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Genes and Genomics of Plants Under Abiotic Stresses
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Genes and Genomics of Plants Under Abiotic Stresses

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

Deadline for manuscript submissions: closed (25 December 2024) | Viewed by 4789

Special Issue Editor

Prof. Dr. Yong-Jun Shu

E-Mail Website
Guest Editor
College of Life Science and Technology, Harbin Normal University, Harbin, China
Interests: genomics; transcriptomics; proteomics; metabolomics; abiotic stress; abiotic tolerance; high-throughput sequencing

Special Issue Information

Dear Colleagues,

High-throughput sequencing technologies have promoted the development of life science research by generating a large amount of biological data for better understanding biological mechanisms. In plant research, omics methods have been broadly integrated to explore plant growth and development phenomena, especially in plant adaption to abiotic stress. As sessile organisms, plants are constantly challenged by various abiotic stressors, including cold, drought, salt, water logging, etc.; these stresses can decrease plant growth and development and even threatened plant survival. Therefore, plants have adopted numerous biological pathways to confer these stresses. Recently, with the development of HTS technologies, many biological data, such as genome sequences, transcriptome sequences, proteomics data, and metabolomics data, have been obtained, which are helpful for demonstrating the molecular mechanisms of plant responses to various abiotic stressors and tolerance from genotype to phenotype.

This Special Issue is dedicated to exploring the molecular mechanisms of plant responses to various abiotic stress, including cold, drought, salt, or other abiotic stresses, even complex abiotic stress. Research improving our understanding of plant adaption to abiotic stresses is welcome, particularly studies involving state-of-the-art high-throughput experiments to investigate plant genomics to abiotic stresses.

Prof. Dr. Yong-Jun Shu
Guest Editor

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Keywords

  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • abiotic stress
  • abiotic tolerance
  • high-throughput sequencing

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Published Papers (4 papers)

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Research

18 pages, 2989 KiB  
Article
Genetic Diversity Analysis and Comprehensive Evaluation of “M82” in EMS-Mutagenized Tomato
by Yanchao Yang, Zhanming Tan, Shuang Liang, Wei Cheng, Yihuan Sun, Yunxia Cheng, Yu Song, Yongming Wang, Jialong Wu and Qi Wang
Genes 2025, 16(2), 179; https://doi.org/10.3390/genes16020179 - 1 Feb 2025
Viewed by 603
Abstract
Background: Ethyl methyl sulfonate (EMS) mutagenesis is widely used because of its advantages of inducing point mutations and no need for genetic transformation. To identify germplasm resources of processed tomatoes with superior comprehensive traits suitable for cultivation in Xinjiang. Methods: In this study, [...] Read more.
Background: Ethyl methyl sulfonate (EMS) mutagenesis is widely used because of its advantages of inducing point mutations and no need for genetic transformation. To identify germplasm resources of processed tomatoes with superior comprehensive traits suitable for cultivation in Xinjiang. Methods: In this study, tomato seeds were treated with 2% EMS reagent for 12 h, 21 quality traits and 20 quantitative traits of 33 processed tomatoes derived from EMS-mutagenized“M82”were evaluated. Results: The results indicated that for traits such as hypocotyl color, growth habit, plant type, leaf type, and leaf shape, the range of quantitative trait variation was 8.45–37.25%, with a genetic diversity index ranging from 1.25 to 2.07. Conclusions: Cluster analysis of quantitative traits categorized the 33 EMS-mutagenized “M82” processed tomato resources into five groups: Group I contained 22 robust germplasm samples; Group II consisted of a single potential high-quality germplasm; Group III comprised five germplasm with a small and extreme plant type; Group IV included four high-yield germplasm; and Group V represented one moderate, conventional germplasm. Raw data from 15 quantitative traits across the 33 accessions were standardized using the “extreme method” to extract six comprehensive factors. The top 10 germplasm resources based on the comprehensive score were 76, 137, 97, 102, 19, 104, 21, 108, 17, and 147. It provides some theoretical basis for realizing the high-yield and high-quality cultivation and variety breeding of processed tomatoes in Xinjiang. Full article
(This article belongs to the Special Issue Genes and Genomics of Plants Under Abiotic Stresses)
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21 pages, 7226 KiB  
Article
Genome-Wide Identification, Conservation, and Expression Pattern Analyses of the BBR-BPC Gene Family Under Abiotic Stress in Brassica napus L.
by Long Wang, Wei Chen, Zhi Zhao, Huaxin Li, Damei Pei, Zhen Huang, Hongyan Wang and Lu Xiao
Genes 2025, 16(1), 36; https://doi.org/10.3390/genes16010036 - 29 Dec 2024
Viewed by 978
Abstract
Background: The BBR-BPC gene family is a relatively conservative group of transcription factors, playing a key role in plant morphogenesis, organ development, and responses to abiotic stress. Brassica napus L. (B. napus), commonly known as oilseed rape, is an allopolyploid plant [...] Read more.
Background: The BBR-BPC gene family is a relatively conservative group of transcription factors, playing a key role in plant morphogenesis, organ development, and responses to abiotic stress. Brassica napus L. (B. napus), commonly known as oilseed rape, is an allopolyploid plant formed by the hybridization and polyploidization of Brassica rapa L. (B. rapa) and Brassica oleracea L. (B. oleracea), and is one of the most important oil crops. However, little is known about the characteristics, conservation, and expression patterns of this gene family in B. napus, especially under abiotic stress. Methods: To explore the characteristics and potential biological roles of the BBR-BPC gene family members in B. napus, we conducted identification based on bioinformatics and comparative genomics methods. We further analyzed the expression patterns through RNA-seq and qRT-PCR. Results: We identified 25 BBR-BPC members, which were classified into three subfamilies based on phylogenetic analysis, and found them to be highly conserved in both monocots and dicots. The conserved motifs revealed that most members contained Motif 1, Motif 2, Motif 4, and Motif 8. After whole-genome duplication (WGD), collinearity analysis showed that BBR-BPC genes underwent significant purifying selection. The promoters of most BBR-BPC genes contained cis-acting elements related to light response, hormone induction, and stress response. RNA-seq and qRT-PCR further indicated that BnBBR-BPC7, BnBBR-BPC15, BnBBR-BPC20, and BnBBR-BPC25 might be key members of this family. Conclusions: This study provides a theoretical foundation for understanding the potential biological functions and roles of the BBR-BPC gene family, laying the groundwork for resistance breeding in B. napus. Full article
(This article belongs to the Special Issue Genes and Genomics of Plants Under Abiotic Stresses)
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14 pages, 3551 KiB  
Article
Genome-Wide Identification and Expression Analysis of SNAP Gene Family in Wheat
by Xiaohan Zhang, Yanan Yu, Yumeng Sun, Yan Bai, Yongjun Shu and Changhong Guo
Genes 2024, 15(10), 1311; https://doi.org/10.3390/genes15101311 - 11 Oct 2024
Viewed by 1486
Abstract
Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, [...] Read more.
Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, physicochemical properties, conserved motifs, and cis-acting elements of the TaSNAP family members. Results: The TaSNAP family comprises members that encode proteins ranging between 120 and 276 amino acids, with isoelectric points spanning from 4.87 to 7.92. Phylogenetic analysis elucidated the categorization of the eight TaSNAP into three distinct subfamilies, wherein members of the same subfamily display marked similarities in their gene structures. Chromosomal mapping revealed the distribution of TaSNAP family members across chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. Utilizing the Plant CARE tool, we identified ten elements linked to plant hormones and four associated with stress responses. Expression analysis via qRT-PCR was performed to assess the levels of the eight TaSNAP genes in various tissues and under diverse abiotic stress conditions. The results indicated heightened expression of most genes in roots compared to spikes. Notably, under ABA stress, the majority of genes exhibited upregulation, whereas certain genes were downregulated under PEG stress, implying a substantial role for SNAP protein in wheat growth and development. Conclusions: This study conducted a comprehensive bioinformatics analysis of each member of the wheat SNAP family, laying a crucial foundation for future functional investigations. Full article
(This article belongs to the Special Issue Genes and Genomics of Plants Under Abiotic Stresses)
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18 pages, 2977 KiB  
Article
Silicon Modifies Photosynthesis Efficiency and hsp Gene Expression in European Beech (Fagus sylvatica) Seedlings Exposed to Drought Stress
by Justyna Nowakowska, Monika Dang, Piotr Kiełtyk, Marzena Niemczyk, Tadeusz Malewski, Wiesław Szulc, Beata Rutkowska, Piotr Borowik and Tomasz Oszako
Genes 2024, 15(9), 1233; https://doi.org/10.3390/genes15091233 - 21 Sep 2024
Cited by 1 | Viewed by 1185
Abstract
Background: Climate change is leading to severe and long-term droughts in European forest ecosystems. can have profound effects on various physiological processes, including photosynthesis, gene expression patterns, and nutrient uptake at the developmental stage of young trees. Objectives: Our study aimed to test [...] Read more.
Background: Climate change is leading to severe and long-term droughts in European forest ecosystems. can have profound effects on various physiological processes, including photosynthesis, gene expression patterns, and nutrient uptake at the developmental stage of young trees. Objectives: Our study aimed to test the hypothesis that the application of silica (SiO2) influences photosynthetic efficiency and gene expression in 1- to 2-year-old Fagus sylvatica (L.) seedlings. Additionally, we aimed to assess whether silicon application positively influences the structural properties of leaves and roots. To determine whether the plant physiological responses are genotype-specific, seedlings of four geographically different provenances were subjected to a one-year evaluation under greenhouse conditions. Methods: We used the Kruskal–Wallis test followed by Wilcoxon’s test to evaluate the differences in silicon content and ANOVA followed by Tukey’s test to evaluate the physiological responses of seedlings depending on treatment and provenance. Results: Our results showed a significantly higher Si content in the roots compared with the leaves, regardless of provenance and treatment. The most significant differences in photosynthetic performance were found in trees exposed to Si treatment, but the physiological responses were generally nuanced and provenance-dependent. Expression of hsp70 and hsp90 was also increased in leaf tissues of all provenances. These results provide practical insights that Si can improve the overall health and resilience of beech seedlings in nursery and forest ecosystems, with possible differences in the beneficial role of silicon application arising from the large differences in wild populations of forest tree species. Full article
(This article belongs to the Special Issue Genes and Genomics of Plants Under Abiotic Stresses)
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