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Genetic Breeding of Trees
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Genetic Breeding of Trees

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 October 2025 | Viewed by 8186

Special Issue Editors

Dr. Wenhao Bo

E-Mail Website
Guest Editor
State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
Interests: forest genomics; forest phenomics; genetic improvement in forest
Prof. Dr. Jinhuan Chen

E-Mail Website
Guest Editor
State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
Interests: trees breeding; tree genetics; plant stress response

Special Issue Information

Dear Colleagues,

Forests provide multitude of resources such as timber, paper, medicinal materials, food, and industrial materials, which play a vital role in soil and water conservation, climate regulation, and the maintenance of biodiversity, forming an essential part of terrestrial ecosystems. With the impacts of climate change and increasing demands from human populations, the genetic improvement of forest trees becomes increasingly crucial for both basic research and applications in forestry. It can enhance the adaptability, growth rate, and production and quality of timber, food, and medicinal products of tree species, as well as the ability to resist biotic and abiotic stresses. This Special Issue aims to collect and showcase the latest research findings and advancements in the field of the genetic breeding of trees.

Topics of interest for the issue include but are not limited to:

  • New strategies and methods for the genetic improvement of tree species;
  • Evaluation of tree genetic resources;
  • Application of molecular markers and genomics in tree species improvement;
  • The biotechnology in the genetic improvement of forest trees;
  • Genetic basis studies on the adaptability of forest trees to environmental changes;
  • Genetic breeding for resistance to biotic and abiotic stresses;
  • The relationship between forest ecosystem services and genetic breeding.
  • Flowering and pollination rules and its molecular mechanism of forest plants

We invite researchers, scholars, and practitioners from around the globe to submit their original research and review articles on tree species genetic improvement, genomics, molecular biology, the management and conservation of genetic resources, and related fields.

Dr. Wenhao Bo
Prof. Dr. Jinhuan Chen
Guest Editors

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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • tree genomics
  • tree species genetic improvement
  • adaptive genetics in forestry
  • forest genetic resources
  • biotechnology in tree breeding
  • molecular markers in forestry
  • biotic and abiotic stress resistance in trees
  • forest biodiversity conservation
  • wood quality improvement
  • forest tree phenotyping
  • genetic diversity and tree conservation

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Published Papers (9 papers)

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Research

16 pages, 2320 KiB  
Article
Transposon-Associated Small RNAs Involved in Plant Defense in Poplar
by Cui Long, Yuxin Du, Yumeng Guan, Sijia Liu and Jianbo Xie
Plants 2025, 14(8), 1265; https://doi.org/10.3390/plants14081265 - 21 Apr 2025
Viewed by 340
Abstract
Utilizing high-throughput Illumina sequencing, we examined how small RNA (sRNA) profiles vary in Chinese white poplar (Populus tomentosa) across two pivotal infection stages by the rust fungus Melampsora larici-populina: the biotrophic growth phase (T02; 48 h post infection) and the [...] Read more.
Utilizing high-throughput Illumina sequencing, we examined how small RNA (sRNA) profiles vary in Chinese white poplar (Populus tomentosa) across two pivotal infection stages by the rust fungus Melampsora larici-populina: the biotrophic growth phase (T02; 48 h post infection) and the urediniospore development and dispersal phase (T03; 168 h), both essential for plant colonization and prolonged biotrophic engagement. Far exceeding random expectations, siRNA clusters predominantly arose from transposon regions, with pseudogenes also contributing significantly, and infection-stage-specific variations were notably tied to these transposon-derived siRNAs. As the infection advanced, clusters of 24 nt siRNAs in transposon and intergenic regions exhibited pronounced abundance shifts. An analysis of targets indicated that Populus sRNAs potentially regulate 95% of Melampsora larici-populina genes, with pathogen effector genes showing heightened targeting by sRNAs during the biotrophic and urediniospore phases compared to controls, pointing to selective sRNA-target interactions. In contrast to conserved miRNAs across plant species, Populus-specific miRNAs displayed a markedly greater tendency to target NB-LRR genes. These observations collectively highlight the innovative roles of sRNAs in plant defense, their evolutionary roots, and their dynamic interplay with pathogen coevolution. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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15 pages, 4608 KiB  
Article
Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in Populus euphratica
by Yunzhu Shi, Zixuan Mu, Xiangyu Meng, Xiang Li, Lingxuan Zou, Xuli Zhu and Wenhao Bo
Plants 2025, 14(8), 1248; https://doi.org/10.3390/plants14081248 - 19 Apr 2025
Viewed by 319
Abstract
Auxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF [...] Read more.
Auxin response factor (ARF) is a plant-specific transcription factor that responds to changes in auxin levels, regulating various biological processes in plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF gene family in Populus euphratica Oliv. using bioinformatics analysis, examining their conserved structural domains, gene structure, expression products, and evolutionary relationships. We found that the 34 PeARF genes were unevenly distributed on 19 chromosomes of P. euphratica. All 56 PeARF proteins were hydrophilic and unstable proteins localized in the nucleus, with secondary structures containing α-helices, extended strands, random coils, and β-turns but lacking transmembrane helices (TM-helices) and signal peptides. Evolutionary analysis divided the PeARF proteins into five subfamilies (A–E), with high conservation observed in the order and number of motifs, domains, gene structure, and other characteristics within each subfamily. Expression pattern analysis revealed that 17 PeARF genes were upregulated during cell growth and heterophylly development. This comprehensive analysis provides insights into the molecular mechanisms of ARF genes in P. euphratica growth, development, and stress response, serving as a basis for further studies on the auxin signaling pathway in P. euphratica. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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15 pages, 9095 KiB  
Article
Genome-Wide Identification of the CYP78A Gene Family in Lycium and Functional Characterization of LrCYP78A5
by Yiru Zhao, Shupei Rao, Guoli Dai and Jinhuan Chen
Plants 2025, 14(8), 1152; https://doi.org/10.3390/plants14081152 - 8 Apr 2025
Viewed by 378
Abstract
The CYP78A gene family, a plant-specific subfamily of cytochrome P450 enzymes, plays pivotal roles in plant growth, development, and stress responses. Although the CYP78A genes in many plants have been widely studied, little is known about them in Lycium. In this study, [...] Read more.
The CYP78A gene family, a plant-specific subfamily of cytochrome P450 enzymes, plays pivotal roles in plant growth, development, and stress responses. Although the CYP78A genes in many plants have been widely studied, little is known about them in Lycium. In this study, we identified six CYP78A genes in both Lycium barbarum and Lycium ruthenicum through comprehensive bioinformatics analysis. These genes exhibited high conservation in protein structure, gene organization, and conserved motifs. Phylogenetic analysis revealed they are close in terms of homology to CYP78A genes in Arabidopsis, tomato, and eggplant. Cis-acting element analysis of the promoter regions indicated that CYP78A genes are involved in light, hormone, and stress responses, with tissue-specific expression patterns observed across different developmental stages. Subcellular localization experiments confirmed that LrCYP78A5 is localized in the endoplasmic reticulum. Overexpression of LrCYP78A5 in L. ruthenicum resulted in a significant increase in chlorophyll content, indicating the former’s potential role in plant growth. These findings provide valuable insights into the functional roles of the CYP78A gene family in goji, highlighting their potential involvement in growth regulation and metabolic processes. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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19 pages, 2093 KiB  
Article
Comparative Study on Growth Characteristics and Early Selection Efficiency of Hybrid Offspring of Populus deltoides ‘DD-109’ and P. maximowiczii in Liaoning, China
by Wei Liu, Chenggong Liu, Yan Zhang, Jinhua Li, Jiabao Ji, Xiaorui Qin, Fenfen Liu, Chengcheng Gao, Nairui Wang, Xueli Zhang, Ning Liu, Rusheng Peng and Qinjun Huang
Plants 2025, 14(1), 111; https://doi.org/10.3390/plants14010111 - 2 Jan 2025
Viewed by 717
Abstract
Poplar is an important tree species for timber supply and ecological protection in northern China. Cultivating and selecting high-quality varieties and germplasm resources suitable for cultivation are key factors in enhancing the quality and productivity of poplar plantations in the arid and semi-arid [...] Read more.
Poplar is an important tree species for timber supply and ecological protection in northern China. Cultivating and selecting high-quality varieties and germplasm resources suitable for cultivation are key factors in enhancing the quality and productivity of poplar plantations in the arid and semi-arid northern regions with shorter growing seasons. This study conducted a field cultivation experiment on 10 progeny clones from the direct cross (D × M) of imported Populus deltoides ‘DD-109’ with Populus maximowiczii and 7 progeny clones from the reciprocal cross (M × D) using one-year-old rooted cuttings planted at a 4 m × 8 m spacing. Based on 17 years of annual growth observations, the study systematically compared growth characteristics, age of quantitative maturity, path relationships between traits, and early selection efficiency in the hybrid offspring. The results indicated that the D × M population had superior diameter at breast height (DBH), tree height (H), and volume (V) compared to the M × D population, while the height-to-diameter ratio (HDR) was lower. The growth rate of the 17 clones peaked from 10 to 14 years, with annual volume growth increments (PAIs) higher than mean annual volume increments (MAIs) during the early growth stages; the quantitative maturity age ranged between 12 and 16 years. The D × M population generally reached quantitative maturity earlier than the M × D population, with the fastest clone maturing in 12 years. Four clones (DM-9-17, DM-9-18, DM-9-14, and MD-61) showed values for V, DBH, H, and HDR above the hybrid group average. Path analysis demonstrated that DBH had the most significant direct and indirect effects on V, suggesting it as the best predictor for V. Using DBH as a reference, correlation and early selection efficiency analysis showed a strong relationship between growth characteristics at planting years 4–5 and later-stage performance, indicating this as the optimal period for early selection. These findings contribute to evaluating the production potential of P. deltoides ‘DD-109’ and P. maximowiczii germplasm in northern China and provide valuable guidance for selecting poplar clones suitable for local cultivation, accelerating breeding processes, and informing management planning for poplar plantations. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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14 pages, 2240 KiB  
Article
Simultaneous Down-Regulation of Dominant Cinnamoyl CoA Reductase and Cinnamyl Alcohol Dehydrogenase Dramatically Altered Lignin Content in Mulberry
by Shuai Huang, Xiaoru Kang, Rumeng Fu, Longyan Zheng, Peijun Li, Fengjuan Tang, Nan Chao and Li Liu
Plants 2024, 13(24), 3512; https://doi.org/10.3390/plants13243512 - 16 Dec 2024
Viewed by 800
Abstract
Mulberry (Morus alba L.) is a significant economic tree species in China. The lignin component serves as a critical limiting factor that impacts both the forage quality and the conversion efficiency of mulberry biomass into biofuel. Cinnamoyl CoA reductase (CCR; EC 1.21.1.44) [...] Read more.
Mulberry (Morus alba L.) is a significant economic tree species in China. The lignin component serves as a critical limiting factor that impacts both the forage quality and the conversion efficiency of mulberry biomass into biofuel. Cinnamoyl CoA reductase (CCR; EC 1.21.1.44) and cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.95) are the key enzymes that catalyze the final two reductive steps in the biosynthesis of monolignols. In this study, we conducted a comprehensive functional analysis to validate the predominant CCR genes involved in monolignol biosynthesis. In this study, we initially validated the predominant CCR genes implicated in monolignol biosynthesis through an extensive functional analysis. Phylogenetic analysis, tissue-specific expression profiling and enzymatic assays indicated that MaCCR1 is the authentic CCR involved in lignin biosynthesis. Furthermore, the expression level of MaCCR1 exhibited a significant positive correlation with lignin content, and the down-regulation of MaCCR1 via virus-induced gene silencing resulted in altered lignin content in mulberry. The down-regulation of MaCCR1 and MaCAD3/4, both individually and concurrently, exhibited markedly different effects on lignin content and mulberry growth. Specifically, the simultaneous down-regulation of MaCCR1 and MaCAD3/4 significantly altered lignin content in mulberry, resulting in dwarfism of the plants. Conversely, the down-regulation of MaCAD3/4 alone not only decreased lignin content but also led to an increase in biomass. These findings offer compelling evidence elucidating the roles of MaCCRs in mulberry and identify specific target genes, thereby providing a crucial foundation for the genetic modification of lignin biosynthesis. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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21 pages, 8595 KiB  
Article
Genome-Wide Identification of Xyloglucan Endotransglucosylase/Hydrolase Multigene Family in Chinese Jujube (Ziziphus jujuba) and Their Expression Patterns Under Different Environmental Stresses
by Mohamed Refaiy, Muhammad Tahir, Lijun Jiao, Xiuli Zhang, Huicheng Zhang, Yuhan Chen, Yaru Xu, Shuang Song and Xiaoming Pang
Plants 2024, 13(24), 3503; https://doi.org/10.3390/plants13243503 - 15 Dec 2024
Viewed by 1258
Abstract
The Xyloglucan endotransglucosylase/hydrolase (XTH) family, a group of cell wall-modifying enzymes, plays crucial roles in plant growth, development, and stress adaptation. The quality and yield of Chinese jujube (Ziziphus jujuba) fruit are significantly impacted by environmental stresses, including excessive salinity, drought, [...] Read more.
The Xyloglucan endotransglucosylase/hydrolase (XTH) family, a group of cell wall-modifying enzymes, plays crucial roles in plant growth, development, and stress adaptation. The quality and yield of Chinese jujube (Ziziphus jujuba) fruit are significantly impacted by environmental stresses, including excessive salinity, drought, freezing, and disease. However, there has been no report of the XTH encoding genes present in the Chinese jujube genome and their response transcription level under various stresses. This study provides an in-depth analysis of ZjXTH genes in the genome of Chinese jujube and elucidates their structural motifs, regulatory networks, and expression patterns under various stresses. A total of 29 ZjXTH genes were identified from the Ziziphus jujuba genome. Phylogenetic analysis classifies ZjXTH genes into four distinct groups, while conserved motifs and domain analyses reveal coordinated xyloglucan modifications, highlighting key shared motifs and domains. Interaction network predictions suggest that ZjXTHs may interact with proteins such as Expansin-B1 (EXPB1) and Pectin Methylesterase 22 (PME22). Additionally, cis-regulatory element analysis enhances our understanding of Chinese jujube plant’s defensive systems, where TCA- and TGACG-motifs process environmental cues and orchestrate stress responses. Expression profiling revealed that ZjXTH1 and ZjXTH5 were significantly upregulated under salt, drought, freezing, and phytoplasma infection, indicating their involvement in biotic and abiotic stress responses. Collectively, these findings deepen our understanding of the functional roles of Chinese jujube XTHs, emphasizing their regulatory function in adaptive responses in Chinese jujube plants. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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14 pages, 2123 KiB  
Article
Parental Reconstruction from a Half-Sib Population of Stoneless Jujube Ziziphus jujuba Mill. Based on Individual Specific SNP Markers Using Multiplex PCR
by Muhammad Tahir, Yue Ren, Bo Wu, Meiyu Li, Mohamed Refaiy, Ming Cao, Decang Kong and Xiaoming Pang
Plants 2024, 13(22), 3163; https://doi.org/10.3390/plants13223163 - 11 Nov 2024
Viewed by 976
Abstract
The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in [...] Read more.
The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between ‘Wuhezao’ and ‘JingZao 39’, segregating for stone and stoneless fruit. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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13 pages, 4416 KiB  
Article
Genome-Wide Characterization and Development of Simple Sequence Repeat Markers for Molecular Diversity Analyses in Yellowhorn (Xanthoceras sorbifolium Bunge)
by Xiaoming Yang, Yuan Wang, Yuewen Yang, Tuya Shareng, Yukun Xing, Gaowa Bai, Zhongyu Xing, Yuanyuan Ji, Liling Liu and Gongxiang Cao
Plants 2024, 13(19), 2794; https://doi.org/10.3390/plants13192794 - 5 Oct 2024
Viewed by 954
Abstract
Yellowhorn (Xanthoceras sorbifolium Bunge) is a valuable ornamental, medicinal, and woody oilseed species that is indigenous to China. The breeding improvement of yellowhorn has been hindered by a lack of suitable markers and sufficient information regarding the molecular diversity of this species. [...] Read more.
Yellowhorn (Xanthoceras sorbifolium Bunge) is a valuable ornamental, medicinal, and woody oilseed species that is indigenous to China. The breeding improvement of yellowhorn has been hindered by a lack of suitable markers and sufficient information regarding the molecular diversity of this species. In this study, we conducted a comprehensive analysis of the yellowhorn genome to characterize the simple sequence repeat (SSR) loci. A total of 4,007,201 SSRs were successfully identified. Among these markers, mono-nucleotide SSRs were most abundant in the genome, while the tri-nucleotide SSRs accounted for the highest proportion in coding sequences. The GO and KEGG function enrichment analysis revealed that most SSR loci in coding sequences were associated with potential biological functions. Additionally, we used 30 pairs of primers to amplify SSR markers to gain a better understanding of the genetic variation in yellowhorn germplasms. The average values of observed heterozygosity and polymorphism information content were 0.625 and 0.517, respectively. Population structure, phylogeny and principal component analyses identified two distinct subclusters. Furthermore, yellowhorn germplasms with the same geographical distribution tended to group together. Moreover, a total of 26 yellowhorn core collections, which accounted for approximately 14.94% of the total yellowhorn germplasms, effectively represented the genetic diversity of all original germplasms. Our findings not only unveiled the genetic diversity and population structure of yellowhorn germplasms but also investigated the yellowhorn core collection, which will serve as a strong basis for yellowhorn management and genetic improvement. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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14 pages, 2551 KiB  
Article
Identification of Key Genes of Fruit Shape Variation in Jujube with Integrating Elliptic Fourier Descriptors and Transcriptome
by Yue Ren, Wenqing Fu, Yi Gao, Yuhan Chen, Decang Kong, Ming Cao, Xiaoming Pang and Wenhao Bo
Plants 2024, 13(9), 1273; https://doi.org/10.3390/plants13091273 - 5 May 2024
Cited by 1 | Viewed by 1506
Abstract
Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and [...] Read more.
Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) for gene discovery remain scarce. In this study, six cultivars of jujube fruits with distinct shapes were selected, and samples were collected from the fruit set period to the white mature stage across five time points for shape analysis and transcriptome studies. By combining EFDs with WGCNA and STEM, the study aimed to identify the critical periods and key genes involved in the formation of jujube fruit shape. The findings indicated that the D25 (25 days after flowering) is crucial for the development of jujube fruit shape. Moreover, ZjAGL80, ZjABI3, and eight other genes have been implicated to regulate the shape development of jujubes at different periods of fruit development, through seed development and fruit development pathway. In this research, EFDs were employed to precisely delineate the shape of jujube fruits. This approach, in conjunction with transcriptome, enhanced the precision of gene identification, and offered an innovative methodology for fruit shape analysis. This integration facilitates the advancement of research into the morphological characteristics of plant fruits, underpinning the development of a refined framework for the genetic underpinnings of fruit shape variation. Full article
(This article belongs to the Special Issue Genetic Breeding of Trees)
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