Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, ...with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.
Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia ...infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C
-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, ...mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
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.
Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While ...C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the
transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include
introns 2/3/4,
intron 3,
introns 2/3,
intron 1, and
intron 1. A greater splicing efficiency of
intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III
were also observed in nodules, although the causal relationship between these observations requires further investigation.
Natural antisense transcripts (NATs) have been generally reported as negative regulators of their sense counterparts. Multidrug and toxic compound extrusion (MATE) proteins mediate the transport of ...various substrates. Although
s have been identified genome-wide in various plant species, their transcript regulators remain unclear. Here, using the publicly available strand-specific RNA-seq datasets of
(wild soybean) which have the data from various tissues including developing pods, developing seeds, embryos, cotyledons and hypocotyls, roots, apical buds, stems, and flowers, we identified 35 antisense transcripts of
s from 28 gene loci after transcriptome assembly. Spearman correlation coefficients suggested the positive expression correlations of eight
antisense and sense transcript pairs. By aligning the identified transcripts with the reference genome of
(cultivated soybean), the
antisense and sense transcript pairs were identified. Using soybean C08 (
), in developing pods and seeds, the positive correlations between
antisense and sense transcript pairs were shown by RT-qPCR. These findings suggest that soybean antisense transcripts are not necessarily negative transcription regulators of their sense counterparts. This study enhances the existing knowledge on the transcription regulation of MATE transporters by uncovering the previously unknown
antisense transcripts and their potential synergetic effects on sense transcripts.
MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean Glycine max (L.) Merr., we ...identified high‐confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium‐inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA‐seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high‐affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole‐plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole‐plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi–nitrogen balance to promote SNF in nodules.
Core Ideas
Expression of some miRNAs in soybean roots or nodules is tissue specific.
Some miRNAs regulate nutrient flow for nitrogen fixation in mature soybean nodules.
MiR399b is highly induced in nodules and soybean roots inoculated with Sinorhizobium fredii.
MiR399b can enhance phosphate and ureide contents in the whole soybean plant.
MiR399b overexpression improves overall plant growth in soybean.
Display omitted
•Cellulose fibers were separated from licorice residues by pulping and bleaching.•Cellulose nanofibril from licorice residues was got by enzymatic hydrolysis method.•Effects of ...enzymatic pretreatment on CNF were investigated.•ETCNF showed clear nanofibrillar structure and good colloidal stability.•Chitosan nanofibril and lignin nanoparticles were incorporated into ETCNF films.
It is important to make full utilization of industrial biomass residues. Pulp was prepared from licorice residues by soda-anthraquinone pulping followed by peroxyacetic acid bleaching. Cellulose nanofibril was obtained by enzymatic pretreatment followed by homogenization of the pulp (ETCNF). The effects of enzymatic pretreatment on ETCNF were investigated. Chitosan nanofibril (CHN) and lignin nanoparticles (LNPs) were prepared and used for ETCNF composites, respectively. The results showed that ETCNF exhibited clear nanofibrillar structure and a highly relative colloidal stability, and a much higher crystallinity index and thermal stability compared to TEMPO-medicated oxidized one; the cellulose composite films incorporated with CHN or LNPs exhibited good thermal stability and hydrophobicity. Compared with ETCNF film, ETCNF@LNPs-5.0% film showed higher UV-blocking ability and thermal stability, but reduced light transmittance, while ETCNF@CHN-5.0% film showed improved mechanical properties and similar light transmittance. This study would expend licorice residues as potential materials for CNF and its applications.
Soybean can establish symbiosis with soil-borne bacteria, rhizobia. Following rhizobium infection, soybean roots undergo organogenesis to form nodules, where rhizobia take shelter and carry out ...symbiotic nitrogen fixation (SNF). SNF in soybeans can provide the soybean plant with nitrogen and also significantly enrich the bioavailable nitrogen content of the soil which can reduce the nitrogen fertilizer application in agriculture. In recent years, microRNAs (miRNAs) are verified to be important regulators in nodule formation. However, roles of miRNA in mature nodule are not well studied. In this research, I aimed to identify miRNAs in roots and nodules that are important for nitrogen fixation in both cultivated (Glycine max) and wild soybeans (Glycine soja) 28 days post inoculation with rhizobia (Sinorhizobium fredii). Uninfected roots, infected roots with nodules removed and nodules were harvested from cultivated (C08) and wild (W05) soybeans 28 days after inoculation with rhizobia for small RNA. Hierarchical clustering analysis identified miRNA expressions exhibit tissue-specificity, suggesting a universal regulatory role of miRNAs on root and nodule functions in both soybean species. There were also some miRNA expressions showing variety-specificity, indicating a different response to rhizobium infection between two soybean varieties. After miRNA target prediction, differential expressions of miRNAs that are functionally associated with plant hormone signaling, nodulation processes and nutrient transportation in soybean roots and mature nodules were identified. Amongst these miRNAs, miR4407 showed higher expression in C08 and could regulated the soybean nodule number. Except miR4407, members of miR399 family were strongly induced in inoculated roots and nodules upon rhizobium infection. MiR399 was predicted to target PHO2, which encodes a negative regulator of phosphate transporter. It was found that miR399 could be induced by both nodulation and phosphate starvation. Furthermore, miR399 also affects nitrate transportation through regulating transcription of NITRATE TRANSPORTER1.1 (NRT1.1), NRT2.4 and NRT2.5. Three nitrate reductase encoding genes were also down-regulated by miR399. Transgenic alteration of miR399 expression significantly influenced the whole plant phosphate concentration, nitrogen fixation efficiency and plant growth in the rhizobia-infected soybeans. These findings suggested an important role of miRNAs in nutrient allocation in soybean roots and nodules that is essential for effective nitrogen fixation.
PDF
