers)

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Research

21 pages, 3163 KiB  
Article
Stability Analysis and Multi-Trait Selection of Flowering Phenology Parameters in Olive Cultivars Under Multi-Environment Trials
by Jinhua Li, Dongxu Jia, Zhenyuan Zhou, Jincheng Du, Qiangang Xiao and Mingrong Cao
Plants 2025, 14(13), 1906; https://doi.org/10.3390/plants14131906 - 20 Jun 2025
Viewed by 156
Abstract
Flowering represents the most important process in the reproductive stage of fruit trees, including olive trees. Previous studies have demonstrated that the genotype–environment interaction (GEI) has a considerable influence on olive flowering time. This study investigated the GEI and genetic parameters influencing olive [...] Read more.
Flowering represents the most important process in the reproductive stage of fruit trees, including olive trees. Previous studies have demonstrated that the genotype–environment interaction (GEI) has a considerable influence on olive flowering time. This study investigated the GEI and genetic parameters influencing olive flowering phenology in Southwestern China (a non-Mediterranean region), using multi-trait-based stability selection methods. Sixteen olive cultivars from five countries were evaluated over two years in two distinct climatic regions of Southwestern China. Flowering phenology was assessed based on three parameters: full-bloom date (FBD), flowering-period length (FP), and full-bloom-period length (FBP). In the analyses, the best linear unbiased prediction (BLUP) to predict genetic value and genotype + genotype by environment interaction (GGE) biplot methods to visualize and assess stability and performance were employed across four environments. The results showed that genotype, environment, and GEI had highly significant effects on flowering traits, with GEI accounting for 54.12% to 89.62% of the variance. Heritability values were low (0.0589 to 0.262), indicating that genetic factors had limited control over flowering phenology compared to environmental factors. A stability analysis using a mean performance and stability (MPS) index identified genotypes with earlier flowering dates and longer flowering periods. Multi-trait selection using a multi-trait mean performance and stability (MTMPS) index further highlighted six superior genotypes with high performance and stability across environments. The findings emphasize the critical role of environmental factors on olive flowering phenology, highlighting the challenges in breeding for stable flowering traits. This study demonstrates the effectiveness of multi-trait selection methods in identifying genotypes with superior performance and stability under different environmental conditions. These results provide valuable insights for olive breeding programs, particularly in non-Mediterranean regions, suggesting that targeted selection and multi-trait evaluation could enhance the adaptability and productivity of olive cultivars under changing climatic conditions. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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17 pages, 1432 KiB  
Article
Genomic Prediction in a Self-Fertilized Progenies of Eucalyptus spp.
by Guilherme Ferreira Melchert, Filipe Manoel Ferreira, Fabiana Rezende Muniz, Jose Wilacildo de Matos, Thiago Romanos Benatti, Itaraju Junior Baracuhy Brum, Leandro de Siqueira and Evandro Vagner Tambarussi
Plants 2025, 14(10), 1422; https://doi.org/10.3390/plants14101422 - 9 May 2025
Viewed by 579
Abstract
Genomic selection in Eucalyptus enables the identification of superior genotypes, thereby reducing breeding cycles and increasing selection intensity. However, its efficiency may be compromised due to the complex structures of breeding populations, which arise from the use of multiple parents from different species. [...] Read more.
Genomic selection in Eucalyptus enables the identification of superior genotypes, thereby reducing breeding cycles and increasing selection intensity. However, its efficiency may be compromised due to the complex structures of breeding populations, which arise from the use of multiple parents from different species. In this context, partial inbred lines have emerged as a viable alternative to enhance efficiency and generate productive clones. This study aimed to apply genomic selection to a self-fertilized population of different Eucalyptus spp. Our objective was to predict the genomic breeding values (GEBVs) of individuals lacking phenotypic information, with a particular focus on inbred line development. The studied population comprised 662 individuals, of which 600 were phenotyped for diameter at breast height (DBH) at 36 months in a field experiment. The remaining 62 individuals were located in a hybridization orchard and lacked phenotypic data. All individuals, including progeny and parents, were genotyped using 10,132 SNP markers. Genomic prediction was conducted using four frequentist models—GBLUP, GBLUP dominant additive, HBLUP, and ABLUP—and five Bayesian models—BRR, BayesA, BayesB, BayesC, and Bayes LASSO—using k-fold cross-validation. Among the GS models, GBLUP exhibited the best overall performance, with a predictive ability of 0.48 and an R2 of 0.21. For mean squared error, the Bayes LASSO presented the lowest error (3.72), and for the other models, the MSE ranged from 3.72 to 15.50. However, GBLUP stood out as it presented better precision in predicting individual performance and balanced performance in the studied parameter. These results highlight the potential of genomic selection for use in the genetic improvement of Eucalyptus through inbred lines. In addition, our model facilitates the identification of promising individuals and the acceleration of breeding cycles, one of the major challenges in Eucalyptus breeding programs. Consequently, it can reduce breeding program production costs, as it eliminates the need to implement experiments in large planted areas while also enhancing the reliability in selection of genotypes. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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24 pages, 7987 KiB  
Article
Systematic Analysis of the Betula platyphylla TCP Gene Family and Its Expression Profile Identifies Potential Key Candidate Genes Involved in Abiotic Stress Responses
by Shengzhou Guo, Yuan Xu, Yi Zhou, Ronglin Liu, Yongkang Wang, Ling Yao, Syed Muhammad Azam, Huanhuan Ma, Xiaomin Liu, Shijiang Cao and Kang Wang
Plants 2025, 14(6), 880; https://doi.org/10.3390/plants14060880 - 11 Mar 2025
Viewed by 736
Abstract
The TCP transcription factor (TF) family is a vital set of plant-specific regulators involved in plant growth, development, and responses to environmental stresses. Despite the extensive research on TCP transcription factors in numerous plant species, the functions they fulfill in Betula platyphylla are [...] Read more.
The TCP transcription factor (TF) family is a vital set of plant-specific regulators involved in plant growth, development, and responses to environmental stresses. Despite the extensive research on TCP transcription factors in numerous plant species, the functions they fulfill in Betula platyphylla are still not well understood. In this study, 21 BpTCP genes were identified via genome-wide analysis. Bioinformatics analysis was used to examine the physicochemical properties of these transcription factors, including molecular weight, isoelectric point, chromosomal distribution, and predicted subcellular localization. We expected that most BpTCP transcription factors would be located in the nucleus. Collinearity analysis revealed that gene fragment duplication events played a major role in the evolutionary expansion and diversification of the BpTCP gene family. Promoter analysis identified diverse cis-acting elements in BpTCP, suggesting that they play a role in stress responses, hormonal regulation, and plant growth and development. qRT-PCR analysis showed that BpTCP genes displayed tissue-specific expression patterns in the roots, stems, and leaves, displaying remarkable differences in expression levels when subjected to abiotic stresses, including drought and high- and low-temperature conditions. Notably, BpTCP17 and BpTCP18 showed markedly higher expression levels under multiple stress conditions. Subcellular localization experiments confirmed that both BpTCP17 and BpTCP18 localize in the nucleus, consistent with bioinformatic predictions. These findings emphasize the potential roles of BpTCP17 and BpTCP18 in mediating abiotic stress responses, highlighting their potential as candidate genes for improving stress tolerance in B. platyphylla. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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20 pages, 15436 KiB  
Article
Genome-Wide Identification and Expression Pattern Analysis of Nuclear Factor Y B/C Genes in Pinus koraiensis, and Functional Identification of LEAFY COTYLEDON 1
by Xiuyue Xu, Xin He, Qun Zhang and Ling Yang
Plants 2025, 14(3), 438; https://doi.org/10.3390/plants14030438 - 2 Feb 2025
Viewed by 913
Abstract
The nuclear factor Y (NF-Y) transcription factor is widely involved in various plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress responses. This study presents a comprehensive genome-wide identification and expression profile of transcription factors NF-YB and NF-YC in Pinus [...] Read more.
The nuclear factor Y (NF-Y) transcription factor is widely involved in various plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress responses. This study presents a comprehensive genome-wide identification and expression profile of transcription factors NF-YB and NF-YC in Pinus koraiensis. Eight NF-YB and seven NF-YC transcription factors were identified through bioinformatics analysis, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. We evaluate the expression patterns of NF-YB/C genes in various tissues and somatic embryo maturation processes through the transcriptomics of ABA-treated tissues from multiple nutritional tissues, reproductive tissues, and somatic embryo maturation processes. The Leafy cotyledon1 (LEC1) gene belongs to the LEC1-type gene in the NF-YB family, numbered PkNF-YB7. In this study, we characterized the function of PkLEC1 during somatic embryonic development using genetic transformation techniques. The results indicate that PkNF-YB/C transcription factors are involved in the growth and development of nutritional tissues and reproductive organs, with specific high expression in PkNF-YB7 embryogenic callus, somatic embryos, zygotic embryos, and macropores. Most PkNF YB/C genes do not respond to ABA treatment during the maturation culture process. Compared with the absence of ABA, PkNF-YB8 was up-regulated in ABA treatment for one week (4.1 times) and two weeks (11.6 times). However, PkNF-YC5 was down-regulated in both one week (0.6 times) and two weeks (0.36 times) of culture, but the down-regulation trend was weakened in tissues treated with ABA (0.72–0.83 times). In addition, the promoter of PkNF YB/Cs was rich in elements that respond to various plant hormones, indicating their critical role in hormone pathways. The overexpression of PkLEC1 stimulated the generation of early somatic embryos from callus tissue with no potential for embryogenesis, enhancing the somatic embryogenesis ability of P. koraiensis callus tissue. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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18 pages, 5428 KiB  
Article
Phylogenetic and Expression Analysis of SBP-Box Gene Family to Enhance Environmental Resilience and Productivity in Camellia sinensis cv. Tie-guanyin
by Yusen Gao, Yingxin Wen, Qinmin Lin, Yizhuo Feng, Xinying Shi, Siyao Xiao, Elisabeth Tumukunde, Kehui Zheng and Shijiang Cao
Plants 2025, 14(3), 422; https://doi.org/10.3390/plants14030422 - 1 Feb 2025
Viewed by 760
Abstract
Tieguanyin tea, a renowned oolong tea, is one of the ten most famous teas in China. The Squamosa Promoter Binding Protein (SBP)-box transcription factor family, widely present in plants, plays a crucial role in plant development, growth, and stress responses. In this study, [...] Read more.
Tieguanyin tea, a renowned oolong tea, is one of the ten most famous teas in China. The Squamosa Promoter Binding Protein (SBP)-box transcription factor family, widely present in plants, plays a crucial role in plant development, growth, and stress responses. In this study, we identify and analyze 22 CsSBP genes at the genome-wide level. These genes were distributed unevenly across 11 chromosomes. Using Arabidopsis thaliana and Solanum lycopersicum L. as model organisms, we constructed a phylogenetic tree to classify these genes into six distinct subfamilies. Collinearity analysis revealed 20 homologous gene pairs between AtSBP and CsSBP, 21 pairs between SiSBP and CsSBP, and 14 pairs between OsSBP and CsSBP. Cis-acting element analysis indicated that light-responsive elements were the most abundant among the CsSBP genes. Protein motif, domain, and gene architecture analyses demonstrated that members of the same subgroup shared similar exon–intron structures and motif arrangements. Furthermore, we evaluated the expression profiles of nine CsSBP genes under light, shade, and cold stress using qRT-PCR analysis. Notably, CsSBP1, CsSBP17, and CsSBP19 were significantly upregulated under all three stresses. This study provides fundamental insights into the CsSBP gene family and offers a novel perspective on the mechanisms of SBP transcription factor-mediated stress responses, as well as Tieguanyin tea’s adaptation to environmental variations. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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20 pages, 6952 KiB  
Article
Genetic Diversity Analysis and Polyploid Induction Identification of Idesia polycarpa
by Xiaomei Luo, Yunke Liu, Yuting Lei, Zhoujian He, Xiao Gong, Meng Ye and Qiangang Xiao
Plants 2024, 13(23), 3394; https://doi.org/10.3390/plants13233394 - 3 Dec 2024
Viewed by 1239
Abstract
Idesia polycarpa from Sichuan is a valuable germplasm with high economic potential, but it faces variety scarcity. To address this, this study collected 16 varieties (lines), identifying IpHT1 as a promising parent due to its high oil content (38.5%) and red fruits. Polyploid [...] Read more.
Idesia polycarpa from Sichuan is a valuable germplasm with high economic potential, but it faces variety scarcity. To address this, this study collected 16 varieties (lines), identifying IpHT1 as a promising parent due to its high oil content (38.5%) and red fruits. Polyploid induction via adding 0.50% colchicine to Murashige and Skoog (MS) medium yielded 520 IpHT1 mutagenized seedlings. Subsequently, flow cytometry (FCM) was performed on 401 morphologically variant seedlings which had been initially screened, resulting in the identification of 15 suspected triploids, 35 suspected tetraploids, and 3 chimeras. Furthermore, fluorescence in situ hybridization (FISH) analysis found that the probe (AG3T3)3 had terminal signals at both ends of each chromosome, allowing for the counting of 42 chromosomes in diploids and 84 in tetraploids. The probe 5S rDNA showed 2, 3, and 4 hybridization signals in the interphase nuclei of diploid, triploid, and tetraploid cells, respectively, but the probe (GAA)6 failed to produce any signal on I. polycarpa chromosomes. Ultimately, 18 polyploids were selected, including 7 triploids and 11 tetraploids. Triploids and tetraploids showed significant leaf morphological and physiological differences from diploids. Consequently, this study successfully established a polyploid breeding system for I. polycarpa, thereby enhancing its genetic diversity and breeding potential. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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10 pages, 2597 KiB  
Communication
Screening and Functional Evaluation of Four Larix kaempferi Promoters
by Chen-Yi Zhang, Zha-Long Ye, Li-Wang Qi, Ling Yang and Wan-Feng Li
Plants 2024, 13(19), 2777; https://doi.org/10.3390/plants13192777 - 3 Oct 2024
Cited by 2 | Viewed by 1447
Abstract
Promoters are powerful tools for breeding new varieties using transgenic technology. However, the low and unstable expression of target genes is still a limiting factor in Larix kaempferi (Lamb.) Carr (Japanese larch) genetic transformation. In this study, we analyzed L. kaempferi transcriptome data, [...] Read more.
Promoters are powerful tools for breeding new varieties using transgenic technology. However, the low and unstable expression of target genes is still a limiting factor in Larix kaempferi (Lamb.) Carr (Japanese larch) genetic transformation. In this study, we analyzed L. kaempferi transcriptome data, screened out highly expressed genes, cloned their promoters, and constructed plant expression vectors containing the β-glucuronidase (GUS) reporter gene driven by these promoters. Recombinant vectors were introduced into the L. kaempferi embryogenic callus by means of the Agrobacterium-mediated transient or stable genetic transformation method, and the promoter activity was then determined by measuring GUS expression and its enzyme activity in the transformed materials. Four highly expressed genes were identified: L. kaempferi Zhang Chen Yi-1 (LaZCY-1), Zhang Chen Yi-2 (LaZCY-2), Translationally Controlled Tumor Protein (LaTCTP), and ubiquitin (LaUBQ). The 2000 bp fragments upstream of ATG in these sequences were cloned as promoters and named pLaZCY-1, pLaZCY-2, pLaTCTP, and pLaUBQ. Semi-quantitative and quantitative RT-PCR analyses of transient genetic transformation materials showed that all four promoters could drive GUS expression, indicating that they have promoter activities. Semi-quantitative and quantitative RT-PCR analyses and the histochemical staining of stable genetic transformation materials showed that the pLaUBQ promoter had higher activity than the other three L. kaempferi promoters and the CaMV35S promoter. Thus, the pLaUBQ promoter was suggested to be used in larch genetic transformation. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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16 pages, 2294 KiB  
Article
Economic Evaluation of Conservation through Use of an Araucaria angustifolia Provenance and Progeny Test
by José Arimatéia Rabelo Machado, Miguel Luiz Menezes Freitas, Daniela Ivana Paiva, Bruno Marchetti de Souza, Valderês Aparecida De Sousa, Karina Martins, Edilson Batista Oliveira and Ananda Virginia De Aguiar
Plants 2024, 13(18), 2580; https://doi.org/10.3390/plants13182580 - 14 Sep 2024
Cited by 2 | Viewed by 900
Abstract
Araucaria angustifolia is a species known for its valuable wood and nuts, but it is threatened with extinction. The plantation of forests for genetic resource conservation is a complementary strategy designed to reduce the species’ genetic variability loss. This study aimed to evaluate [...] Read more.
Araucaria angustifolia is a species known for its valuable wood and nuts, but it is threatened with extinction. The plantation of forests for genetic resource conservation is a complementary strategy designed to reduce the species’ genetic variability loss. This study aimed to evaluate the technical and economic viability of A. angustifolia for genetic conservation through use. The analyzed provenance and progeny trial was established in 1982 in Itapeva, Brazil. It was structured using a compact family blocks design with 110 open-pollinated progenies from five natural populations, three replicates, ten plants per subplot, and 3.0 m × 2.0 m spacing. After 33 years, the trial was evaluated for total height, diameter at breast height, wood volume, and survival. The variance components and genetic parameter estimates were performed using Restricted Maximum Likelihood/Best Linear Unbiased Prediction methods (REML/BLUP) methods with the Selegen software (version 2014). The production and management scenarios were obtained using the SisAraucaria software (version 2003). Sensitivity analysis and economic parameter estimates were obtained through various economic evaluation methods using the Planin software (version 1995). In general, the genetic parameters indicated that the population has enough variability for both conservation and breeding purposes, suggesting technical viability for the establishment of a seed orchard. The economic parameters indicated that the commercialization of wood and araucaria nuts proved to be more profitable than wood production by itself. In conclusion, araucaria genetic conservation through use is a technically and economically viable ex situ conservation strategy. Full article
(This article belongs to the Special Issue Advances in Forest Tree Genetics and Breeding)
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