Introduction: Heterosis is a critical phenomenon in crop improvement. Cytoplasmic male sterility (CMS) and Restorer gene (Rf) systems are essential components for heterosis-based breeding. However, the molecular mechanism underlying CMS remains largely unclear in soybean.Methods: We integrated a morphological investigation with comparative analyses of transcriptomic and proteomic changes in pollen from the CMS line W931A and its maintainer line, W931B, at the uninucleate microspore (UM) and binucleate pollen (BP) stages.Results: Compared to W931B, which had healthy, oval pollen grains, W931A showed shrunken or degraded pollen grains with an irregularly thickened endothelium and decreased starch accumulation. Transcriptomic comparisons revealed a total of 865 differentially expressed genes (DEGs) in W931A over the two stages. These genes were primarily associated with pentose and glucuronate interconversions, sphingolipid metabolism, and glycerolipid metabolism. Proteomic analysis revealed 343 differentially expressed proteins (DEPs), which were mainly involved in carbon metabolism, glycolysis/gluconeogenesis, and nitrogen metabolism. Consistently, Gene Ontology (GO) biological process terms related to pollen development were enriched among DEGs at the UM and BP stages. Notably, four genes with demonstrated roles in pollen development were differentially expressed, including AGAMOUS-LIKE 104, PROTEIN-TYROSINE-PHOSPHATASE 1, and PHOSPHOLIPASE A2. A total of 53 genes and the corresponding proteins were differentially expressed in W931A at both the UM and BP stages, and many of these were pectinesterases, polygalacturonases, peroxidases, and ATPases.Discussion: The results of this study suggest that pollen development in W931A is likely regulated through suppression of the identified DEGs and DEPs. These findings increase our understanding of the molecular mechanism underlying CMS in soybean, aiding future research into soybean fertility and promoting the efficient use of heterosis for soybean improvement.

Stay-green syndrome (SGS) is an important factor that causes soybean (Glycine max) yield reduction. Despite progress being made, the regulatory mechanism remains largely unclear. Therefore, in this study, an SGS-sensitive soybean variety, “HD0702”, was employed to investigate the underlying mechanism. Transcriptomic analyses were performed in a tissue-specific manner to investigate differentially expressed genes (DEGs) in soybeans impacted by SGS and in those without SGS. A total of 1858 DEGs were identified in the pods, and 2814 DEGs were identified in the leaves. Further investigation revealed that SGS mainly affected the expression levels of key genes involved in the regulation of photosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. To support this finding, the chlorophyll content of the pods was to be found increased by 320% for chlorophyll a and 260% for chlorophyll b. In leaves, soluble sugar levels significantly increased, whereas phytohormones IAA and ABA decreased in SGS pods. DEGs were classified using gene ontology (GO) terms, and photosynthesis-related genes α-glucosidase, β-mannosidase, β-amylase 5 (GmBAM5), and starch synthase 2 (GmSS2) were up-regulated. This study demonstrates a molecular and physiological basis for SGS that merits further investigation to allow for SGS management.