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Recent Advances in Soybean Molecular Breeding
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Recent Advances in Soybean Molecular Breeding

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: 30 November 2025 | Viewed by 3593

Special Issue Editor

Dr. Dong Cao

E-Mail Website
Guest Editor
Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan 430062, China
Interests: soybean; molecular breeding; plant architecture

Special Issue Information

Dear Colleagues,

Soybean, an economically relevant legume crop, is widely cultivated due to its edible oil and protein content. In recent years, researchers have endeavored to increase the yield of soybean under various growth conditions.

This Special Issue, entitled “Recent Advances in Soybean Molecular Breeding”, aims to promote strategies that enhance the yield of soybean in response to the growth of the global population and changing climatic conditions. We therefore welcome contributions that address the following topics:

  • Altering plant architecture to improve yield performance;
  • Improving varieties to expand cultivation areas;
  • Enhancing nutritional quality;
  • Increasing tolerance to stress;
  • Genetic engineering for soybean improvement.

This Special Issue aims to highlight recent breakthroughs and innovative methods related to the breeding and genetics of soybean.

Dr. Dong Cao
Guest Editor

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

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • soybean
  • plant architecture
  • adaptation
  • yield improvement, molecular breeding
  • nutritional quality traits
  • stress tolerance

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Published Papers (4 papers)

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Research

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14 pages, 3746 KB  
Article
Multi-Stage Transcriptome Analysis Identifies Key Molecular Pathways for Soybean Under Phosphorus-Limited Conditions
by Xiulin Liu, Sobhi F. Lamlom, Xueyang Wang, Chunlei Zhang, Fengyi Zhang, Kezhen Zhao, Rongqiang Yuan, Bixian Zhang and Honglei Ren
Int. J. Mol. Sci. 2025, 26(17), 8385; https://doi.org/10.3390/ijms26178385 - 28 Aug 2025
Viewed by 613
Abstract
Phosphorus deficiency significantly limits soybean production across 74% of China’s arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis [...] Read more.
Phosphorus deficiency significantly limits soybean production across 74% of China’s arable land. This study investigated the molecular mechanisms enabling soybean to access insoluble phosphorus through transcriptome sequencing of the Heinong 48 variety across four developmental stages (Trefoil, Flower, Podding, and Post-podding). RNA-Seq analysis identified 2755 differentially expressed genes (DEGs), with 2506 up-regulated and 249 down-regulated genes. Notably, early developmental stages showed the most substantial transcriptional reprogramming, with 3825 DEGs in the Trefoil stage and 10,660 DEGs in the Flower stage, compared to only 523 and 393 DEGs in the Podding and Post-podding stages, respectively. Functional enrichment analysis revealed 44 significantly enriched GO terms in the Trefoil stage and 137 in the Flower stage, with 13 GO terms shared between both stages. KEGG pathway analysis identified 8 significantly enriched pathways in the Trefoil stage and 21 in the Flower stage, including key pathways related to isoflavonoid biosynthesis, alpha-linolenic acid metabolism, and photosynthesis. Among 87 differentially expressed transcription factors from 31 families, bHLH (8.08%), bZIP (7.18%), and WRKY (5.94%) were most prevalent. These findings provide genetic targets for developing soybean varieties with improved phosphorus acquisition capacity, potentially reducing fertilizer requirements and supporting more sustainable agricultural practices. Full article
(This article belongs to the Special Issue Recent Advances in Soybean Molecular Breeding)
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14 pages, 1052 KB  
Article
Regulatory Mechanism of the GmMYB14 Transcription Factor on Auxin-Related Proteins in Soybean
by Lihua Peng, Yangyan Liu, Hongli Yang, Wei Guo, Qingnan Hao, Shuilian Chen, Songli Yuan, Chanjuan Zhang, Zhonglu Yang, Bei Han, Yi Huang, Zhihui Shan, Limiao Chen and Haifeng Chen
Int. J. Mol. Sci. 2025, 26(16), 7763; https://doi.org/10.3390/ijms26167763 - 11 Aug 2025
Viewed by 465
Abstract
In a previous study, GmMYB14 overexpressing (GmMYB14-OX) transgenic soybean plants displayed a semi-dwarfism and compact phenotype, which was regulated by the brassinosteroid (BR) pathway. However, the phenotype of GmMYB14-OX plants could be partly rescued after spraying them with exogenous BR. This [...] Read more.
In a previous study, GmMYB14 overexpressing (GmMYB14-OX) transgenic soybean plants displayed a semi-dwarfism and compact phenotype, which was regulated by the brassinosteroid (BR) pathway. However, the phenotype of GmMYB14-OX plants could be partly rescued after spraying them with exogenous BR. This indicates that other hormones, in addition to BR, also play a role in regulating the architecture of GmMYB14-OX plants. We observed a significant decrease in the content of endogenous indole-3-acetic acid (IAA) in transgenic soybean lines (OX9 and OX12) compared to wild type (WT) plants. The plant height, leaf area, leaf petiole length, and leaf petiole angle of GmMYB14-OX plants could also be partly rescued after applying exogenous IAA for two weeks. Transcriptome sequencing analysis revealed that the expression of many genes within the Aux/IAA gene family underwent alterations in the GmMYB14-OX transgenic soybean plants. Among them, Glyma.02G000500 (GmIAA1) showed the highest expression in GmMYB14-OX plants. Furthermore, the results of electrophoretic mobility shift assay and dual-luciferase reporter indicate that GmMYB14 protein could bind to the promoter of GmIAA1. In summary, a decrease in endogenous IAA content may be one of the factors contributing to the compact and dwarfed architecture of GmMYB14-OX plants. GmMYB14 also acts as a transcriptional activator of GmIAA1 to potentially block IAA effects. Our findings provide a theoretical basis for further investigation of the regulatory mechanism of GmMYB14 on soybean plant architecture. Full article
(This article belongs to the Special Issue Recent Advances in Soybean Molecular Breeding)
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17 pages, 4291 KB  
Article
Natural Variations in Key Maturity Genes Underpin Soybean Cultivars Adaptation Beyond 50° N in Northeast China
by Hongchang Jia, Baiquan Sun, Bingjun Jiang, Peiguo Wang, Mahmoud Naser, Shuqing Qian, Liwei Wang, Lixin Zhang, Mikhail Sinegovskii, Shi Sun, Wencheng Lu, Valentina Sinegovskaya, Jiangping Bai and Tianfu Han
Int. J. Mol. Sci. 2025, 26(7), 3362; https://doi.org/10.3390/ijms26073362 - 3 Apr 2025
Cited by 1 | Viewed by 700
Abstract
Expanding soybean planting is vital for food security both in China and globally. The 50° N latitude serves as the northern boundary of major soybean regions. However, enhancing the adaptability of soybean to photothermal conditions enables the potential to extend cultivation to higher [...] Read more.
Expanding soybean planting is vital for food security both in China and globally. The 50° N latitude serves as the northern boundary of major soybean regions. However, enhancing the adaptability of soybean to photothermal conditions enables the potential to extend cultivation to higher latitudes and altitudes. Understanding the genetic basis of super-early maturity of soybean is crucial to achieving this goal. In this study, 438 soybean germplasms collected from high-latitude regions were evaluated in Heihe (HH) (50°15′ N, 127°28′ E, 154 m), Beijicun (BJC) (53°28′ N, 122°21′ E, 295 m) and Labudalin (LBDL) (50°15′ N, 120°19′ E, 577 m). Using resequencing data, we analyzed natural variation and haplotypes in 35 key genes associated with flowering time and maturity. The results showed that the relative maturity groups (RMGs) for BJC, HH, and LBDL were −1.0, 0.0, and −1.2, respectively. Among the 35 genes analyzed, 23 had identical allelic variations, while 12 genes exhibited 19 SNPs and four InDels. Functional mutations were identified in E1, E2, E3, and E4. Notably, all cultivars carried the e1-as allele of E1, which is likely critical for high-latitude adaptation. Additional mutations included a single-base substitution in E2 (16142 A > T) and E3 (5203 C > T), causing premature codon termination, along with frameshift mutations in E4 (3726 and 4099) and E3 (2649). Haplotype analysis revealed significant differences in growth stages among nine gene haplotypes. The higher frequency of early-maturing haplotypes in BJC and LBDL highlights the role of gene accumulation in soybean adaptation. These findings offer valuable insights for improving soybean maturity and expanding its cultivation in high-latitude regions of China. Full article
(This article belongs to the Special Issue Recent Advances in Soybean Molecular Breeding)
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Review

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26 pages, 2404 KB  
Review
CRISPR/Cas-Mediated Optimization of Soybean Shoot Architecture for Enhanced Yield
by Nianao Li, Xi Yuan, Bei Han, Wei Guo and Haifeng Chen
Int. J. Mol. Sci. 2025, 26(16), 7925; https://doi.org/10.3390/ijms26167925 - 16 Aug 2025
Viewed by 1298
Abstract
Plant architecture is a crucial agronomic trait significantly impacting soybean (Glycine max) yield. Traditional breeding has made some progress in optimizing soybean architecture, but it is limited in precision and efficiency. The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein [...] Read more.
Plant architecture is a crucial agronomic trait significantly impacting soybean (Glycine max) yield. Traditional breeding has made some progress in optimizing soybean architecture, but it is limited in precision and efficiency. The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein (CRISPR/Cas) system, a revolutionary gene-editing technology, provides unprecedented opportunities for plant genetic improvement. This review outlines CRISPR’s development and applications in crop improvement, focusing specifically on progress regulating soybean architecture traits affecting yield, such as node number, internode length, branching, and leaf morphology. It also discusses the technical challenges for CRISPR technology in enhancing soybean architecture, including that the regulatory network of soybean plant architecture is complex and the development of multi-omics platforms helps gene mining. The application of CRISPR enables precise the regulation of gene expression through promoter editing. Meanwhile, it is also faced with technical challenges such as the editing of homologous genes caused by genome polyploidy, the efficiency of editing tools and off-target effects, and low transformation efficiency. New delivery systems such as virus-induced genome editing bring hope for solving some of these problems. The review emphasizes the great potential of CRISPR technology in breeding next-generation soybean varieties with optimized architecture to boost yield potential. Full article
(This article belongs to the Special Issue Recent Advances in Soybean Molecular Breeding)
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