Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.

Background: Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. Results: In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as “Photosynthesis”, “Carbon metabolism”, and “Fatty acid metabolism”, were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. Conclusions: Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.

Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean genotypes with different P-efficiencies. The DNA methylation levels were slightly higher under low-P stress in both genotypes. Integrative methylation and transcription analysis suggested a complex regulatory relationship between DNA methylation and gene expression that may be associated with the type, region, and extent of methylation. Association analysis of low-P-induced differential methylation and gene expression showed that transcriptional alterations of a small part of genes were associated with methylation changes. Dynamic methylation alterations in transposable element (TE) regions in the CHH methylation context correspond with changes in the amount of siRNA under low-P conditions, indicating an important role of siRNAs in modulating TE activity by guiding CHH methylation in TE regions. Together, these results could help to elucidate the epigenetic regulation mechanisms governing the responses of plants to abiotic stresses.

This data descriptor introduces the dataset of the transcriptome of low-phosphorus tolerant soybean (Glycine max) variety NN94-156 under phosphorus-deficient and -sufficient conditions. This data is comprised of the transcriptome datasets (four libraries) acquired from roots and leaves of the soybean plants challenged with low-phosphorus, which allows further analysis whether systemic tolerance response to low phosphorus stress occurred. We describe the detailed procedure of how plants were prepared and treated and how the data were generated and pre-processed. Further analyses of this data would be helpful to improve our understanding of molecular mechanisms of low-phosphorus stress in soybean.

Soybean cyst nematode (SCN) is one of the most harmful pests, causing major reductions in soybean yield globally. The validation and functional characterization of SCN resistance genes are crucial to improving soybean yield worldwide. Herein, we describe an SCN resistance gene, GmERF071 ( Glyma.19g262700 ). GmERF071 is a hydrophilic, unstable protein with an AP2/ERF subfamily ethylene response transcription factor domain, which is localized in the nucleus. Overexpression of GmERF071 enhanced SCN resistance in the soybean stable genetic transformation and root systems. RNA‐seq analysis revealed 394 upregulated and 132 downregulated differentially expressed genes (DEGs) in GmERF071 overexpression transgenic plants. The DEGs participated in plant‐pathogen interactions, mitogen‐activated protein kinase signaling, plant hormone signal transduction, response to chitin, response to carbohydrates, response to wounding in starch and sucrose metabolism, phenylpropionic acid biosynthesis, and flavonoid biosynthesis. Nine candidate DEGs were verified using real‐time quantitative reverse transcription PCR. These results suggest that GmERF071 plays a key role in SCN resistance and could be used in genomics‐assisted breeding to develop soybean varieties with increased resistance to SCN.