Background: Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and identification of P efficiency genes are important strategies for increasing soybean yield. Results: Genome-wide association analysis (GWAS) with NJAU 355 K SoySNP array was performed to identify single nucleotide polymorphisms (SNPs) significantly associated with three shoot P efficiency-related traits of a natural population of 211 cultivated soybeans and relative values of these traits under normal P (+P) condition and P deficiency (−P) condition. A total of 155 SNPs were identified significantly associated with P efficiency-related traits. SNPs that were significantly associated with shoot dry weight formed a SNP cluster on chromosome 11, while SNPs that were significantly associated with shoot P concentration formed a SNP cluster on chromosome 10. Thirteen haplotypes were identified based on 12 SNPs, and Hap9 was considered as the optimal haplotype. Four SNPs (AX-93636685, AX-93636692, AX-93932863, and AX-93932874) located on chromosome 10 were identified to be significantly associated with shoot P concentration under +P condition in two hydroponic experiments. Among these four SNPs, two of them (AX-93636685 and AX-93932874) were also significantly associated with the relative values of shoot P concentration under two P conditions. One SNP AX-93932874 was detected within 5′-untranslated region of Glyma.10 g018800, which contained SPX and RING domains and was named as GmSPX-RING1. Furthermore, the function research of GmSPX-RING1 was carried out in soybean hairy root transformation. Compared with their respective controls, P concentration in GmSPX-RING1 overexpressing transgenic hairy roots was significantly reduced by 32.75% under +P condition; In contrast, P concentration in RNA interference of GmSPX-RING1 transgenic hairy roots was increased by 38.90 and 14.51% under +P and -P conditions, respectively. Conclusions: This study shows that the candidate gene GmSPX-RING1 affects soybean phosphorus efficiency by negatively regulating soybean phosphorus concentration in soybean hairy roots. The SNPs and candidate genes identified should be potential for improvement of P efficiency in future soybean breeding programs.

Phosphorus (P) deficiency is one of the major factors limiting soybean production, and approximately 90% of P absorbed by plants occurs during the reproductive stage. Thus, it is important to understand the genetic mechanism underlying soybean low-P tolerance, especially in the mature period. Here, we evaluated six P-efficiency-related traits at maturity of 219 soybean accessions, namely, plant height (PH), node number of the main shoot (NN), branch number of the main shoot (BN), pod number per plant (PN), 100-seed weight (100SW), and seed yield per plant (SY), under normal-phosphorus (NP) and low-phosphorus (LP) conditions across two environments. Then, a genome-wide association study (GWAS) in conjunction with a high-density NJAU 355 K SoySNP array was performed. As a result, 27 P-efficiency-related single nucleotide polymorphisms (SNPs) were identified. Furthermore, two repeated SNPs, AX-93897192 and AX-93897200, located on chromosome 19 that were associated with both PH and NN were considered as stable SNPs associated with P deficiency, and the candidate gene GmABCG39 was identified. This work will be helpful in breeding high-P-efficiency soybean varieties.

Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes. The transcriptomes of two wild accessions (W11 and W99) with different resistance to CCW were analyzed at early- and late-induction time points. After induction, the susceptible accession W11 differentially expressed 1268 and 508 genes at the early and late time points, respectively. Compared with W11, the resistant accession W99 differentially expressed 1270 genes at the early time point and many more genes (2308) at the late time point. In total, 3836 non-redundant genes were identified in both lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) in W99 at the late time point were mostly associated with specific processes and pathways. Among the non-redundant genes, 146 genes were commonly up-regulated in the treatment condition compared with the control condition at the early- and late-induction time points in both accessions used in this experiment. Approximately 40% of the common DEGs were related to secondary metabolism, disease resistance, and signal transduction based on their putative function. Excluding the common DEGs, W99 expressed more unique DEGs than W11. Further analysis of the 3836 DEGs revealed that the induction of CCW not only up-regulated defense-related genes, including 37 jasmonic acid (JA)-related genes, 171 plant-pathogen-related genes, and 17 genes encoding protease inhibitors, but also down-regulated growth-related genes, including 35 photosynthesis-related genes, 48 nutrition metabolism genes, and 28 auxin metabolism genes. Therefore, representative defense-related and growth-related genes were chosen for binding site prediction via co-expression of transcription factors (TFs) and spatial expression pattern analyses. In total, 53 binding sites of 28 TFs were identified based on 3 defense-related genes and 3 growth-related genes. Phosphate transporter PT1, which is a representative growth-related gene, was transformed into soybean, and the transgenic soybean plants were susceptible to CCW. In summary, we described transcriptome reprograming after herbivore induction in wild soybean, identified the susceptibility of growth-related genes, and provided new resources for the breeding of herbivore-resistant cultivated soybeans.

Plants have evolved complex mechanisms to respond to the fluctuation of available nitrogen (N) in soil, but the genetic mechanisms underlying the N response in crops are not well-documented. In this study, we generated a time series of NO₃⁻-mediated transcriptional profiles in roots of maize and sorghum, respectively. Using weighted gene co-expression network analysis, we identified modules of co-expressed genes that related to NO₃⁻ treatments. A cross-species comparison revealed 22 conserved modules, of which four were related to hormone signaling, suggesting that hormones participate in the early nitrate response. Three other modules are composed of genes that are mainly upregulated by NO₃⁻ and involved in nitrogen and carbohydrate metabolism, including NRT, NIR, NIA, FNR, and G6PD2. Two G2-like transcription factors (ZmNIGT1 and SbNIGT1), induced by NO₃⁻ stimulation, were identified as hub transcription factors (TFs) in the modules. Transient assays demonstrated that ZmNIGT1 and SbNIGT1 are transcriptional repressors. We identified the target genes of ZmNIGT1 by DNA affinity-purification sequencing (DAP-Seq) and found that they were significantly enriched in catalytic activity, including carbon, nitrogen, and other nutrient metabolism. A set of ZmNIGT1 targets encode transcription factors (ERF, ARF, and AGL) that are involved in hormone signaling and root development. We propose that ZmNIGT1 and SbNIGT1 are negative regulators of nitrate responses that play an important role in optimizing nutrition metabolism and root morphogenesis. Together with conserved N responsive modules, our study indicated that, to encounter N variation in soil, maize and sorghum have evolved an NO₃⁻-regulatory network containing a set of conserved modules and transcription factors.

Forest fine root litter enters agricultural soils in some cases and its decomposition would change the soil’s properties. However, how this process further influences the ammonia (NH₃) volatilization and nitrous oxide (N₂O) emission from agricultural soil receiving fertilizer nitrogen (N) is unknown. Here, we conducted a soil pot experiment to investigate the responses of the aforementioned gaseous N losses during wheat season to fine root litters derived from Populus deltoides (RP) and Metasequoia glyptostroboides (RM) incorporations. The results showed that two forest fine root litters reduced total NH₃ losses by 30.6−31.9% from 180 kg N ha⁻¹ applied to farmland soil, and this effect was attributed to decreased soil urease activity and ammonium-N during the basal N fertilization period. Whether receiving fertilizer N or not, N₂O emissions from farmland soil were significantly (p < 0.05) mitigated by 62.8–68.2% and 43.0−50.0% following the RP and RM incorporation, respectively. Lower N₂O emission was ascribed to increased soil pH but decreased soil nitrate-N and bulk density. In addition, less AOA and AOB amoA but more nosZ gene abundances explained the fine root litter-induced N₂O mitigation effect. Neither forest fine root litter exerted a negative effect on wheat grain yield and crop N use efficiency in N-added agriculture soil. In conclusion, forest fine root litter incorporation could help to mitigate gaseous N losses via NH₃ volatilization and N₂O emission from fertilizer-N-applied agricultural soils, and without crop production loss.