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Genetics and Novel Techniques for Soybean Pivotal Characters
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Genetics and Novel Techniques for Soybean Pivotal Characters

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 June 2025 | Viewed by 17474

Special Issue Editors

Prof. Dr. Qingshan Chen

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Guest Editor
College of Agriculture, Northeast Agricultural University, Harbin, China
Interests: soybean resources innovation; soybean molecular assisted breeding; soybean biological information
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dawei Xin

E-Mail Website
Guest Editor
National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
Interests: symbiosis; soybean; type III effector; genetic population
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soybean is a worldwide pivotal crop, providing human food, animal feed and industrial materials. Soybean also plays an important role in bio-nitrogen fixation. To meet the ever-growing global population, more than 361.00 million metric tons of soybean have been produced in recent years. With the increasing plant area and yield of soybean, more production problems have been raised and attracted the attention of people. How to breed novel and excellent cultivars and varieties to improve the soybean yield, quality and adaptation to the environment urgently needs to be addressed for human food security.

Currently, the high-quality, reference genome of soybean has been released. However, numerous works are still required to dissect gene functions, signaling networks and regulation mechanisms for the improvement of agronomy traits. Genomics, transcriptomics, proteomics, phenomics and metabolomics technology had been applied to determine gene functions. However, their use in soybean breeding and modification has been limited, and there is huge space for the further development and improvement of breeding, biological function detection and technology application. Compared to rice and maize, there are too many gaps needed to be filled for soybean. Moreover, the mechanisms of symbiosis, the specific traits of legume crops, are still largely unclear. We expect that molecular breeding approaches will be more extensively studied and used in soybean genetic improvement. This Special Issue will provide a forum to address this problem and present new progress in related research.

The research topic will cover basic and application-oriented basic studies that support and facilitate soybean breeding and improvement. Both research articles and review articles are welcome. The following issues will be expected to be addressed:

  • QTL mapping and marker-assisted selection;
  • GWAS and genomic selection/prediction;
  • Molecular breeding by design;
  • Germplasm application;
  • Domestication and selection signatures;
  • Genotype x environment interaction;
  • Improvement of seed quality and/or nutritional quality traits;
  • Nitrogen efficiency modification;
  • Symbiosis mechanism detection;
  • Breeding for tolerance to biotic stresses;
  • Soybean–pathogen interaction
  • Increasing the adaptation to the environment.

This special issue is supervised by Prof. Dr. Qingshan Chen and assisted by our Topical Advisory Panel Member Prof. Dr. Dawei Xin (Northeast Agricultural University).

Prof. Dr. Qingshan Chen
Prof. Dr. Dawei Xin
Guest Editors

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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

  • QTL mapping and marker-assisted selection
  • GWAS and genomic selection/prediction
  • molecular breeding by design
  • germplasm application
  • domestication and selection signatures
  • genotype x environment interaction
  • improvement of seed quality and/or nutritional quality traits
  • nitrogen efficiency modification
  • symbiosis mechanism detection
  • breeding for tolerance to biotic stresses
  • soybean–pathogen interaction
  • increasing the adaptation to the environment

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Published Papers (9 papers)

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Research

16 pages, 4054 KiB  
Article
Hormone Regulation Effect of Blue Light on Soybean Stem Internode Growth Based on the Grey Correlation Analysis Model
by Chang Wang, Shuo Huang, Baiyang Yu, Fuxin Shan, Xiaochen Lyu, Chao Yan, Chunmei Ma and Baiwen Jiang
Int. J. Mol. Sci. 2025, 26(9), 4411; https://doi.org/10.3390/ijms26094411 - 6 May 2025
Viewed by 259
Abstract
Blue light serves as a critical environmental cue regulating Glycine max (soybean) stem morphology, yet the hormonal mechanisms underlying varietal differences remain unclear. Previous studies have highlighted the role of blue light in modulating plant architecture, but the specific hormone interactions driving morphological [...] Read more.
Blue light serves as a critical environmental cue regulating Glycine max (soybean) stem morphology, yet the hormonal mechanisms underlying varietal differences remain unclear. Previous studies have highlighted the role of blue light in modulating plant architecture, but the specific hormone interactions driving morphological divergence between soybean varieties remain underexplored. Two soybean varieties with contrasting stem phenotypes—Henong 60 (HN60, tall) and Heinong 48 (HN48, dwarf)—were subjected to 0% (full light) and 30% (shade) transmittance conditions, supplemented with blue light (450 nm, 45.07 ± 0.03 μmol·m−2·s−1). Stem anatomical traits (xylem area, cell length), hormone profiles, and proteomic changes were analyzed. Grey correlation analysis quantified relationships between hormone ratios and plant height. Blue light increased soybean stem xylem area and diameter while reducing plant height and cell longitudinal length. This treatment concurrently reduced growth-promoting hormones (gibberellin A3 (GA3), indole-3-acetic acid (IAA), brassinolide (BR)) and increased growth-inhibiting hormones (salicylic acid (SA), jasmonic acid (JA), strigolactones (SLs)), thereby inhibiting stem elongation. Although exogenous GA3 promoted hypocotyl elongation, it failed to counteract blue-light-induced inhibition. Proteomic analysis identified 16 differentially expressed proteins involved in hormone signal transduction pathways. Grey correlation analysis highlighted cultivar-specific hormone ratio impacts: GA3/JA, GA3/SA, and BR/SLs significantly influenced HN60 plant height, while GA3/SLs, IAA/SLs, and BR/SLs were critical for HN48, demonstrating highly significant positive correlations. The differential sensitivity of growth-promoting/inhibiting hormone ratios to blue light drives varietal morphological divergence in soybean stems. This study establishes a hormonal regulatory framework for blue-light-mediated stem architecture, offering insights for crop improvement under light-limited environments. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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17 pages, 3574 KiB  
Article
Genome-Wide Identification and Expression Analyses of Glycoside Hydrolase Family 18 Genes During Nodule Symbiosis in Glycine max
by Rujie Li, Chuanjie Gou, Ke Zhang, Milan He, Lanxin Li, Fanjiang Kong, Zhihui Sun and Huan Liu
Int. J. Mol. Sci. 2025, 26(4), 1649; https://doi.org/10.3390/ijms26041649 - 14 Feb 2025
Viewed by 598
Abstract
Glycoside hydrolase family 18 (GH18) proteins can hydrolyze the β-1,4-glycosidic bonds of chitin, which is a common structure component of insect exoskeletons and fungal cell walls. In this study, 36 GH18 genes were identified and subjected to bioinformatic analysis based on the genomic [...] Read more.
Glycoside hydrolase family 18 (GH18) proteins can hydrolyze the β-1,4-glycosidic bonds of chitin, which is a common structure component of insect exoskeletons and fungal cell walls. In this study, 36 GH18 genes were identified and subjected to bioinformatic analysis based on the genomic data of Glycine max. They were distributed in 16 out of 20 tested soybean chromosomes. According to the amino acid sequences, they can be further divided into five subclades. Class III chitinases (22 members) and class V chitinases (6 members) are the major two subclades. The amino acid size of soybean GH18 proteins ranges from 173 amino acids (aa) to 820 aa and the molecular weight ranges from 19.46 kDa to 91.01 kDa. From an evolutionary perspective, soybean GH18 genes are closely related to Medicago (17 collinear loci with soybean) and Lotus (23 collinear loci with soybean). Promoter analysis revealed that GH18 genes could be induced by environmental stress, hormones, and embryo development. GmGH18-15, GmGH18-24, and GmGH18-33 were screened out due to their nodulation specific expression and further verified by RT-qPCR. These results provide an elaborate reference for the further characterization of specific GH18 genes, especially during nodule formation in soybean. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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17 pages, 4991 KiB  
Article
GmbZIP4a/b Positively Regulate Nodule Number by Affecting Cytokinin Biosynthesis in Glycine max
by Yongjie Meng, Nan Wang, Xin Wang, Zhimin Qiu, Huaqin Kuang and Yuefeng Guan
Int. J. Mol. Sci. 2024, 25(24), 13311; https://doi.org/10.3390/ijms252413311 - 11 Dec 2024
Viewed by 995
Abstract
Legumes have the capability to form nodules that facilitate symbiotic nitrogen fixation (SNF) with rhizobia. Given the substantial energy consumption during the process of SNF, legumes need to optimize nodule number in response to everchanging environmental scenarios. The TGACG BINDING FACTOR1/4 (TGA1/4) are [...] Read more.
Legumes have the capability to form nodules that facilitate symbiotic nitrogen fixation (SNF) with rhizobia. Given the substantial energy consumption during the process of SNF, legumes need to optimize nodule number in response to everchanging environmental scenarios. The TGACG BINDING FACTOR1/4 (TGA1/4) are key players in the basal immune response of plants. In this study, both β-glucuronidase staining and quantitative reverse transcription PCR (qRT-PCR) demonstrated that both GmbZIP4a and GmbZIP4b are inducible upon rhizobial inoculation. To investigate their roles further, we constructed gmbzip4a/b double mutants using CRISPR/Cas9 system. Nodulation assessments revealed that these double mutants displayed a reduction in the number of infection threads, which subsequently resulted in a decreased nodule number. However, the processes associated with nodule development including nodule fresh weight, structural characteristics, and nitrogenase activity, remained unaffected in the double mutants. Subsequent transcriptome analyses revealed that zeatin biosynthesis was downregulated in gmbzip4a/b mutants post rhizobial inoculation. Supporting these findings, genes associated with cytokinin (CTK) signaling pathway were upregulated in Williams 82 (Wm82), but this upregulation was not observed in the double mutants after rhizobial treatment. These results suggest that GmbZIP4a/b positively influences nodule formation by promoting the activation of the CTK signaling pathway during the early stages of nodule formation. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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19 pages, 5733 KiB  
Article
Multi-Omics Analysis of a Chromosome Segment Substitution Line Reveals a New Regulation Network for Soybean Seed Storage Profile
by Cholnam Jong, Zhenhai Yu, Yu Zhang, Kyongho Choe, Songrok Uh, Kibong Kim, Chol Jong, Jinmyong Cha, Myongguk Kim, Yunchol Kim, Xue Han, Mingliang Yang, Chang Xu, Limin Hu, Qingshan Chen, Chunyan Liu and Zhaoming Qi
Int. J. Mol. Sci. 2024, 25(11), 5614; https://doi.org/10.3390/ijms25115614 - 21 May 2024
Cited by 2 | Viewed by 1790
Abstract
Soybean, a major source of oil and protein, has seen an annual increase in consumption when used in soybean-derived products and the broadening of its cultivation range. The demand for soybean necessitates a better understanding of the regulatory networks driving storage protein accumulation [...] Read more.
Soybean, a major source of oil and protein, has seen an annual increase in consumption when used in soybean-derived products and the broadening of its cultivation range. The demand for soybean necessitates a better understanding of the regulatory networks driving storage protein accumulation and oil biosynthesis to broaden its positive impact on human health. In this study, we selected a chromosome segment substitution line (CSSL) with high protein and low oil contents to investigate the underlying effect of donor introgression on seed storage through multi-omics analysis. In total, 1479 differentially expressed genes (DEGs), 82 differentially expressed proteins (DEPs), and 34 differentially expressed metabolites (DEMs) were identified in the CSSL compared to the recurrent parent. Based on Gene Ontology (GO) term analysis and the Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG), integrated analysis indicated that 31 DEGs, 24 DEPs, and 13 DEMs were related to seed storage functionality. Integrated analysis further showed a significant decrease in the contents of the seed storage lipids LysoPG 16:0 and LysoPC 18:4 as well as an increase in the contents of organic acids such as L-malic acid. Taken together, these results offer new insights into the molecular mechanisms of seed storage and provide guidance for the molecular breeding of new favorable soybean varieties. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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13 pages, 2354 KiB  
Article
Bowman–Birk Inhibitor Mutants of Soybean Generated by CRISPR-Cas9 Reveal Drastic Reductions in Trypsin and Chymotrypsin Inhibitor Activities
by Won-Seok Kim, Jason D. Gillman, Sunhyung Kim, Junqi Liu, Madhusudhana R. Janga, Robert M. Stupar and Hari B. Krishnan
Int. J. Mol. Sci. 2024, 25(11), 5578; https://doi.org/10.3390/ijms25115578 - 21 May 2024
Cited by 2 | Viewed by 2196
Abstract
Despite the high quality of soybean protein, raw soybeans and soybean meal cannot be directly included in animal feed mixtures due to the presence of Kunitz (KTi) and Bowman–Birk protease inhibitors (BBis), which reduces animal productivity. Heat treatment can substantially inactivate trypsin and [...] Read more.
Despite the high quality of soybean protein, raw soybeans and soybean meal cannot be directly included in animal feed mixtures due to the presence of Kunitz (KTi) and Bowman–Birk protease inhibitors (BBis), which reduces animal productivity. Heat treatment can substantially inactivate trypsin and chymotrypsin inhibitors (BBis), but such treatment is energy-intensive, adds expense, and negatively impacts the quality of seed proteins. As an alternative approach, we have employed CRISPR/Cas9 gene editing to create mutations in BBi genes to drastically lower the protease inhibitor content in soybean seed. Agrobacterium-mediated transformation was used to generate several stable transgenic soybean events. These independent CRISPR/Cas9 events were examined in comparison to wild-type plants using Sanger sequencing, proteomic analysis, trypsin/chymotrypsin inhibitor activity assays, and qRT-PCR. Collectively, our results demonstrate the creation of an allelic series of loss-of-function mutations affecting the major BBi gene in soybean. Mutations in two of the highly expressed seed-specific BBi genes lead to substantial reductions in both trypsin and chymotrypsin inhibitor activities. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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15 pages, 3616 KiB  
Article
QTL Mapping and Data Mining to Identify Genes Associated with Soybean Epicotyl Length Using Cultivated Soybean and Wild Soybean
by Lin Chen, Shengnan Ma, Fuxin Li, Lanxin Li, Wenjun Yu, Lin Yu, Chunshuang Tang, Chunyan Liu, Dawei Xin, Qingshan Chen and Jinhui Wang
Int. J. Mol. Sci. 2024, 25(6), 3296; https://doi.org/10.3390/ijms25063296 - 14 Mar 2024
Cited by 1 | Viewed by 1629
Abstract
Soybean (Glycine max) plants first emerged in China, and they have since been established as an economically important oil crop and a major source of daily protein for individuals throughout the world. Seed emergence height is the first factor that ensures [...] Read more.
Soybean (Glycine max) plants first emerged in China, and they have since been established as an economically important oil crop and a major source of daily protein for individuals throughout the world. Seed emergence height is the first factor that ensures seedling adaptability to field management practices, and it is closely related to epicotyl length. In the present study, the Suinong 14 and ZYD00006 soybean lines were used as parents to construct chromosome segment substitution lines (CSSLs) for quantitative trait loci (QTL) identification. Seven QTLs were identified using two years of epicotyl length measurement data. The insertion region of the ZYD00006 fragment was identified through whole genome resequencing, with candidate gene screening and validation being performed through RNA-Seq and qPCR, and Glyma.08G142400 was ultimately selected as an epicotyl length-related gene. Through combined analyses of phenotypic data from the study population, Glyma.08G142400 expression was found to be elevated in those varieties exhibiting longer epicotyl length. Haplotype data analyses revealed that epicotyl data were consistent with haplotype typing. In summary, the QTLs found to be associated with the epicotyl length identified herein provide a valuable foundation for future molecular marker-assisted breeding efforts aimed at improving soybean emergence height in the field, with the Glyma.08G142400 gene serving as a regulator of epicotyl length, offering new insight into the mechanisms that govern epicotyl development. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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12 pages, 2650 KiB  
Article
Genome-Wide Association Study and Identification of Candidate Genes Associated with Seed Number per Pod in Soybean
by Qiong Wang, Wei Zhang, Wenjing Xu, Hongmei Zhang, Xiaoqing Liu, Xin Chen and Huatao Chen
Int. J. Mol. Sci. 2024, 25(5), 2536; https://doi.org/10.3390/ijms25052536 - 22 Feb 2024
Cited by 4 | Viewed by 2082
Abstract
Soybean (Glycine max [L.] Merr.) is one of the primary sources of plant protein and oil for human foods, animal feed, and industrial processing. The seed number per pod generally varies from one to four and is an important component of seed [...] Read more.
Soybean (Glycine max [L.] Merr.) is one of the primary sources of plant protein and oil for human foods, animal feed, and industrial processing. The seed number per pod generally varies from one to four and is an important component of seed number per unit area and seed yield. We used natural variation in 264 landraces and improved cultivars or lines to identify candidate genes involved in the regulation of seed number per pod in soybean. Genome-wide association tests revealed 65 loci that are associated with seed number per pod trait. Among them, 11 could be detected in multiple environments. Candidate genes were identified for seed number per pod phenotype from the most significantly associated loci, including a gene encoding protein argonaute 4, a gene encoding histone acetyltransferase of the MYST family 1, a gene encoding chromosome segregation protein SMC-1 and a gene encoding exocyst complex component EXO84A. In addition, plant hormones were found to be involved in ovule and seed development and the regulation of seed number per pod in soybean. This study facilitates the dissection of genetic networks underlying seed number per pod in soybean, which will be useful for the genetic improvement of seed yield in soybean. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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12 pages, 5470 KiB  
Article
The Resistance of Soybean Variety Heinong 84 to Apple Latent Spherical Virus Is Controlled by Two Genetic Loci
by Tingshuai Ma, Ying Zhang, Yong Li, Yu Zhao, Kekely Bruno Attiogbe, Xinyue Fan, Wenqian Fan, Jiaxing Sun, Yalou Luo, Xinwei Yu, Weiqin Ji, Xiaofei Cheng and Xiaoyun Wu
Int. J. Mol. Sci. 2024, 25(4), 2034; https://doi.org/10.3390/ijms25042034 - 7 Feb 2024
Viewed by 4799
Abstract
Apple latent spherical virus (ALSV) is widely used as a virus-induced gene silencing (VIGS) vector for function genome study. However, the application of ALSV to soybeans is limited by the resistance of many varieties. In this study, the genetic locus linked to the [...] Read more.
Apple latent spherical virus (ALSV) is widely used as a virus-induced gene silencing (VIGS) vector for function genome study. However, the application of ALSV to soybeans is limited by the resistance of many varieties. In this study, the genetic locus linked to the resistance of a resistant soybean variety Heinong 84 was mapped by high-throughput sequencing-based bulk segregation analysis (HTS–BSA) using a hybrid population crossed from Heinong 84 and a susceptible variety, Zhonghuang 13. The results showed that the resistance of Heinong 84 to ALSV is controlled by two genetic loci located on chromosomes 2 and 11, respectively. Cleaved amplified polymorphic sequence (CAPS) markers were developed for identification and genotyping. Inheritance and biochemical analyses suggest that the resistance locus on chromosome 2 plays a dominant dose-dependent role, while the other locus contributes a secondary role in resisting ALSV. The resistance locus on chromosome 2 might encode a protein that can directly inhibit viral proliferation, while the secondary resistance locus on chromosome 11 may encode a host factor required for viral proliferation. Together, these data reveal novel insights on the resistance mechanism of Heinong 84 to ALSV, which will benefit the application of ALSV as a VIGS vector. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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19 pages, 11370 KiB  
Article
NopC/T/L Signal Crosstalk Gene GmPHT1-4
by Zikun Zhu, Tong Yu, Fuxin Li, Yu Zhang, Chunyan Liu, Qingshan Chen and Dawei Xin
Int. J. Mol. Sci. 2023, 24(22), 16521; https://doi.org/10.3390/ijms242216521 - 20 Nov 2023
Viewed by 1756
Abstract
Symbiotic nodulation between leguminous plants and rhizobia is a critical biological interaction. The type III secretion system (T3SS) employed by rhizobia manipulates the host’s nodulation signaling, analogous to mechanisms used by certain bacterial pathogens for effector protein delivery into host cells. This investigation [...] Read more.
Symbiotic nodulation between leguminous plants and rhizobia is a critical biological interaction. The type III secretion system (T3SS) employed by rhizobia manipulates the host’s nodulation signaling, analogous to mechanisms used by certain bacterial pathogens for effector protein delivery into host cells. This investigation explores the interactive signaling among type III effectors HH103ΩNopC, HH103ΩNopT, and HH103ΩNopL from SinoRhizobium fredii HH103. Experimental results revealed that these effectors positively regulate nodule formation. Transcriptomic analysis pinpointed GmPHT1-4 as the key gene facilitating this effector-mediated signaling. Overexpression of GmPHT1-4 enhances nodulation, indicating a dual function in nodulation and phosphorus homeostasis. This research elucidates the intricate regulatory network governing Rhizobium–soybean (Glycine max (L.) Merr) interactions and the complex interplay between type III effectors. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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