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Genes
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Forest Genetics and Forest-Tree Breeding
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Forest Genetics and Forest-Tree Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 6644

Special Issue Editors

Dr. Changjun Ding

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Guest Editor
Institute of Forestry, Chinese Academy of Forestry, Beijing, China
Interests: drought and salt tolerance in poplar; heterosis; genetic mechanisms
Special Issues, Collections and Topics in MDPI journals
Dr. Weixi Zhang

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Guest Editor
Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
Interests: transgenic breeding; gene editing breeding; tree breeding; forest genetics; biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Presently, climate change is an important global challenge. Forest trees represent the main body of terrestrial ecosystems. It is widely accepted that accelerating the process of forest tree breeding and enhancing forest biomass production will be helpful in responding to climate change.

The forthcoming Special Issue aims to outline the latest topics of forest genetics and tree breeding research, focusing on the molecular mechanisms of the formation of important traits, such as forest yield, quality and resistance, by using multi-omics methods. Priority will also be given to works that elucidate the changes in plant growth, development and yield induced by environmental stress, or that report on the molecular basis of the plastic phenotypic response of plants to the environment. Moreover, studies on the genetic and epigenetic regulatory networks that underpin plant responses to single or combined stresses, including abiotic stress, are also welcome. Topics also include the phenotypic and molecular evaluation of forest tree germplasm in relation to biotic stress, the detection and validation of genes or genomic regions involved in plant–stress interactions, and breeding efforts to increase tolerance or resistance that also use biotechnological and genomic approaches.

Dr. Changjun Ding
Dr. Weixi Zhang
Guest Editors

Manuscript Submission Information

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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. Genes 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

  • forest genetics
  • tree breeding
  • hybridization breeding
  • hybrid vigor
  • germplasm resources
  • genotypic diversity
  • omics

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Published Papers (3 papers)

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Research

15 pages, 2997 KiB  
Article
Genome-Wide Identification, Characterization, and Expression Analysis of the HD-Zip Gene Family in Lagerstroemia for Regulating Plant Height
by Hang Lin, Xinqiang Jiang, Cheng Qian, Yue Zhang, Xin Meng, Nairui Liu, Lulu Li, Jingcai Wang and Yiqian Ju
Genes 2024, 15(4), 428; https://doi.org/10.3390/genes15040428 - 28 Mar 2024
Cited by 1 | Viewed by 1301
Abstract
The Homeodomain leucine zipper (HD-Zip) family of transcription factors is crucial in helping plants adapt to environmental changes and promoting their growth and development. Despite research on the HD-Zip family in various plants, studies in Lagerstroemia (crape myrtle) have not been reported. This [...] Read more.
The Homeodomain leucine zipper (HD-Zip) family of transcription factors is crucial in helping plants adapt to environmental changes and promoting their growth and development. Despite research on the HD-Zip family in various plants, studies in Lagerstroemia (crape myrtle) have not been reported. This study aimed to address this gap by comprehensively analyzing the HD-Zip gene family in crape myrtle. This study identified 52 HD-Zip genes in the genome of Lagerstroemia indica, designated as LinHDZ1-LinHDZ52. These genes were distributed across 22 chromosomes and grouped into 4 clusters (HD-Zip I-IV) based on their phylogenetic relationships. Most gene structures and motifs within each cluster were conserved. Analysis of protein properties, gene structure, conserved motifs, and cis-acting regulatory elements revealed diverse roles of LinHDZs in various biological contexts. Examining the expression patterns of these 52 genes in 6 tissues (shoot apical meristem, tender shoot, and mature shoot) of non-dwarf and dwarf crape myrtles revealed that 2 LinHDZs (LinHDZ24 and LinHDZ14) and 2 LinHDZs (LinHDZ9 and LinHDZ35) were respectively upregulated in tender shoot of non-dwarf crape myrtles and tender and mature shoots of dwarf crape myrtles, which suggested the important roles of these genes in regulate the shoot development of Lagerstroemia. In addition, the expression levels of 2 LinHDZs (LinHDZ23 and LinHDZ34) were significantly upregulated in the shoot apical meristem of non-dwarf crape myrtle. These genes were identified as key candidates for regulating Lagerstroemia plant height. This study enhanced the understanding of the functions of HD-Zip family members in the growth and development processes of woody plants and provided a theoretical basis for further studies on the molecular mechanisms underlying Lagerstroemia plant height. Full article
(This article belongs to the Special Issue Forest Genetics and Forest-Tree Breeding)
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14 pages, 2561 KiB  
Article
RNA-Sequencing Reveals the Involvement of Sesquiterpene Biosynthesis Genes and Transcription Factors during an Early Response to Mechanical Wounding of Aquilaria sinensis
by Jieru Xu, Ruyue Du, Yue Wang and Jinhui Chen
Genes 2023, 14(2), 464; https://doi.org/10.3390/genes14020464 - 11 Feb 2023
Cited by 7 | Viewed by 2536
Abstract
Plants respond to wounding by reprogramming the expression of genes involved in secondary metabolism. Aquilaria trees produce many bioactive secondary metabolites in response to wounding, but the regulatory mechanism of agarwood formation in the early response to mechanical wounding has remained unclear. To [...] Read more.
Plants respond to wounding by reprogramming the expression of genes involved in secondary metabolism. Aquilaria trees produce many bioactive secondary metabolites in response to wounding, but the regulatory mechanism of agarwood formation in the early response to mechanical wounding has remained unclear. To gain insights into the process of transcriptome changes and to determine the regulatory networks of Aquilaria sinensis to an early response (15 days) to mechanical wounding, we collected A. sinensis samples from the untreated (Asc1) and treated (Asf1) xylem tissues and performed RNA sequencing (RNA-seq). This generated 49,102,523 (Asc1) and 45,180,981 (Asf1) clean reads, which corresponded to 18,927 (Asc1) and 19,258 (Asf1) genes, respectively. A total of 1596 differentially expressed genes (DEGs) were detected in Asf1 vs. Asc1 (|log2 (fold change)| ≥ 1, Padj ≤ 0.05), of which 1088 were up-regulated and 508 genes were down-regulated. GO and KEGG enrichment analysis of DEGs showed that flavonoid biosynthesis, phenylpropanoid biosynthesis, and sesquiterpenoid and triterpenoid biosynthesis pathways might play important roles in wound-induced agarwood formation. Based on the transcription factor (TF)-gene regulatory network analysis, we inferred that the bHLH TF family could regulate all DEGs encoding for farnesyl diphosphate synthase, sesquiterpene synthase, and 1-deoxy-D-xylulose-5-phosphate synthase (DXS), which contribute to the biosynthesis and accumulation of agarwood sesquiterpenes. This study provides insight into the molecular mechanism regulating agarwood formation in A. sinensis, and will be helpful in selecting candidate genes for improving the yield and quality of agarwood. Full article
(This article belongs to the Special Issue Forest Genetics and Forest-Tree Breeding)
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16 pages, 5236 KiB  
Article
PyuARF16/33 Are Involved in the Regulation of Lignin Synthesis and Rapid Growth in Populus yunnanensis
by Zhixu Hu, Dan Zong, Qin Zhang, Xiaolin Zhang, Yu Lu and Chengzhong He
Genes 2023, 14(2), 278; https://doi.org/10.3390/genes14020278 - 21 Jan 2023
Cited by 5 | Viewed by 2034
Abstract
(1) Background: Lignin is a unique component of the secondary cell wall, which provides structural support for perennial woody plants. ARFs are the core factors of the auxin-signaling pathway, which plays an important role in promoting plant growth, but the specific relationship between [...] Read more.
(1) Background: Lignin is a unique component of the secondary cell wall, which provides structural support for perennial woody plants. ARFs are the core factors of the auxin-signaling pathway, which plays an important role in promoting plant growth, but the specific relationship between auxin response factors (ARFs) and lignin has not been fully elucidated with regard to rapid plant growth in forest trees. (2) Objectives: This study aimed to investigate the relationship between ARFs and lignin with regard to rapid plant growth in forest trees. (3) Methods: We used bioinformatics analysis to investigate the PyuARF family, find genes homologous to ARF6 and ARF8 in Populus yunnanensis, and explore the changes in gene expression and lignin content under light treatment. (4) Results: We identified and characterized 35 PyuARFs based on chromosome-level genome data from P. yunnanensis. In total, we identified 92 ARF genes in P. yunnanensis, Arabidopsis thaliana, and Populus trichocarpa, which were subsequently divided into three subgroups based on phylogenetic analysis and classified the conserved exon–intron structures and motif compositions of the ARFs into the same subgroups. Collinearity analysis suggested that segmental duplication and whole-genome duplication events were majorly responsible for the expansion of the PyuARF family, and the analysis of Ka/Ks indicated that the majority of the duplicated PyuARFs underwent purifying selection. The analysis of cis-acting elements showed that PyuARFs were sensitive to light, plant hormones, and stress. We analyzed the tissue-specific transcription profiles of PyuARFs with transcriptional activation function and the transcription profiles of PyuARFs with high expression under light in the stem. We also measured the lignin content under light treatment. The data showed that the lignin content was lower, and the gene transcription profiles were more limited under red light than under white light on days 1, 7, and 14 of the light treatments. The results suggest that PyuARF16/33 may be involved in the regulation of lignin synthesis, thereby promoting the rapid growth of P. yunnanensis. (5) Conclusions: Collectively, this study firstly reports that PyuARF16/33 may be involved in the regulation of lignin synthesis and in promoting the rapid growth in P. yunnanensis. Full article
(This article belongs to the Special Issue Forest Genetics and Forest-Tree Breeding)
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