Explore the vast range of titles available.

Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress‐resilient crops is crucial for ensuring global food security. Because of their nitrogen‐fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next‐generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions. Core Ideas Epigenetic mechanisms play an important role in abiotic stress responses in plants. Epigenetic changes in abiotic stress responses in legumes is an emerging study focus. Epigenetic changes under abiotic stress are dynamic and vary among legume species. Epigenetic optimization can be used to enhance abiotic stress tolerance in legumes.

Background Climate change induces perturbation in the global water cycle, profoundly impacting water availability for agriculture and therefore global food security. Water stress encompasses both drought (i.e. water scarcity) that causes the drying of soil and subsequent plant desiccation, and flooding, which results in excess soil water and hypoxia for plant roots. Terrestrial plants have evolved diverse mechanisms to cope with soil water stress, with the root system serving as the first line of defense. The responses of roots to water stress can involve both structural and physiological changes, and their plasticity is a vital feature of these adaptations. Genetic methodologies have been extensively employed to identify numerous genetic loci linked to water stress-responsive root traits. This knowledge is immensely important for developing crops with optimal root systems that enhance yield and guarantee food security under water stress conditions. Results This review focused on the latest insights into modifications in the root system architecture and anatomical features of legume roots in response to drought and flooding stresses. Special attention was given to recent breakthroughs in understanding the genetic underpinnings of legume root development under water stress. The review also described various root phenotyping techniques and examples of their applications in different legume species. Finally, the prevailing challenges and prospective research avenues in this dynamic field as well as the potential for using root system architecture as a breeding target are discussed. Conclusions This review integrated the latest knowledge of the genetic components governing the adaptability of legume roots to water stress, providing a reference for using root traits as the new crop breeding targets.

Background Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations. Results This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population. Conclusion The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics.

Soybeans are nutritionally important as human food and animal feed. Apart from the macronutrients such as proteins and oils, soybeans are also high in health-beneficial secondary metabolites and are uniquely enriched in isoflavones among food crops. Isoflavone biosynthesis has been relatively well characterized, but the mechanism of their transportation in soybean cells is largely unknown. Using the yeast model, we showed that GmMATE1 and GmMATE2 promoted the accumulation of isoflavones, mainly in the aglycone forms. Using the tobacco BrightYellow-2 (BY-2) cell model, GmMATE1 and GmMATE2 were found to be localized in the vacuolar membrane. Such subcellular localization supports the notion that GmMATE1 and GmMATE2 function by compartmentalizing isoflavones in the vacuole. Expression analyses showed that GmMATE1 was mainly expressed in the developing soybean pod. Soybean mutants defective in GmMATE1 had significantly reduced total seed isoflavone contents, whereas the overexpression of GmMATE1 in transgenic soybean promoted the accumulation of seed isoflavones. Our results showed that GmMATE1, and possibly also GmMATE2, are bona fide isoflavone transporters that promote the accumulation of isoflavones in soybean seeds.

The capability of a plant to protect itself from stress-related damages is termed “adaptability” and the phenomenon of showing better performance in subsequent stress is termed “stress memory”. While drought is one of the most serious disasters to result from climate change, the current understanding of drought stress priming in soybean is still inadequate for effective crop improvement. To fill this gap, in this study, the drought memory response was evaluated in cultivated soybean (Glycine max). To determine if a priming stress prior to a drought stress would be beneficial to the survival of soybean, plants were divided into three treatment groups: the unprimed group receiving one cycle of stress (1S), the primed group receiving two cycles of stress (2S), and the unstressed control group not subjected to any stress (US). When compared with the unprimed plants, priming led to a reduction of drought stress index (DSI) by 3, resulting in more than 14% increase in surviving leaves, more than 13% increase in leaf water content, slight increase in shoot water content and a slower rate of loss of water from the detached leaves. Primed plants had less than 60% the transpiration rate and stomatal conductance compared to the unprimed plants, accompanied by a slight drop in photosynthesis rate, and about a 30% increase in water usage efficiency (WUE). Priming also increased the root-to-shoot ratio, potentially improving water uptake. Selected genes encoding late embryogenesis abundant (LEA) proteins and MYB, NAC and PP2C domain-containing transcription factors were shown to be highly induced in primed plants compared to the unprimed group. In conclusion, priming significantly improved the drought stress response in soybean during recurrent drought, partially through the maintenance of water status and stronger expression of stress related genes. In sum, we have identified key physiological parameters for soybean which may be used as indicators for future genetic study to identify the genetic element controlling the drought stress priming.

ABSTRACT Recently, considerable progress has been made in understanding how cultivated rice adapts to phosphate (Pi) deficiency stress. However, little has been achieved in the genetic exploration of wild rice accessions, which are crucial for the development of new varieties adapted to Pi‐limited soils. In this study, we evaluated a collection of wild rice accessions for their phosphorus (P) absorption efficiencies using a hydroponic system, and identified Oryza brachyantha, a distant relative of the cultivated rice, as a promising candidate. Our investigation of phosphate transporters (PTs) in this wild species uncovered 31 ObPT genes across five families and analyzed their corresponding protein sequences. Phylogenetic and synteny analyses revealed that these ObPT proteins were highly conserved with their counterparts in cultivated rice (Oryza sativa), but six OsPT orthologs were lost from the O. brachyantha genome during its natural adaptation to the African savanna. Notably, only 24 out of 31 ObPTs were detectable by qRT‐PCR assays, and these genes showed different expression patterns in roots and leaves following prolonged Pi deprivation of up to 12 days. This dynamic expression pattern suggested an efficient reutilization of high P storage in roots and leaves for an extended period, potentially explaining the superior Pi utilization strategy by O. brachyantha. In conclusion, our study identified a wild rice species with high Pi uptake efficiency and provided novel insights into the genetic diversity and evolution of PT genes in a wild rice relative, illuminating their functions in Pi homeostasis. Oryza brachyantha, a wild rice species, was identified as highly efficient in phosphorus (P) uptake. Genome‐wide analysis revealed 31 phosphate transporter (ObPT) genes, with several ortholog losses and dynamic expression under Pi starvation. These findings highlight the evolutionary divergence and potential of wild rice in enhancing P use efficiency.

Climate change has brought severe challenges to agriculture. It is anticipated that there will be a drop in crop yield – including that of soybean – due to climatic stress factors that include drastic fluctuations in temperature, drought, flooding and high salinity. Genomic information on soybean has been accumulating rapidly since initial publication of its reference genome, providing a valuable tool for the improvement of cultivated soybean. Not only are many molecular markers that are associated with important quantitative trait loci now identified, but we also have a more detailed picture of the genomic variations among soybean germplasms, enabling us to utilize these as tools to assist crop breeding. In this review, we will summarize and discuss the currently available soybean genomic approaches, including whole-genome sequencing, sequencing-based genotyping, functional genomics, proteomics, and epigenomics. The information uncovered through these techniques will help further pinpoint important gene candidates and genomic loci associated with adaptive traits, as well as achieving a better understanding of how soybeans cope with the changing climate.

Plant acyl-CoA-binding proteins (ACBPs) form a highly conserved protein family that binds to acyl-CoA esters as well as other lipid and protein interactors to function in developmental and stress responses. This protein family had been extensively studied in non-leguminous species such as Arabidopsis thaliana (thale cress), Oryza sativa (rice), and Brassica napus (oilseed rape). However, the characterization of soybean ( Glycine max ) ACBPs, designated GmACBPs, has remained unreported although this legume is a globally important crop cultivated for its high oil and protein content, and plays a significant role in the food and chemical industries. In this study, 11 members of the GmACBP family from four classes, comprising Class I (small), Class II (ankyrin repeats), Class III (large), and Class IV (kelch motif), were identified. For each class, more than one copy occurred and their domain architecture including the acyl-CoA-binding domain was compared with Arabidopsis and rice. The expression profile, tertiary structure and subcellular localization of each GmACBP were predicted, and the similarities and differences between GmACBPs and other plant ACBPs were deduced. A potential role for some Class III GmACBPs in nodulation, not previously encountered in non-leguminous ACBPs, has emerged. Interestingly, the sole member of Class III ACBP in each of non-leguminous Arabidopsis and rice had been previously identified in plant-pathogen interactions. As plant ACBPs are known to play important roles in development and responses to abiotic and biotic stresses, the in silico expression profiles on GmACBPs, gathered from data mining of RNA-sequencing and microarray analyses, will lay the foundation for future studies in their applications in biotechnology.

Transcription activation is tightly associated with the openness of chromatin, which allows direct contact between transcriptional regulators, such as transcription factors, and their targeted DNA for downstream gene activation. However, the annotation of open chromatin regions (OCRs) in the wild soybean (Glycine soja) genome is limited. We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and successfully identified 22,333 OCRs in the leaf of W05 (a wild soybean accession). These OCRs were enriched in gene transcription start sites (TSS) and were positively correlated with downstream gene expression. Several known transcription factor (TF)-binding motifs were also enriched at the OCRs. A potential regulatory network was constructed using these transcription factors and the OCR-marked genes. Furthermore, by overlapping the OCR distribution with those of histone modifications from chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that the distribution of the activation histone mark, H3K4me3, but not that of the repressive H3K27me3 mark, was closely associated with OCRs for gene activation. Several putative enhancer-like distal OCRs were also found to overlap with LincRNA-encoding loci. Moreover, our data suggest that homologous OCRs could potentially influence homologous gene expression. Hence, the duplication of OCRs might be essential for plant genome architecture as well as for regulating gene expression.