Flowers and pod abscission significantly reduces soybean yield. This study aims to identify the main signaling pathways and key candidate genes in soybean leaves that affect flower and pod abscission under shade conditions. This information will be useful for the localization and cloning of genes related to abscission. Two soybean cultivars with different abscission rates (Liaodou 32 and Shennongdou 28) were used in this experiment. The soybean leaves were subjected to 50% shading treatment and the transcriptome and metabolome was sequenced during the light-sensitive period. The effects of weak light at different growth stages on the metabolic pathways of soybean leaves and organ abscission were investigated by analyzing plant phenotype and physiological changes. The results showed that both two cultivars triggered the same molecular mechanism and similar metabolite accumulation mode by shading, but the regulations of the two cultivars were different. The key candidate genes identified for soybean flower and pod abscission caused by shading were DIV, MYB06, MYB44, MY1R1, MYBS3, WRKY6, WRK53, WRK70, WRK40, DOF14, CDF3, CDF2, GATA5, DREB3 and ERF3; the differentially expressed genes that caused the variation between the cultivars were SRM1, MYB16, WRK24, COL16, MYB61 and TRB1. The main metabolic pathways involved in soybean flower and pod abscission caused by shading were secondary metabolite biosynthesis pathway, metabolic pathway, cofactor biosynthesis pathway, phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, fatty acid biosynthesis pathway and amino acid biosynthesis pathway; the DEMs that caused the differences among the cultivars were carbon metabolism, glutathione metabolism, biotin metabolism, nucleotide metabolism, purine metabolism, plant hormone signaling, flavone and flavonol biosynthesis, lysine degradation, arginine and proline metabolism, amino sugars and nucleotide sugars metabolism, etc. In conclusion, shading treatment in the light-sensitive period of soybean changed the physiological response and gene expression level of leaves, inhibited carbohydrate metabolism and transport and biosynthesis of secondary metabolites, and thereby leading to increased competition and hormonal disruption, which promoted the abscission of soybean flowers/pods and reduced grain yield.

Premature leaf failure is one of the major factors contributing to crop yield reduction. High-yielding soybean cultivars exhibit a longer leaf lifespan during the reproductive period, promoting higher yields. In this experiment, physiological indexes and transcriptomics analysis were carried out on leaves of different canopy parts of two soybean cultivars with different senescence sensitivities of LD32 and SND28 as test materials. The results showed that the leaf senescence rates of the two soybean cultivars, tested at the grain-filling stage, were significantly different, and the senescence rates of the upper and middle canopy leaves of LD32 were significantly lower than those of SND28. In comparison to SND28, LD32 exhibited slower decreases in chlorophyll, net photosynthetic rate, and SPAD values in the upper and middle canopy leaves. The differentially expressed genes for senescence of upper and middle canopy leaves of both cultivars were enriched in four pathways: the photosynthesis pathway, the photosynthesis–antenna protein pathway, the MAPK signaling pathway–plant hormone signal transduction pathway, and the plant hormone signal transduction pathway. The differential expression of 20 genes (Ribose-5-phosphate isomerase, fructose-1,6-bisphosphatase, etc.) in the “carbon fixation in photosynthetic organisms” pathway of LD32 may be involved in the regulation of reducing the rate of leaf senescence in the middle of the canopy at the grain-filling stage of LD32. Ribose-5-phosphate isomerase and fructose-1,6-bisphosphatase in LD32 may reduce the rate of leaf senescence in the middle of the canopy during seed filling.

A high pod abscission rate in soybean plants results in a significant decrease in the yield per plant. Under dense planting conditions, dense tolerant soybean cultivars had a relatively low rate of pod abscission, thereby facilitating higher yield. In this experiment, two planting densities were used to analyze the differentially expressed genes and metabolites between the abscised and non-abscised flowers of two soybean cultivars on the basis of transcriptomic and metabolomic techniques. The flower abscission rate of LD32 was significantly lower than that of SND28. Both cultivars were enriched in the photosynthesis, sugar, and starch metabolism; MAPK signaling; and phenylalanine metabolism pathways at different planting densities. However, under dense planting, the trend of differential gene changes in the density-tolerant CV LD32 was opposite to that of the conventional CV SND28. The results of the joint analysis indicated that the co-regulation of cytokinin dehydrogenase 6 (CKX6) and cis-zeatin riboside monophosphate (CZRM) in the zeatin biosynthesis pathway of LD32 under dense planting conditions was the main factor for the relatively low rate of pod abscission under dense planting conditions.