Background: Shading includes low light intensity and varying quality. However, a low red/far-red (R/Fr) ratio of light is a signal that affects plant growth in intercropping and close- planting systems. Thus, the low R/Fr ratio uncoupling from shading conditions was assessed to identify the effect of light quality on photosynthesis and CO₂ assimilation. Soybean plants were grown in a growth chamber with natural solar radiation under four treatments, that is, normal (N, sunlight), N + Fr, Low (L) + Fr, and L light. Results: Low R/Fr ratio significantly increased the total biomass, leaf area, starch and sucrose contents, chlorophyll content, net photosynthetic rate, and quantum efficiency of the photosystem II compared with normal R/Fr ratio under the same light level (P < 0.05). Proteomic analysis of soybean leaves under different treatments was performed to quantify the changes in photosynthesis and CO₂ assimilation in the chloroplast. Among the 7834 proteins quantified, 12 showed a > 1.3-fold change in abundance, of which 1 was related to porphyrin and chlorophyll metabolism, 2 were involved in photosystem I (PS I), 4 were associated with PS II, 3 proteins participated in photosynthetic electron transport, and 2 were involved in starch and sucrose metabolism. The dynamic change in these proteins indicates that photosynthesis and CO₂ assimilation were maintained in the L treatment by up-regulating the component protein levels compared with those in N treatment. Although low R/Fr ratio increased the photosynthetic CO₂ assimilation parameters, the differences in most protein expression levels in N + Fr and L + Fr treatments compared with those in N treatment were insignificant. Similar trends were found in gene expression through quantitative reverse transcription polymerase chain reaction excluding the gene expression of sucrose synthase possible because light environment is one of the factors affecting carbon assimilation. Conclusions: Low R/Fr ratio (high Fr light) can increase the photosynthetic CO₂ assimilation in the same light intensity by improving the photosynthetic efficiency of the photosystems.

Shading created by intercropping reduces the photosynthetic capacity of soybean plants but also directly affects the pod setting process of soybean. However, which of the changed aspects induce the yield differences in intercropped soybean cultivars is still unknown. Four soybean cultivars with similar yield and growth and development processes in monoculture were selected by a pre-experiment. Field experiments were carried out from 2015 to 2017 to investigate the leaf photosynthetic parameters, total biomass, reproductive characteristics, yield and yield components of soybean. The yield of soybean cultivars was significantly decreased in intercropping systems and the yield of cultivars (cvs.) ZH39 and QH34 were considerably higher than those of cvs. HD19 and HD20. Besides, the pod and seed number and harvest index were also reduced by intercropping and the yield components of cvs. ZH39 and QH34 in intercropping were significantly higher than those of cvs. HD19 and HD20, other than the seed size. Although the parameters of leaf photosynthetic capacity (leaf area index, net photosynthetic rate, and chlorophyll content) of soybean were changed by intercropping, there was no significant difference among cultivars. Additionally, the CGR_R1–R5 (crop growth rate between R1 and R5) of intercropped soybean was lower than that of monoculture, while no significant differences were observed in different cultivars. The reproductive biomass at R5 was significantly different among soybean cultivars, and the reproductive partitioning and seed set efficiency of different cultivars were varied by the reproductive biomass at R5. Therefore, high-yielding cultivars in intercropping can achieve higher yield due to more reproductive structures survived at R5.

The fruiting stage of soybean (Glycine max L.) is critical for determining both its yield and quality, thereby influencing global production. While some studies have provided partial explanations for the occurrence of Fusarium species on soybean seeds and pods, the fungal diversity affecting soybean pods in Sichuan Province, a major soybean cultivation region in Southwestern China, remains inadequately understood. In this study, 182 infected pods were collected from a maize–soybean relay strip intercropping system. A total of 10 distinct pod-infecting fungal genera (132 isolates) were identified, and their pathogenic potential on soybean seeds and pods was evaluated. Using morphological characteristics and DNA barcode markers, we identified 43 Fusarium isolates belonging to 8 species, including F. verticillioides, F. incarnatum, F. equiseti, F. proliferatum, F. fujikuroi, F. oxysporum, F. chlamydosporum, and F. acutatum through the analysis of the translation elongation factor gene (EF1-α) and RNA polymerases II second largest subunit (RPB2) gene. Multi-locus phylogenetic analysis, incorporating the Internal Transcribed Spacer (rDNA ITS), β-tubulin (β-tubulin), Glyceraldehyde 3-phosphate dehydrogenase (GADPH), Chitin Synthase 1 (CHS-1), Actin (ACT), Beta-tubulin II (TUB2), and Calmodulin (CAL) genes distinguished 37 isolates as 6 Colletotrichum species, including C. truncatum, C. karstii, C. cliviicola, C. plurivorum, C. boninense, and C. fructicola. Among these, F. proliferatum and C. fructicola were the most dominant species, representing 20.93% and 21.62% of the isolation frequency, respectively. Pathogenicity assays revealed significant damage from both Fusarium and Colletotrichum isolates on soybean pods and seeds, with varying isolation frequencies. Of these, F. proliferatum, F. acutatum, and F. verticillioides caused the most severe symptoms. Similarly, within Colletotrichum genus, C. fructicola was the most pathogenic, followed by C. truncatum, C. karstii, C. cliviicola, C. plurivorum, and C. boninense. Notably, F. acutatum, C. cliviicola, C. boninense, and C. fructicola were identified for the first time as pathogens of soybean pods under the maize–soybean strip intercropping system in Southwestern China. These findings highlight emerging virulent pathogens responsible for soybean pod decay and provide a valuable foundation for understanding the pathogen population during the later growth stages of soybean.

Seed and pod decay significantly threaten to soybean yield and quality during the fruiting stage worldwide. Although, few previous studies partially explained the occurrence of Fusarium species on soybean seeds and pods, However, fungal diversity affecting soybean pods in Sichuan Province China, third-largest soybean cultivation region remains unknown. In this study, we identified pod-infecting fungal communities and evaluated their pathogenic potential on soybean seeds and pods. Using morphological indices and DNA barcode markers, we characterized Fusarium species, including F. verticillioides, F. incarnatum, F. equiseti, F. proliferatum, F. fujikuroi, F. oxysporum, F. chlamydosporum, and F. acutatum through Translation elongation factor gene (EF1-α) and RNA polymerases II second largest subunit (RPB2) gene analysis. Multi-locus phylogeny assay of Internal transcribed spacer (rDNA ITS), β-tubulin (β-tubulin), Glyceraldehyde 3-phosphate dehydrogenase (GADPH), Chitin Synthase 1 (CHS-1), Actin (ACT), Beta-tubulin II (TUB2) and Calmodulin (CAL) distinguished Colletotrichum species as C. truncatum, C. karstii, C. cliviicola, C. plurivorum, C. boninense, and C. fructicola. Pathogenicity assays revealed significant damage from Fusarium and Colletotrichum isolates on soybean pods and seeds, with varying isolation frequencies. Among them, F. proliferatum, F. acutatum, and F. verticillioides caused the most severe symptoms, while C. fructicola was most pathogenic, followed by C. truncatum, C. karstii, C. cliviicola, C. plurivorum, and C. boninense. These findings highlight emerging virulent pathogens responsible for soybean pod decay, paves a valuable foundation for developing resistant cultivars to manage pod associated diseases at the later growth stage of soybean.

Soybean is an important global crop used for oil, food, and feed production. To increase yield and land-use efficiency, growers often plant soybean at a high density or use intercropping systems. Under these systems, soybeans frequently experience shade stress, which directly affects agronomic traits such as plant height. Although researchers have well documented the genetic basis of plant height under normal conditions, the loci responsible for height variation under shade stress remain largely unexplored. Therefore, we performed a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) using SNP linkage disequilibrium block (SNPLDB) markers to identify QTLs associated with soybean plant height under shade stress. We evaluated a natural population of 181 soybean accessions for plant height traits under both normal and shaded conditions across four environments for three years. Using the Soybean40K chip, we derived 11,463 SNPLDB markers and identified 42, 33, and 28 significant SNPLDBs associated with plant height, average internode length, and number of main-stem nodes, respectively. For each SNPLDB, we estimated haplotype (allele) effects and assembled QTL–allele matrices to summarize the population’s genetic composition. Four SNPLDB loci proved stable across multiple environments, exhibiting high −lg(p) values and explaining substantial phenotypic variation. Finally, we projected that 80 candidate genes resided within 180 kb of these stable loci, and we identified four strong candidate genes linked to plant height traits based on combined positional and functional evidence. These results clarify genetic factors that influence soybean height under shading and could aid development of high-yielding soybean varieties.