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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 November 2025 | Viewed by 1636

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Prof. Dr. Zhengjun Xia

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Guest Editor

Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
Interests: soybean; elucidation of gene networks controlling the soybean photoperiodic response; identification of key genes conferring agronomical traits to improve soybean productivity; molecular design and breeding of high-producing soybean varieties

Special Issue Information

Dear Colleagues,

Soybean, as a major staple crop, plays a crucial role in both scientific research and people’s daily lives. It is not only a significant source of edible oil and protein but also serves as animal feed and a provider of bioactive substances beneficial to human health. In the context of molecular biology, the study of soybean molecular biology holds great potential.

We welcome submissions to this Special Issue, titled “Molecular Biology of Soybean”, from scientific researchers. This topic aims to promote in-depth research of every aspect of soybean molecular biology, including its growth and development, disease resistance, nodulation, and the interaction between soybeans, microorganisms, and the environment in terms of physiological and biochemical features.

Scope of submissions includes the following themes:

Growth and Development: Studies on the molecular mechanisms underlying soybean growth stages, such as germination, flowering, and seed formation. Understanding how genes regulate these processes can provide valuable insights.
Disease Resistance: Research on the molecular basis of soybean's defense against various diseases. This can help in developing disease-resistant soybean varieties.
Nodulation: Exploration of molecular interactions between soybeans and nitrogen-fixing bacteria during nodule formation, which is vital for nitrogen uptake.
Interaction with Microorganisms and the Environment: Analyses of how soybeans respond to different environmental factors and interact with surrounding microorganisms at the molecular level.

By focusing on these areas, we aim to uncover the regulatory mechanisms of soybeans at the molecular level. This will provide important target-functional genes for breeders, resulting in facilitation of breeding of improved soybean varieties with better traits.

Prof. Dr. Zhengjun Xia
Guest Editor

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

soybean
growth and development
disease resistance
nodulation
nolecular mechanism
plant interaction

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26 pages, 31747 KiB

Open AccessArticle

Genome-Wide Identification of GmARF9b/GmARF2a Negatively Regulate Root Growth in Soybean

by Di Li, Tianle Miao, Hong Liao and Yongjia Zhong

Int. J. Mol. Sci. 2025, 26(10), 4547; https://doi.org/10.3390/ijms26104547 - 9 May 2025

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Abstract

Auxin is the most important phytohormone, regulating root growth and development in plants. ARFs function as central regulators in auxin signaling in model plants, and the functions of ARF activators have been widely investigated, while the functions of ARF repressors remain elusive. In this study, we investigated the family of GmARFs in soybean through a genome-wide expression pattern and functional study of roots highly expressing ARFs. In total, we identified 59 GmARF members in the soybean genome. GmARFs harbor canonical B3 DNA-binding (B3), ARF (Aux rep), and PB1 functional protein domains. We identified two potential repressor genes, GmARF9b (Glyma.03G070500) and GmARF2a (Glyma.05G200800), which are specifically or highly expressed in the roots. Histochemical staining suggested that both genes are primarily expressed in the stele, root tips, and lateral root primordia. Subcellular localization analysis showed they were mainly localized in the nucleus. Overexpression of GmARF9b and GmARF2a significantly inhibited root growth using a transgenic hairy root assay. Root section analysis further suggested that GmARF9b and GmARF2a negatively regulated cortical cell layers and the longitudinal cell length of roots, thereby modulating root growth. Overall, this study has preliminarily identified two GmARFs that inhibit root growth in soybean. This discovery has deepened our understanding of the functions of ARFs in root development and has provided guidance for breeding crop roots with improved nutrient use efficiency. Full article

(This article belongs to the Special Issue Molecular Biology of Soybean)

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12 pages, 4261 KiB

Open AccessArticle

Functional Verification of the Soybean Pseudo-Response Factor GmPRR7b and Regulation of Its Rhythmic Expression

by Ziye Song, Jia Liu, Xueyan Qian, Zhengjun Xia, Bo Wang, Nianxi Liu, Zhigang Yi, Zhi Li, Zhimin Dong, Chunbao Zhang, Bo Zhang, Million Tadege, Yingshan Dong and Yuqiu Li

Int. J. Mol. Sci. 2025, 26(6), 2446; https://doi.org/10.3390/ijms26062446 - 9 Mar 2025

Viewed by 570

Abstract

The pseudo response regulator (PRR) gene is an important component of the core oscillator involved in plant circadian rhythms and plays an important role in regulating plant growth and development and stress responses. In this study, we investigated the function of GmPRR7b by overexpression and gene editing approaches. It was found that GmPRR7b plays a role in delaying flowering. While GmPRR7b overexpressing plants showed significantly delayed flowering compared to untransformed WT, GmPRR7b edited plants flowered earlier than the control WT. On the basis of previous research results and bioinformatics analysis, we re-identified 14 soybean PRR genes and analysed their rhythmic expression. Based on the rhythmic expression pattern, we found that GmPRR5/9a and GmPRR5/9b interacted with GmPRR7b by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments. Combined with the expression regulatory networks of the GmPRR7b, we inferred a possible regulatory mechanism by which GmPRR7b affects flowering through quit rhythm expression. These research elements provide valuable references for understanding growth, development, and circadian regulation in soybean. Full article

(This article belongs to the Special Issue Molecular Biology of Soybean)

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20 pages, 3542 KiB

Open AccessArticle

Genome-Wide Analysis of Soybean Apyrase Gene Family and Functional Characterization of GmAPY1-4 Responses to Aluminum Stress

by Yanyu Yu, Shengnan Ma, Lanxin Li, Zhen Song, Lin Yu, Chunshuang Tang, Chunyan Liu, Qingshan Chen, Dawei Xin and Jinhui Wang

Int. J. Mol. Sci. 2025, 26(5), 1919; https://doi.org/10.3390/ijms26051919 - 23 Feb 2025

Viewed by 449

Abstract

Apyrases (APYs) directly regulate intra- and extra-cellular ATP homeostasis and play a key role in the process of plants adapting to various stresses. In this study, we identified and characterized soybean APY (GmAPY) family members at the genomic level. The results identified a total of 18 APYRASE homologous genes with conserved ACR domains. We conducted a bioinformatics analysis of GmAPYs, including sequence alignment, phylogenetic relationships, and conserved motifs. According to the phylogenetic and structural characteristics, GmAPYs in soybeans are mainly divided into three groups. The characteristics of these GmAPYs were systematically evaluated, including their collinearity, gene structure, protein motifs, cis-regulatory elements, tissue expression patterns, and responses to aluminum stress. A preliminary analysis of the function of GmAPY1-4 was also conducted. The results showed that GmAPY1-4 was localized in the nucleus, presenting relatively high levels in roots and root nodules and demonstrating high sensitivity and positive responses under aluminum stress circumstances. Further functional characterization revealed that the overexpression of GmAPY1-4 in hairy roots not only induced root growth under normal growth conditions but also significantly prevented root growth inhibition under aluminum stress conditions and contributed to maintaining a relatively higher fresh root weight. By contrast, RNAi interference with the expression of GmAPY1-4 in hairy roots inhibited root growth under both normal and aluminum stress conditions, but it exerted no significant influence on the dry or fresh root weight. To sum up, these findings support the significant functional role of GmAPY1-4 in root growth and the aluminum stress response. These findings not only enhance our comprehension of the aluminum stress response mechanism by identifying and characterizing the APY gene family in the soybean genome but also provide a potential candidate gene for improving aluminum tolerance in soybeans in the future. Full article

(This article belongs to the Special Issue Molecular Biology of Soybean)

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