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Agronomy
Special Issues
Functional Genomics and Molecular Breeding of Soybeans—2nd Edition
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Functional Genomics and Molecular Breeding of Soybeans—2nd Edition

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 4629

Special Issue Editors

Prof. Dr. Fang Huang

E-Mail Website
Guest Editor
National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
Interests: soybean molecualr biology; soybean molecular genetics and breeding for yield and quality
Special Issues, Collections and Topics in MDPI journals
Dr. Lin Zhao

E-Mail Website
Guest Editor Assistant
Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
Interests: soybean molecualr biology; genetic improvement of soybean growth period
Prof. Dr. Xiaobo Wang

E-Mail Website
Guest Editor Assistant
School of Agronomy, Anhui Agricultural University, Hefei 230036, China
Interests: soybean molecular breeding; functional genomics; gene editing

Special Issue Information

Dear Colleagues,

Soybean (Glycine max (L.) Merr.) is one of the most important grain and oil crops worldwide. With the extensive exploitation of soybean gene resources, research on soybean functional genomics using genomic information and phenotypic group information has become increasingly important. With the continuous development of biotechnology, modern breeding techniques, such as whole genome selection breeding and genome editing breeding, are changing rapidly, and the selection of excellent soybean varieties has shifted towards soybean molecular design breeding. This Special Issue will collect cutting-edge research on soybean functional genomics and molecular breeding to further promote their molecular design and breeding.

Prof. Dr. Fang Huang
Guest Editor

Dr. Lin Zhao
Prof. Dr. Xiaobo Wang
Guest Editor Assistants

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 250 words) can be sent to the Editorial Office for assessment.

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. Agronomy is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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
  • functional genomics
  • molecular breeding

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Related Special Issue

Published Papers (6 papers)

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Research

21 pages, 2695 KB  
Article
Marker-Assisted Breeding for Pyramiding Multiple Resistance to Soybean Fungal Diseases
by Carla María Lourdes Rocha, María Gabriela García, Esteban Mariano Pardo, José Ramón Sánchez, Atilio Pedro Castagnaro and María Amalia Chiesa
Agronomy 2026, 16(7), 754; https://doi.org/10.3390/agronomy16070754 - 2 Apr 2026
Viewed by 404
Abstract
Fungal diseases such as soybean stem canker (SSC), frogeye leaf spot (FLS), and sudden death syndrome (SDS) cause substantial yield losses in soybean worldwide. This study aimed to pyramid major resistance genes and QTLs against these diseases through marker-assisted backcrossing (MABC). Diagnostic SSR [...] Read more.
Fungal diseases such as soybean stem canker (SSC), frogeye leaf spot (FLS), and sudden death syndrome (SDS) cause substantial yield losses in soybean worldwide. This study aimed to pyramid major resistance genes and QTLs against these diseases through marker-assisted backcrossing (MABC). Diagnostic SSR markers, linked to Rdm4 (SSC), Rcs3 (FLS), and SDS resistance QTLs, were validated and successfully employed for foreground and background selection in crosses between the elite cultivar A8100RR and the resistant donor ‘Forrest’. Molecular analyses confirmed the effective introgression and fixation of multiple resistance loci in BC2F5 lines. Under artificial inoculation, lines R30-11 and R25-13 displayed high resistance levels to Diaporthe aspalathi, Cercospora sojina, Fusarium virguliforme, and F. tucumaniae. Genotype R30-11 exhibited the most consistent resistance across pathogens, while R25-13 combined multi-disease resistance with glyphosate tolerance and stable agronomic performance under field conditions comparable to commercial cultivars. These results represent, to our knowledge, the first report of successful pyramiding genes and QTLs against three distinct fungal diseases (SSC, FLS, and SDS) in soybean through MABC. The developed lines constitute valuable germplasm for breeding programs designed to achieve broad-spectrum, durable and sustainable disease management. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans—2nd Edition)
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21 pages, 4886 KB  
Article
Comparative Transcriptome Analysis Reveals Novel Insights into Regulatory Mechanisms of Seed Protein and Oil Accumulation in Soybeans
by Chaoyue Zhao, Dagang Wang, Ekaterina Shor, Xiangjin Chen and Hengyou Zhang
Agronomy 2026, 16(5), 562; https://doi.org/10.3390/agronomy16050562 - 4 Mar 2026
Cited by 1 | Viewed by 477
Abstract
Soybean seed quality is defined by an inverse relationship between oil and protein content. Understanding the spatiotemporal regulation of this trade-off is crucial for breeding. This study aims to dissect the transcriptomic networks governing carbon and nitrogen partitioning during seed development. Here, transcriptomic [...] Read more.
Soybean seed quality is defined by an inverse relationship between oil and protein content. Understanding the spatiotemporal regulation of this trade-off is crucial for breeding. This study aims to dissect the transcriptomic networks governing carbon and nitrogen partitioning during seed development. Here, transcriptomic and co-expression network analyses were performed on cotyledon and seedcoat tissues of high-protein (HP) and low-protein (LP) soybean cultivars across three seed developmental stages. We identified 4910 HP/LP-specific differentially expressed genes (DEGs), with striking transcriptional alterations in the early developmental stage. Notably, some important DEGs were enriched in carbon/lipid metabolism, protein folding, and hormone/circadian signaling pathways, among which key gene families (e.g., OLEs, SWEETs, HSPs), core regulators (e.g., LACS, L1L, ABF1), and QTL-localized candidate genes (e.g., FA9) were characterized. Mechanistically, C/VIF1-mediated post-translational inhibition of CWINV1 may restrict carbon flux to oil synthesis in HP seeds; upstream circadian/hormone signaling and L1L-sHSPs jointly promote protein deposition, uncoupling the oil–protein trade-off and enabling HP trait formation. In contrast, LP cultivars upregulated SWEETs, OLEs, and LTPs to facilitate high carbon flux into lipid biosynthesis and storage. These findings provide valuable genetic targets for precision breeding programs aimed at optimizing resource allocation. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans—2nd Edition)
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20 pages, 3094 KB  
Article
The PIN-LIKES Auxin Transport Genes Involved in Regulating Yield in Soybean
by Siming Wei, Jiayin Han, Chun Tang, Lei Zhang, Mingliang Yang, Fubin Cao, Yuyao Zhao, Xinghua Li, Hao Xu, Zhaoming Qi and Qingshan Chen
Agronomy 2026, 16(2), 226; https://doi.org/10.3390/agronomy16020226 - 17 Jan 2026
Viewed by 500
Abstract
PIN-LIKES (PILS) auxin transport genes play key roles in plant development, but their functions and molecular mechanism in soybean yield remain unclear. Here, we characterized the 44-member soybean GmPILS genes via comprehensive analyses. Phylogenetic analysis classified GmPILS into three subfamilies, with [...] Read more.
PIN-LIKES (PILS) auxin transport genes play key roles in plant development, but their functions and molecular mechanism in soybean yield remain unclear. Here, we characterized the 44-member soybean GmPILS genes via comprehensive analyses. Phylogenetic analysis classified GmPILS into three subfamilies, with most proteins being hydrophobic, stable, and membrane-localized. Chromosomal distribution showed random scattering across 17 chromosomes, with gene duplication driving family expansion. Expression profiling identified GmPILS36 and GmPILS40 as seed-specific and differentially expressed between cultivated Suinong14 (SN14) and wild ZYD00006 (ZYD06) soybeans. Population genetic analyses revealed GmPILS40 experienced a domestication bottleneck without yield-related superior haplotypes, while GmPILS36 underwent selection during landrace-to-improved variety domestication. A coding region CC/TT natural variation in GmPILS36 (S/A substitution) was significantly associated with seed weight per plant and 100-seed weight, with the TT genotype conferring superior traits. This study provides insights into GmPILS genes’ evolution and identifies GmPILS36 as an important candidate gene for further functional study and investigation of the molecular mechanisms regulating soybean yield. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans—2nd Edition)
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12 pages, 2837 KB  
Article
Identification of Wild Segments Related to High Seed Protein Content Under Multiple Environments and Analysis of Its Candidate Genes in Soybean
by Ning Li, Mengdan Cai, Wei Luo, Wei Han, Cheng Liu, Jianbo He, Fangdong Liu, Lei Sun, Guangnan Xing, Junyi Gai and Wubin Wang
Agronomy 2025, 15(12), 2902; https://doi.org/10.3390/agronomy15122902 - 17 Dec 2025
Viewed by 536
Abstract
Annual wild soybean is characterized by a high protein content. To elucidate the genetic basis, this study utilized a chromosome segment substitution line population (177 lines) constructed with cultivated soybean NN1138-2 as the recipient and wild soybean N24852 as the donor. Phenotypic analyses [...] Read more.
Annual wild soybean is characterized by a high protein content. To elucidate the genetic basis, this study utilized a chromosome segment substitution line population (177 lines) constructed with cultivated soybean NN1138-2 as the recipient and wild soybean N24852 as the donor. Phenotypic analyses across three environments revealed significant variation in protein content ranging from 42.86% to 49.08%, with a high heritability of 0.70, indicating strong genetic control. Through high-throughput sequencing, six wild segments associated with high protein content were detected on chromosomes 3, 6, 9, 15, and 20, with phenotypic variation explained (PVE) by individual segments ranged from 3.58% to 22.46%, with segments on chromosomes 9, 15, and 20 as large-effect segments with PVE > 10%. All wild segments exhibited positive additive effects (0.42–1.09%), consistent with the characteristic of a high protein content in wild soybean. Compared with previous studies, five segments overlapped with reported loci, while qPro6.1 on chromosome 6 was a novel discovery. Integration of genomic and transcriptomic data identified 10 genes involved in nucleic acid binding, transmembrane protein transport, and amino acid synthesis pathway, with homologs validated in soybean, rice, and rapeseed. This research deepens the understanding of wild soybean’s high protein and offers new gene resources for breeding high-protein cultivated soybean. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans—2nd Edition)
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16 pages, 1262 KB  
Article
Fine Mapping of Phytophthora sojae PNJ1 Resistance Locus Rps15 in Soybean (Glycine max (L.) Merr.)
by Bo Chen, Si Bai, Ximeng Yang, Chanyu Niu, Qiuju Xia, Zhandong Cai, Jia Jia, Qibin Ma, Tengxiang Lian, Hai Nian and Yanbo Cheng
Agronomy 2025, 15(12), 2736; https://doi.org/10.3390/agronomy15122736 - 27 Nov 2025
Viewed by 770
Abstract
Phytophthora root rot (PRR), which is caused by the oomycete pathogen Phytophthora sojae (P. sojae), is one of the most devastating diseases affecting global soybean production. The deployment of resistance (Rps) genes through molecular breeding is a sustainable strategy [...] Read more.
Phytophthora root rot (PRR), which is caused by the oomycete pathogen Phytophthora sojae (P. sojae), is one of the most devastating diseases affecting global soybean production. The deployment of resistance (Rps) genes through molecular breeding is a sustainable strategy to control this disease. In this study, we finely mapped a novel resistance gene using two recombinant inbred line (RIL) populations: one comprising 248 F8:11 lines from a cross between the resistant cultivar ‘Guizao 1’ and the susceptible ‘B13’, and another consisting of 196 F7:8 lines from a cross between ‘Wayao’ (resistant) and ‘Huachun 2’ (susceptible). The gene in ‘Guizao 1’, designated as Rps15, was delimited to a 78 kb genomic interval on chromosome 3 (bin31), spanning the physical positions from 4,292,416 to 4,370,772 bp. This region contains eight predicted genes. Similarly, the resistance locus in ‘Wayao’ was mapped to a broader region on chromosome 3 (approximately 324 kb; 3,968,039–4,292,863 bp), which encompasses 16 genes. Expression analysis via quantitative real-time PCR of the candidate genes suggested that Glyma.03g036000 is likely involved in the resistance response to PRR. The fine mapping of this novel Rps locus provides a foundation for the future cloning of Rps15 and can be expected to accelerate the development of P. sojae-resistant soybean cultivars through marker-assisted selection. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans—2nd Edition)
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17 pages, 3798 KB  
Article
Negative Regulation of GmNAC35 by miR164 Enhances Drought Tolerance in Soybean
by Wentao Hu, Man Zhang, Jie Lu, Miaomiao Zhang, Reqing He, Youlin Zhu, Dong Wang and Liyun Jiang
Agronomy 2025, 15(6), 1450; https://doi.org/10.3390/agronomy15061450 - 14 Jun 2025
Viewed by 1347
Abstract
Soybean (Glycine max (L.) Merr.) is a critical crop in China, serving as a primary source of food, oil, and animal feed. Drought stress significantly impacts soybean growth and yield. MicroRNAs (miRNAs) play crucial roles in plant drought responses. The miR164 family [...] Read more.
Soybean (Glycine max (L.) Merr.) is a critical crop in China, serving as a primary source of food, oil, and animal feed. Drought stress significantly impacts soybean growth and yield. MicroRNAs (miRNAs) play crucial roles in plant drought responses. The miR164 family is highly conserved across plant species and has been shown to participate in drought responses in a range of plants, yet the function of miR164 in soybean remains unclear. In this study, we identified GmNAC35 as a direct target of miR164 through published degradome sequencing data and 5′ RLM-RACE assays. Under drought stress, miR164 members (e.g., MIR164a, MIR164f, and MIR164k) rapidly down-regulated, reaching their lowest expression at 2 h and returning to basal levels within 6 h. Conversely, GmNAC35 showed an inverse pattern, indicating negative regulation by miR164. Overexpression of GmNAC35 enhanced drought tolerance in transgenic soybean plants, as evidenced by higher survival rates and reduced water loss. Transcriptomic analysis revealed that GmNAC35 modulates stress-responsive pathways, including ABA signaling and phenylpropanoid biosynthesis. Our findings indicate that miR164 negatively regulates GmNAC35, a positive regulator of drought tolerance. This enhances our understanding of the molecular mechanisms of drought tolerance in soybean and may inform strategies for breeding drought-resistant varieties. Full article
(This article belongs to the Special Issue Functional Genomics and Molecular Breeding of Soybeans—2nd Edition)
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