Transcriptome-wide m6A methylation profiling identifies GmAMT1;1 as a promoter of lead and cadmium tolerance in soybean nodules

GmWRKY33a is a hub gene responsive to brassinosteroid signaling that suppresses nodulation in soybean (Glycine max)

Brassinosteroids (BRs) are key phytohormones influencing soybean development, yet their role in symbiosis remains unclear. Here, the RNA-Seq was used to identify important gene associated with BRs and symbiotic nitrogen fixation, and the function of candidate gene was verified by transgenic hairy roots. The result shows that the RNA-Seq analysis was conducted in which BR signaling was found to suppress nodule formation and many DEGs enriched in immunity-related pathways. WGCNA analyses led to the identification of GmWRKY33a as being responsive to BR signaling in the context of symbiosis establishment. Transgenic hairy roots analyses indicated that GmWRKY33a served as a negative regulator of the establishment of symbiosis. The qRT-PCR analysis confirmed that BR signaling upregulates GmWRKY33a, leading to nodulation suppression and activation of soybean immune responses. In summary, our research revealed that BR suppresses root nodule formation by modulating the immune signaling pathway in soybean roots. We further identified that GmWRKY33a, a crucial transcription factor in BR signaling, plays a negative role in the symbiotic establishment.

Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review

Soybean improvement has entered a new era with the advent of multi-omics strategies and bioinformatics innovations, enabling more precise and efficient breeding practices. This comprehensive review examines the application of multi-omics approaches in soybean-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics. We first explore pre-breeding and genomic selection as tools that have laid the groundwork for advanced trait improvement. Subsequently, we dig into the specific contributions of each -omics field, highlighting how bioinformatics tools and resources have facilitated the generation and integration of multifaceted data. The review emphasizes the power of integrating multi-omics datasets to elucidate complex traits and drive the development of superior soybean cultivars. Emerging trends, including novel computational techniques and high-throughput technologies, are discussed in the context of their potential to revolutionize soybean breeding. Finally, we address the challenges associated with multi-omics integration and propose future directions to overcome these hurdles, aiming to accelerate the pace of soybean improvement. This review serves as a crucial resource for researchers and breeders seeking to leverage multi-omics strategies for enhanced soybean productivity and resilience.

NtARF11 positively regulates cadmium tolerance in tobacco by inhibiting expression of the nitrate transporter NtNRT1.1

Heavy metal cadmium (Cd) is widespread in contaminated soil and an important factor limiting plant growth. NO3- (nitrate) affects Cd uptake and thus changes Cd tolerance in plants; however, the underlying molecular regulatory mechanisms have not yet been elucidated. Here, we analyzed a novel gene, NtARF11 (auxin response factor), which regulates Cd tolerance in tobacco via the NO3- uptake pathway, through experiments with NtARF11-knockout and NtARF11-overexpression transgenic tobacco lines. NtARF11 was highly expressed under Cd stress in tobacco plants. Under Cd stress, overexpression of NtARF11 enhanced Cd tolerance in tobacco compared to that in wild-type tobacco, as shown by the low Cd concentration, high chlorophyll concentration, and low accumulation of reactive oxygen species in NtARF11-overexpressing tobacco. Moreover, low NO3- concentrations were observed in NtARF11-overexpressing tobacco plants. Further analyses revealed direct binding of NtARF11 to the promoter of the nitrate transporter NtNRT1.1, thereby negatively regulating its expression in tobacco. Notably, NtNRT1.1 knockout reduced NO3- uptake, which resulted in low Cd concentrations in tobacco. Altogether, these results demonstrate that the NtARF11-NtNRT1.1 module functions as a positive regulator of Cd tolerance by reducing the Cd uptake in tobacco, providing new insights for improving Cd tolerance of plants through genetic engineering.

Interactive effects of ammonium sulfate and lead on alfalfa in rare earth tailings: Physiological responses and toxicity thresholds

Ion-adsorption rare earth ore contains significant levels of leaching agents and heavy metals, leading to substantial co-contamination. This presents significant challenges for ecological rehabilitation, yet there is limited understanding of the toxicity thresholds associated with the co-contamination of ammonium sulfate (AS) and lead (Pb) on pioneer plants. Here, we investigated the toxicity thresholds of various aspects of alfalfa, including growth, ultrastructural changes, metabolism, antioxidant system response, and Pb accumulation. The results indicated that the co-contamination of AS-Pb decreased the dry weight of shoot and root by 26 %-77 % and 18 %-92 %, respectively, leading to irregular root cell morphology and nucleus disintegration. The high concentration and combined exposures to AS and Pb induced oxidative stress on alfalfa, which stimulated the defense of the antioxidative system and resulted in an increase in proline levels and a decrease in soluble sugars. Structural equation modeling analysis and integrated biomarker response elucidated that the soluble sugars, proline, and POD were the key physiological indicators of alfalfa under stresses and indicated that co-exposure induced more severe oxidative stress in alfalfa. The toxicity thresholds under single exposure were 496 (EC5), 566 (EC10), 719 (EC25), 940 (EC50) mg kg-1 for AS and 505 (EC5), 539 (EC10), 605 (EC25), 678 (EC50) mg kg-1 for Pb. This study showed that AS-Pb pollution notably influenced plant growth performance and had negative impacts on the growth processes, metabolite levels, and the antioxidant system in plants. Our findings contribute to a theoretical foundation and research necessity for evaluating ecological risks in mining areas and assessing the suitability of ecological restoration strategies.

Identification of m6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli

Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.

Molecular Mechanism of GmSNE3 Ubiquitin Ligase-Mediated Inhibition of Soybean Nodulation by Halosulfuron Methyl

In this study, the role of E3 ubiquitin ligase GmSNE3 in halosulfuron methyl (HSM) inhibiting soybean nodulation was investigated. GmSNE3 was strongly induced by HSM stress, and the overexpression of GmSNE3 significantly reduced the number of soybean nodules. Further investigation found that GmSNE3 could interact with a nodulation signaling pathway 1 protein (GmNSP1a) and GmSNE3 could mediate the degradation of GmNSP1a. Importantly, GmSNE3-mediated degradation of GmNSP1a could be promoted by HSM stress. Moreover, HSM stress and the overexpression of GmSNE3 resulted in a substantial decrease in the expression of the downstream target genes of GmNSP1a. These results revealed that HSM promotes the ubiquitin-mediated degradation of GmNSP1a by inducing GmSNE3, thereby inhibiting the regulatory effect of GmNSP1a on its downstream target genes and ultimately leading to a reduction in nodulation. Our findings will promote a better understanding of the toxic mechanism of herbicides on the symbiotic nodulation between legumes and rhizobia.