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Plant Genetic Diversity and Omics Research
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Plant Genetic Diversity and Omics Research

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

Deadline for manuscript submissions: 20 October 2024 | Viewed by 3111

Special Issue Editors

Dr. Ying Li

E-Mail Website
Guest Editor
The Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan (ICBR), Beijing, China
Interests: plant genetic diversity; omics; plant biology; bamboo plants
Dr. Mingyang Quan

E-Mail Website
Guest Editor
Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
Interests: forest molecular breeding; plant genomics

Special Issue Information

Dear Colleagues,

Plant genetic diversity plays an important role in maintaining plant ecosystem balance, ensuring the ecological security of forests, and promoting the development of the ecological economy. It is evident that, only by understanding plant genetic diversity and the genetic basis of complex traits, can people better take effective measures to protect and utilize them, so as to determine a sustainable development path.

Omics research is one such favorable technique often employed to study plant diversity. Through the analysis of a large number of biological data, one can study the overall characteristics of plant tissues or individuals, the interaction between them, and the biological mechanism implicated in the formation of certain traits.

This Special Issue will thus be subdivided into contributions focused on the role of omics, including genomics, transcriptomics, proteomics, metabolomics and phenomics, in the identification of key metabolic pathways, vital molecular mechanisms, and causative genes, proteins, metabolites, etc., during plant growth, development, and stress response. Existing problems, the development of trends in omics research on plant diversity conservation and utilization, the evaluation of plant population diversity, and the improvement of specific traits will be discussed.

Finally, we will give attention to the multi-omics integration analysis strategy; this can efficiently identify molecular patterns and genetic interactions, accurately construct the interrelationships and regulatory networks among various biomolecules, study complicated problems from both cause-and-effect levels, and verify their relevance.

Dr. Ying Li
Dr. Mingyang Quan
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. 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

  • genetic diversity
  • omics research
  • population diversity evaluation
  • development
  • stress response

Published Papers (3 papers)

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Research

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19 pages, 2381 KiB  
Article
Comparative Transcriptome Analysis of High- and Low-Growth Genotypes of Eucalyptus urophylla in Response to Long-Term Nitrogen Deficiency
by Xiaohui Yang, Fang Xu, Wen Pan, Weihua Zhang, Huanqin Liao, Baozhu Zhu, Bin Xu, Xinyu Chen and Huixiao Yang
Genes 2024, 15(1), 60; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15010060 - 30 Dec 2023
Cited by 1 | Viewed by 740
Abstract
Nutrients play important roles in the growth and development of most plant species. However, in perennial trees, the function of nutrients in different genotypes is poorly understood. Three different nutrient levels (low, sufficient, and high nutrient levels) were applied to two contrasting Eucalyptus urophylla [...] Read more.
Nutrients play important roles in the growth and development of most plant species. However, in perennial trees, the function of nutrients in different genotypes is poorly understood. Three different nutrient levels (low, sufficient, and high nutrient levels) were applied to two contrasting Eucalyptus urophylla cultivars (a high-growth cultivar ZQUA44 and a low-growth cultivar ZQUB15), and growth and expression levels were analyzed. Although the growth traits of both genotypes under nutrient starvation treatment were much lower than under abundant nutrients, tree height, crown width, and biomass of different ZQUA44 tissues were much higher than those of ZQUB15 at all three nutrient levels. Differentially expressed genes (DEGs) clustered into six subclusters based on their expression patterns, and functional annotation showed that the DEGs involved in glutathione metabolism and flavonoid biosynthesis may be responsible for nutrient starvation across different genotypes, while the DEGs involved in carotenoid biosynthesis and starch and sucrose metabolism may have a range of functions in different genotypes. The DEGs encoding the MYB-related family may be responsible for nutrient deficiency in all genotypes, while B3 may have different functions in different genotypes. Our results demonstrate that different genotypes may form different pathways to coordinate plant survival when they face abiotic stresses. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Omics Research)
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20 pages, 16197 KiB  
Article
Transcriptomic Analysis Reveals CBF-Dependent and CBF-Independent Pathways under Low-Temperature Stress in Teak (Tectona grandis)
by Miaomiao Liu, Guang Yang, Wenlong Zhou, Xianbang Wang, Qiang Han, Jiange Wang and Guihua Huang
Genes 2023, 14(11), 2098; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14112098 - 18 Nov 2023
Cited by 1 | Viewed by 1031
Abstract
Teak is a rare tropical tree with high economic value, and it is one of the world’s main afforestation trees. Low temperature is the main problem for introducing and planting this species in subtropical or temperate zones. Low-temperature acclimation can enhance the resistance [...] Read more.
Teak is a rare tropical tree with high economic value, and it is one of the world’s main afforestation trees. Low temperature is the main problem for introducing and planting this species in subtropical or temperate zones. Low-temperature acclimation can enhance the resistance of teak to low-temperature stress, but the mechanism for this is still unclear. We studied the gene expression of two-year-old teak seedlings under a rapid temperature drop from 20 °C to 4 °C using RNA-seq and WGCNA analyses. The leaves in the upper part of the plants developed chlorosis 3 h after the quick transition, and the grades of chlorosis were increased after 9 h, with the addition of water stains and necrotic spots. Meanwhile, the SOD and proline contents in teak leaves increased with the prolonged cold stress time. We also identified 36,901 differentially expressed genes, among which 1055 were novel. Notably, CBF2 and CBF4 were significantly induced by low temperatures, while CBF1 and CBF3 were not. Furthermore, WGCNA successfully identified a total of fourteen modules, which consist of three modules associated with cold stress response genes, two modules linked to CBF2 and CBF4, and one module correlated with the CBF-independent pathway gene HY5. The transformation experiments showed that TgCBF2 and TgCBF4 improved cold resistance in Arabidopsis plants. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Omics Research)
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13 pages, 2627 KiB  
Brief Report
First Contiguous Genome Assembly of Japanese Lady Bell (Adenophora triphylla) and Insights into Development of Different Leaf Types
by Ji-Nam Kang, Si-Myung Lee, Ji-Weon Choi, Seung-Sik Lee and Chang-Kug Kim
Genes 2024, 15(1), 58; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15010058 - 30 Dec 2023
Viewed by 999
Abstract
Adenophora triphylla is an important medicinal and food plant found in East Asia. This plant is rich in secondary metabolites such as triterpenoid saponin, and its leaves can develop into different types, such as round and linear, depending on the origin of germination [...] Read more.
Adenophora triphylla is an important medicinal and food plant found in East Asia. This plant is rich in secondary metabolites such as triterpenoid saponin, and its leaves can develop into different types, such as round and linear, depending on the origin of germination even within the same species. Despite this, few studies have comprehensively characterized the development processes of different leaf types and triterpenoid saponin pathways in this plant. Herein, we provide the first report of a high-quality genome assembly of A. triphylla based on a combination of Oxford Nanopore Technologies and Illumina sequencing methods. Its genome size was estimated to be 2.6 Gb, and the assembled genome finalized as 2.48 Gb, containing 57,729 protein-coding genes. Genome completeness was assessed as 95.6% using the Benchmarking Universal Single-Copy Orthologs score. The evolutionary divergence of A. triphylla was investigated using the genomes of five plant species, including two other species in the Campanulaceae family. The species A. triphylla diverged approximately 51-118 million years ago from the other four plants, and 579 expanded/contracted gene families were clustered in the Gene Ontology terms. The expansion of the β-amyrin synthase (bAS) gene, a key enzyme in the triterpenoid saponin pathway, was identified in the A. triphylla genome. Furthermore, transcriptome analysis of the two leaf types revealed differences in the activity of starch, sucrose, unsaturated fatty acid pathways, and oxidoreductase enzymes. The heat and endoplasmic reticulum pathways related to plant stress were active in the development of round type leaf, while an enhancement of pyrimidine metabolism related to cell development was confirmed in the development of the linear type leaf. This study provides insight into the evolution of bAS genes and the development of different leaf types in A. triphylla. Full article
(This article belongs to the Special Issue Plant Genetic Diversity and Omics Research)
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