Background:Soybean (Glycine max), is a globally important oilseed crop whose yield and quality are severely constrained by environmental stress. The Sucrose Transporter (SUT) gene family plays a crucial role in sucrose transport, plant growth, and stress adaptation. However, comprehensive identification and functional characterization of SUT family members in soybean remain largely incomplete. Results:In this study, a total of 12 non-redundant GmSUT genes were identified in soybean. The encoded proteins have predicted molecular weights ranging from 11.80 to 65.88 kDa and theoretical isoelectric points (pI) between 5.73 and 9.44. These genes were classified into three subfamilies (SUTI, SUTIIa and SUTIV) by phylogenetic analysis, with SUTI being the largest group. Gene structure and conserved motif analyses showed that motif composition was largely uniform within each subfamily, except for GmSUT4.1, which retained only two motifs. Chromosomal mapping revealed an uneven distribution across seven chromosomes, with Chr16 harboring four SUTI members. Collinearity analysis indicated a closer evolutionary relationship between soybean and Glycine soja than with Arabidopsis thaliana or Medicago truncatula. Cis -regulatory element analysis identified abundant stress- and hormone-responsive motifs (e.g., ABRE, MeJA-responsive elements), with 83% of promoters containing ABA-responsive elements. Moreover, the transcriptional levels of the GmSUT genes were significantly induced under various abiotic stresses (salt, drought, cold and alkaline) and phytohormone treatments (ABA, and MeJA), demonstrating that multiple GmSUT genes play critical roles in soybean stress adaptation. Conclusions:This study provides a comprehensive identification and characterization of the SUT gene family in soybean (Glycine max), revealing 12 GmSUT genes grouped into three subfamilies (SUTI, SUTIIa, SUTIIV). Expression profiling demonstrated that multiple GmSUT members are rapidly upregulated under stress treatment, underscoring their essential functions in sucrose distribution and stress adaptation. These findings offer valuable insights into the regulatory mechanisms of the GmSUT family and suggest candidate genetic targets for enhancing stress tolerance in soybean.

Background: Cytokinin oxidase/dehydrogenase (CKX) can irreversibly degrade cytokinin, regulating the growth and development of plants and helping them cope with environmental stress. Methods: To understand the expression characteristics and the biological functions of CKX in alfalfa (Medicago sativa), a novel gene, designated as MsCKX5 (GenBank: PV934228), was cloned, characterized and overexpressed in Arabidopsis thaliana. Results: qRT-PCR results showed that MsCKX5 gene expression was clearly tissue-specific and had the highest expression level in the stems. In addition, the expression level of MsCKX5 was significantly induced by cold treatments. Heterologous expression of the MsCKX5 gene in A. thaliana could enhance cold tolerance by regulating the activities of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and adjust the relative conductivity and malondialdehyde (MDA) content. The combined analysis of transcriptome and metabolome results indicated that flavone and flavonol biosynthesis as well as the plant hormone signal transduction pathways were the main enriched pathways between wild-type and MsCKX5 overexpressed lines. Conclusions: These results provide an important molecular basis for further elucidating the molecular mechanism of plant cold resistance and the breeding of cold-resistant crop varieties.

Auxin plays a positive role in plant responses to low-phosphorus stress. However, the molecular mechanisms underlying indole-3-acetic acid (IAA)-mediated responses to phosphorus deficiency in alfalfa remain poorly understood. Alfalfa (Medicago sativa L.) cultivar ‘Zhongmu No. 3’ was subjected to two treatments: normal phosphorus (NP, 1000 μM KH2PO4) and low phosphorus supplemented with 1 μM IAA (LP + IAA, 10 μM KH2PO4). Morphological traits, physiological parameters, transcriptomic profiles, and metabolite accumulation were analyzed at 48 h and 10 days following treatment. Compared with the NP group, plants in the LP + IAA group showed marked changes in growth-related traits. At 48 h, plant height increased by 34%, total root length was 1.24-fold that of the NP group, and lateral root number increased by 23.48%. After 10 days, root fresh weight increased by 28%, total root length was 1.25-fold that of the NP group, lateral root number increased by 36.58%, and root volume increased by 22.2%, whereas plant height, stem diameter, and shoot fresh weight remained comparable to those of the NP group. Root acid phosphatase activity was 114.8% higher than that of the NP group at 48 h. Transcriptome analysis identified 1274 and 2277 differentially expressed genes (DEGs) between the NP and LP + IAA groups at 48 h and 10 days, respectively. At 48 h, the up-regulated genes were amino phospholipid ATPase 9 and amino alcohol phosphotransferase 1, whereas phosphate transporter 1 and purple acid phosphatase 12 were up-regulated at 10 days. Metabolomic analysis identified 308 and 1296 differentially accumulated metabolites (DAMs) at 48 h and 10 days, respectively. Early responses were enriched in purine metabolism and involved (5′-phosphoribosyl)-5-formamido-4-imidazolecarboxamide (FAICAR), whereas prolonged treatment involved L-aspartic acid, adenine, and cAMP. Integrated analyses identified tryptophan metabolism, cysteine and methionine metabolism, glycerophospholipid metabolism, and plant hormone signal transduction as major regulatory pathways. CDP-choline accumulation and changes in lipid-remodeling genes further indicated enhanced membrane phospholipid remodeling. Overall, these results provide insight into the morphological, physiological, transcriptional, and metabolic responses of alfalfa to low phosphorus in the presence of exogenous IAA.

Seed oil content is one of the primary breeding objectives in soybean. However, the genetic basis of seed oil content remains largely unexplored. In this study, we employed a recombinant inbred line (RIL) population consisting of 201 lines derived from a cross between Feidong and Guanyun, to identify quantitative trait loci (QTLs) for seed oil content in soybean under five environments. High broad-sense heritability (92.34%) indicates a substantial genetic contribution to phenotypic variation in this population and set of environments. A high-density genetic map containing 11,220 SNP markers was constructed, spanning 2507.62 cM, with an average distance of 0.22 cM between markers. By jointly using five QTL mapping methods, a total of 24 QTLs for seed oil content were identified, including eight stable QTLs detected in at least three environments and seven QTLs identified by all five methods. Out of these QTLs, qOil-5-4, qOil-9-2 and qOil-10-3 were considered as the major and stable QTLs. Within these three major and stable QTL intervals, except that Glyma.05g244100 (GmMFT/GmST05) is an experimentally validated gene, the other six genes that were highly expressed during seed development stages were identified as putative candidate genes requiring further validation. In conclusion, the major stable QTLs and candidate genes identified in this study facilitate the dissection of the genetic architecture underlying seed oil content and hold great potential for application in developing new high-oil soybean cultivars after further fine mapping and validation in independent genetic backgrounds.

Lespedeza potaninii is a species of flowering plant in the legume family. Due to its strong stress tolerance and nitrogen-fixing capacity, Lespedeza potaninii has become a crucial plant species for reseeding and restoring degraded grasslands in China. However, drought stress during the seedling or germination stage severely impacts the effectiveness of Lespedeza potaninii-based grassland restoration efforts. To screen seed-soaking agents enhancing seed germination under sorbitol-simulated drought stress and explore the underlying mechanisms, seed germination, physiological parameters and transcriptomic regulation of Lespedeza potaninii seeds under different seed-soaking treatments were analyzed. The results revealed that sorbitol-simulated drought stress significantly reduced seed germination of Lespedeza potaninii. However, treatments with 0.04% ZnSO4 or 0.10 mg/L ZnO-NPs could significantly enhance germination percentages. 0.04% ZnSO4 and 0.10 mg/L ZnO-NPs treatments notably decreased hydrogen peroxide (H2O2) levels, with 0.10 mg/L ZnO-NPs also increasing glutathione cycle efficiency. Transcriptomic analysis revealed that a 0.10 mg/L ZnO-NPs treatment improved drought resistance by enhancing energy and nutrient metabolism, particularly nitrogen metabolism, which in turn strengthened antioxidant defenses through the glutathione metabolism. In contrast, the ZnSO4 treatment promoted sulfur metabolism, thereby enhancing glutathione metabolism and increasing the biosynthesis of flavonoids and monoterpenes, further improving drought resistance. Both treatments likely involve zinc ions in promoting antioxidant synthesis and maintaining cell membrane stability by regulating antioxidant defense, particularly glutathione metabolism. These findings offer novel insights and strategies for improving seed emergence and establishment in degraded grasslands.

Phytophthora sojae (P. sojae) is a devastating soil-borne oomycete that severely threatens soybean [Glycine max (L.) Merr.] yield and quality. Abscisic acid (ABA) plays critical roles in plant physiology; however, its genetic mechanisms in regulating pathogen resistance remain unclear. Here, we identify ABA as a negative regulator of soybean immunity. The ABA signaling core component Abscisic acid-insensitive 5 (GmABI5) physically interacts with cyclin-dependent kinase 8 (GmCDK8), and they both function as immune suppressors. GmCDK8 stabilizes the GmABI5 protein by partially inhibiting proteasomal degradation, while GmABI5 transcriptionally activates GmCDK8 expression, forming a positive feedback loop that amplifies immune suppression. Furthermore, the GmCDK8-GmABI5 module coregulates overlapping downstream targets to repress pathogen-inducible lignin biosynthesis genes. Our findings highlight the critical roles of GmABI5 and GmCDK8 in P. sojae resistance through interconnection with phytohormone signaling.

Soybean is an important food and oil crop worldwide, but its narrow genetic background constrains the breeding of high-quality varieties. To expand soybean germplasm resources and investigate the effects of polyploidization on soybean agronomic and quality traits, three autotetraploid materials from two cultivated (W82 and JD17) and one wild soybean (W006) were successfully created through colchicine induction. The 12-h treatment of seeds with 0.2 % colchicine solution achieved optimal induction efficiency, with a chromosome doubling success rate of 11.76 %. Compared to diploids, autotetraploid soybeans exhibited significant phenotypic and physiological changes: increase tissue and cell size, thicker leaf with three to five leaflets, 16.71 % increase of chlorophyll content, and 14.52 % increase of photosynthetic rate. The fertility of autotetraploid soybean decreased, the average of single-seed pod ratio increased to 50.64 %, but the hundred-grain weight increased by 43.11 %. Notably, autotetraploid soybeans maintain oil content while achieving 8.89 % average protein content increase, with significant elevations in oleic acid, water-soluble proteins and essential amino acids (e.g., lysine and leucine). For genomic changes, 7457, 41,497, and 110,970 genetic variations were detected in tetraploid W82, JD17, and W006, respectively, these variations including SNP, InDel, and structural variation. The genes containing these variations were rich in defense response, lipid metabolic, DNA repair, transcription regulation, and amino acid synthesis, indicating that the genetic variations may be responsible for the phenotypic variation of tetraploid soybeans, and also indicating that tetraploid soybeans may has great potential in stress resistance. Besides, the chromosome number variation of three tetraploid plants indicating the genome of tetraploid soybeans were unstable. This study first reveals the differentiation in lipid metabolism pathways between diploid and tetraploid soybeans, providing critical germplasm resources and theoretical foundations for deciphering polyploid soybean nutrient synthesis mechanisms and breeding high-protein, high-oleic-acid varieties.

Isoflavonoids, which are abundant in soybeans, increase the utility value of soybean products and mediate plant defenses against diverse stresses. In this study, integrated transcriptomic and ultra-performance liquid chromatography (UPLC) analyses revealed that Phytophthora sojae (P. sojae) infection remodels the isoflavonoid biosynthesis pathway. Exogenous isoflavonoid application significantly increased soybean resistance to P. sojae, suppressing lesion expansion by more than 70% and inhibiting both reactive oxygen species accumulation and host cell death. Resistant evaluation of 228 soybean germplasms revealed 48 germplasms resistant to P. sojae isolate JS08-12, 42 germplasms resistant to isolate W210, and 38 elite germplasms exhibiting resistance against both W210 and JS08-12. Compared with that of the susceptible germplasm (1850.24 μg g-1), the resistant soybean germplasm presented 35.35% higher total isoflavonoids (2504.29 μg g-1), with significant increases in six compounds: 6″-O-malonylgenistin (+33.04%), 6″-O-malonyldaidzin (+43.35%), genistin (+43.34%), daidzin (+43.97%), genistein (+5.99%), and 6″-O-acetylgenistin (+5.48%). Importantly, the elite germplasm YZS180, YZS210, YZS073, and YZS052 presented significantly high levels of seed isoflavonoids (> 3500.00 μg g-1) and strong resistance. We further investigated the crosstalk between abscisic acid (ABA) and isoflavonoids. This study identifies isoflavonoids as defense metabolites against P. sojae and provides elite genetic resources for breeding soybeans with integrated disease resistance and nutritional quality.

High-vigor soybean seeds are critical for efficient production owing to their favorable growth properties and high yield potential. The evaluation and identification of high-vigor germplasms are essential for increasing soybean production capacity. Currently, there is no universally accepted evaluation system to test for soybean seed vigor. In this study, 11 seed vigor-related traits were measured across 126 soybean landraces via an artificial accelerated aging technique. The ratios of these 11 traits, which were calculated before and after artificial accelerated aging, were used as vigor indicators in principal component analysis (PCA), ultimately yielding two principal component factors. These factors were then combined via membership function standardization to calculate a comprehensive seed vigor evaluation value (V value), thereby establishing an evaluation system. Cluster analysis based on the V value was used to classify seed vigor into five levels and identify seven high-vigor germplasms: ZDD12322, ZDD06438, ZDD11951, ZDD08251, ZDD12436, ZDD02315, and ZDD15624. Through stepwise regression analysis, the optimal seed vigor predictive model was defined as V = -0.026 + 0.625 x RSL + 0.485 x RGI. This model revealed that the relative seedling length (RSL) and relative germination index (RGI) had significant positive effects on seed vigor. This study provides a valuable framework for seed quality control and selection, facilitating presowing vigor assessments to increase soybean planting efficiency and yield.

Abiotic stresses severely constrain soybean productivity worldwide. Here we demonstrate that gmeif2b5 (eukaryotic initiation factors) mutants confer dual stress tolerance through coordinated mechanisms. Integrative RNA-Seq and protein interaction analyses revealed that gmeif2b5 mutants increase lignin deposition to increase drought resilience and balanced Na+/K+ homeostasis to enhance salt tolerance; GmeIF2B5 physically interacts with GmPRX4, a plant heme peroxidase; GmPRX4 overexpression increases drought and salt resistance in soybean; GmeIF2B5 plays the predominant role in the GmeIF2B5-GmPRX4 module, and double mutants exhibiting synergistic stress tolerance improvements. Our work uncovers a 'GmeIF2B5-GmPRX4 regulatory axis' that: mobilises lignin-based structural fortification for enhanced drought resistance and orchestrates ionic equilibrium for increased salt tolerance. This study pioneers the role of eIF2B genes in soybean stress adaptation, establishing a multi-tiered regulatory node for precision molecular design of stress-resilient crops.

Seed hardness is an important quality trait of vegetable soybean. To determine the factors underlying seed hardness, two landraces with contrasting seed hardness, Niumaohuang (low seed hardness) and Pixiansilicao (high seed hardness), were selected from 216 soybean accessions originating from 26 provinces in China. The contents of the main components in vegetable soybean seeds such as water, soluble sugar, starch, protein and oil were measured, and transcriptome analyses performed during five stages of seed developmental. Transcriptome analysis indicates that during the middle and late stages of seed development, a large number of genes involved in the synthesis or degradation of starch, storage protein, and fatty acids were differentially expressed, leading to differences in the accumulation of stored substances during seed maturation among Niumaohuang and Pixiansilicao. The activity of cell proliferation and the formation of cell walls in the middle and late stages of seed development may also affect the hardness of seeds to a certain extent. In addition, weighted gene co-expression network analysis (WGCNA) was undertaken to identify co-expressed gene modules and hub genes that regulate seed hardness. Overexpression of a candidate seed hardness regulatory hub gene, GmSWEET2, resulted in increased seed hardness. In this study, the important role of GmSWEET2 in regulating the hardness of vegetable soybean seeds was verified and numerous potential key regulators controlling seed hardness and the proportion of seed components were identified, laying the groundwork for improving the texture of vegetable soybean.

Phytophthora root and stem rot caused by Phytophthora sojae (P. sojae) is one of the most destructive diseases to affect soybean (Glycine max (L.) Merr) pro duction. GmSRC2 that encodes a C2 domain-containing protein can respond to various stresses, however, the molecular mechanism of GmSRC2 in resistance of soybean to P. sojae is yet to be fully elucidated. In this study, GmSRC2 was found to be significantly up-regulated under P. sojae treatment; GmSRC2-overexpression (OE) transgenic lines and GmSRC2-silencing transient plants were generated via Agrobacterium tumefaciens mediated transformation and virus-induced gene silencing (VIGS) system, respectively. Infected leaves and cotyledons of OE-GmSRC2-1 and OE-GmSRC2-2 lines showed significant decreases in the disease symptoms and P. sojae biomass than those of wild type (WT); the activities of superoxide dismutase (SOD) and peroxidase (POD) confirmed the accumulation of reactive oxygen species (ROS) in overexpressed transgenic lines. Whereas, silencing of GmSRC2 severely increased the disease symptoms and the biomass of P. sojae. Further, we confirmed that GmSRC2 interacted with the effector PsAvh23 of P. sojae, and the C2 domain was crucial for the interaction. Overexpression of GmSRC2 upregulated the ADA2/GCN5 module upon P. sojae. The aforementioned results demonstrated that GmSRC2 played vital roles in regulating soybean resistance to oomycetes.

Soybean production is significantly impacted by Phytophthora root rot (PRR), which is caused by Phytophthora sojae. The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean NLR genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the NLR gene (Glyma.18g283200) were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after P. sojae infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and Glyma.18g283200 overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to P. sojae infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to P. sojae at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR.

Rapeseed (Brassica napus L.) is a major agricultural crop with diverse applications, particularly in the production of seed oil for both culinary use and biodiesel. However, its photosynthetic efficiency, a pivotal determinant of yield, remains relatively low compared with other C3 plants such as rice and soybean, highlighting the necessity of identifying the genetic loci and genes regulating photosynthesis in rapeseed. In this study, we investigated 5 photosynthesis traits and 5 leaf morphology traits in a natural population of rapeseed, and conducted a genome-wide association study (GWAS) to identify significantly associated loci and genes. The results showed that the gas-exchange parameters of the dark reactions in photosynthesis exhibited a significant positive correlation with the chlorophyll content, whereas they showed a weaker negative correlation with the leaf area. By GWAS, a total of 538 quantitative trait nucleotides (QTNs) were identified as significantly associated with traits related to both leaf morphology and photosynthesis. These QTNs were classified into 84 QTL clusters, of which, 21 clusters exhibited remarkable stability across different traits and environmental conditions. In addition, a total of 3,129 potential candidate genes were identified to be significantly associated with the above-mentioned 10 traits, most of which were shared by certain traits, further indicating the reliability of the findings. By integrating GWAS data with GO enrichment analysis and gene expression analysis, we further identified 8 key candidate genes that are associated with the regulation of photosynthesis, chlorophyll content, leaf area, and leaf petiole angle. Taken together, this study identified key genetic loci and candidate genes with the potential to improve photosynthetic efficiency in rapeseed. These findings provide a theoretical framework for breeding new rapeseed varieties with enhanced photosynthetic capabilities.

Vegetable soybean is an important legume vegetable. High sucrose content is a significant quality characteristic of vegetable soybean that influences consumers’ taste. However, the genetic basis of sucrose content in vegetable soybean is currently unclear. In this study, the genome-wide association study (GWAS) of sucrose content in vegetable soybean was performed using Chinese soybean mini-core collection. The results showed a wide genetic variation for the sucrose content in the mini-core collection. The sucrose content of genotypes from HHR (Huanghuai region) and SR (Southern region) was higher than that of genotypes from NER (Northeast region) and NR (Northern region). Furthermore, 82,187 high quality SNPs (Single nucleotide polymorphism) were used for GWAS of sucrose content. Based on SNPs detected in multiple environments, the chromosome 8 19,496,314–19,698,413 bp interval was identified as the candidate interval. And Glyma.08g234100 was most likely to affect the sucrose content of vegetable soybean seeds. This study has created new details to be used for breeding for high sucrose content in vegetable soybean.

Soybean (Glycine max L. Merr) production is severely affected by soil salinization as an important crop. The discovery of salt stress-responsive genes is essential for soybean breeding. To our knowledge, cyclophilins (CYPs) play important roles in salt stresses in crops such as rice and cotton, except in soybean. This study cloned GmCYP2 from soybean salt-tolerant cultivar Suxie No. 1 and obtained ten stable transgenic soybean lines overexpressing GmCYP2 by Agrobacterium rhizogenes-mediated transformation. Two of the higher-expressing transgenic lines (OE1 and OE2) were used to compare salt tolerance with the wild type (WT). Under the salt stress, the chlorophyll content, the maximum efficiency of PSII photochemistry (Fv/Fm) and actual photochemical quantum yield [Y(II)] of OE1 and OE2 lines were significantly higher than those of the WT. Meanwhile, the accumulation of malondialdehyde (MDA) in the OE1 and OE2 lines was significantly lower than that in the WT. In addition, the Na+/K+ ratio was also significantly lower than that of the WT in leaves and roots. The results also confirmed that the salt tolerance of GmCYP2-silencing soybean seedlings obtained by virus-induced gene silencing (VIGS) was reduced compared to the control. Subcellular localization showed that GmCYP2 was expressed in the plasma membrane and nucleus of Nicotiana benthamiana. RNA-seq results demonstrated that GmCYP2 is involved in key regulators of the ABA and Ca2+ signaling pathway. Yeast two-hybrid, bimolecular fluorescence complementation (BiFC) and split-luciferase complementation assay demonstrated that GmCYP2 protein interacts with salt-associated halotolerance 3 (HAL3) protein. These results suggest that the GmCYP2-GmHAL3 module enhances salt tolerance of soybean seedlings by maintaining the Na+/K+ ratio and good photosynthetic state and it may be involved in the ABA and Ca2+ signaling pathway.

With the rapid emergence and distribution of red crown rot (RCR) across countries, durable sources of resistance against Calonectria ilicicola in soybean [Glycine max (L.) Merrill] is required to control the disease. We employed two RIL populations for the experiment. We identified 15 and 14 QTLs associated with RCR resistance in ZM6 and MN populations, respectively, totaling 29 QTLs. Six and eight QTLs had phenotypic variation above 10% in ZM6 and MN populations, respectively. We identified six (6) “QTL hotspots” for resistance to RCR from the ZM6 and MN RIL populations on chromosomes 1, 7, 10, 11, 13, and 18. Gene annotations, gene ontology enhancement, and RNA sequencing assessment detected 23 genes located within six “QTL Hotspots” as potential candidate genes that could govern RCR resistance in soybeans. Our data will generally assist breeders in rapidly and effectively incorporating RCR resistance into high-yielding accession through marker-assisted selection.

Red crown rot (RCR) disease caused by Calonectria ilicicola negatively impacts soybean yield and quality. Unfortunately, the knowledge of the genetic architecture of RCR resistance in soybeans is limited. In this study, 299 diverse soybean accessions were used to explore their genetic diversity and resistance to RCR, and to mine for candidate genes via emergence rate (ER), survival rate (SR), and disease severity (DS) by a multi-locus random-SNP-effect mixed linear model of GWAS. All accessions had brown necrotic lesions on the primary root, with five genotypes identified as resistant. Nine single-nucleotide polymorphism (SNP) markers were detected to underlie RCR response (ER, SR, and DS). Two SNPs colocalized with at least two traits to form a haplotype block which possessed nine genes. Based on their annotation and the qRT-PCR, three genes, namely Glyma.08G074600, Glyma.08G074700, and Glyma.12G043600, are suggested to modulate soybean resistance to RCR. The findings from this study could serve as the foundation for breeding RCR-tolerant soybean varieties, and the candidate genes could be validated to deepen our understanding of soybean response to RCR.