Genetic and Omics Insights into Plant Adaptation and Growth

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

Deadline for manuscript submissions: 31 March 2026 | Viewed by 92

Special Issue Editor

The Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan (ICBR), Beijing, China
Interests: cell fate determination; organizational differentiation; stress response; omics research
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Special Issue Information

Dear Colleagues,

Plant growth and development is a process through which adaptive phenotypes are shaped by the combined influence of genetic factors and environmental conditions. Notably, allelic variations, gene expression levels, and physiological and biochemical traits, as well as epigenetic modifications and their respective degrees, can all contribute to the formation of specific phenotypic traits.

Omics-based approaches have emerged as powerful tools for studying plant diversity. By analyzing large-scale biological datasets, researchers can investigate the systemic characteristics of plant tissues or individuals, their interactions, and the underlying biological mechanisms driving trait formation.

This Special Issue will highlight research focusing on the role of omics—including genomics, transcriptomics, proteomics, metabolomics, and phenomics—in identifying key metabolic pathways, molecular mechanisms, and causative genes, proteins, and metabolites involved in plant growth, development, and stress responses. Additionally, we will explore current challenges, emerging trends in omics research for plant diversity conservation and utilization, the assessment of population diversity, and strategies for trait improvement.

Finally, we will emphasize multi-omics integration strategies, which enable efficient identification of molecular patterns and genetic interactions. Such approaches facilitate the precise reconstruction of biomolecular networks, allowing researchers to examine complex biological questions from both causal and effect-based perspectives while validating their functional relevance.

Dr. Ying Li
Guest Editor

Manuscript Submission Information

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Keywords

  • omics research
  • growth and development
  • stress response
  • population diversity evaluation

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Published Papers (1 paper)

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Research

20 pages, 2106 KiB  
Article
Transposon Dynamics Drive Genome Evolution and Regulate Genetic Mechanisms of Agronomic Traits in Cotton
by Zeyu Dong, Shangkun Jin, Yupeng Hao, Ting Zhao, Haihong Shang, Zhiyuan Zhang, Lei Fang, Zhihong Zheng and Jun Li
Plants 2025, 14(16), 2509; https://doi.org/10.3390/plants14162509 - 12 Aug 2025
Abstract
Transposable elements (TEs) serve as important drivers mediating polyploidization events and phenotypic diversification in plant genomes. However, the dynamic changes in various TE subclasses post-polyploidization and their mechanisms of influencing phenotypic variation require further investigation. The allopolyploid Gossypium species, originating from two diploid [...] Read more.
Transposable elements (TEs) serve as important drivers mediating polyploidization events and phenotypic diversification in plant genomes. However, the dynamic changes in various TE subclasses post-polyploidization and their mechanisms of influencing phenotypic variation require further investigation. The allopolyploid Gossypium species, originating from two diploid progenitors, provide an ideal model for studying TE dynamics following polyploidization. This study investigated TE dynamics post-polyploidization based on 21 diploid and 7 polyploid cotton genomes. The Tekay subclass of the Gypsy serves as a major driver of Gossypium genome evolution, as it underwent two burst events in the At-subgenome and its progenitor, exhibiting the highest abundance, longest length, and largest proportion among all TE subclasses. In contrast, the Gopia superfamily Tork subclass has lower abundance but greater genic association, facilitating environmental adaptation and phenotypic variation. Additionally, a pan-TE-related structural variation, the pan-TRV map, was constructed by integrating resequencing data from 256 accessions. Genome-wide analysis of 28 cotton genomes identified 142,802 TRVs, among which 72,116 showed polymorphisms in the 256 G. hirsutum accessions. The Gypsy superfamily, particularly the Tekay subclass, has been identified as a major source of TRVs, while Copia-type elements demonstrate significantly greater enrichment in gene-proximal genomic regions. A total of 334 TRVs exhibiting statistically significant associations with 10 key phenotypic traits, including 164 TRVs affecting yield components and 170 TRVs determining fiber quality. This investigation delineates the evolutionary significance of transposable elements in Gossypium genome diversification while simultaneously providing novel functional markers and potential editing targets for genetic dissection and molecular breeding of key agronomic traits in cotton. Full article
(This article belongs to the Special Issue Genetic and Omics Insights into Plant Adaptation and Growth)
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