Comparative genomic and transcriptomic analyses provide new insight into symbiotic host specificity.

Host specificity plays important roles in expanding the host range of rhizobia, while the genetic information responsible for host specificity remains largely unexplored. In this report, the roots of four symbiotic systems with notable different symbiotic phenotypes and the control were studied at four different post-inoculation time points by RNA sequencning (RNA-seq). The differentially expressed genes (DEGs) were divided into "found only in soybean or ," "only expressed in soybean or ," and "expressed in both hosts" according to the comparative genomic analysis.

RNA-Seq and Comparative Transcriptomic Analyses of Asian Soybean Rust Resistant and Susceptible Soybean Genotypes Provide Insights into Identifying Disease Resistance Genes.

Asian soybean rust (ASR), caused by , is one of the most destructive foliar diseases that affect soybeans. Developing resistant cultivars is the most cost-effective, environmentally friendly, and easy strategy for controlling the disease. However, the current understanding of the mechanisms underlying soybean resistance to remains limited, which poses a significant challenge in devising effective control strategies.

Heterologous expression of the Glycine soja Kunitz-type protease inhibitor GsKTI improves resistance to drought stress and Helicoverpa armigera in transgenic Arabidopsis lines.

Kunitz-like protease inhibitors (KTIs) have been identified to play critical roles in insect defense, but evidence for their involvement in drought stress is sparse. The aim of this study was to identify and functionally characterize a Kunitz-like protease inhibitor, GsKTI, from the wild soybean (Glycine soja) variety ED059. Expression patterns suggest that drought stress and insect herbivory may induce GsKTI transcript levels.

Melatonin Attenuates the Urea-Induced Yields Improvement Through Remodeling Transcriptome and Rhizosphere Microbial Community Structure in Soybean.

Foliar application of nitrogen to enhance crop productivity has been widely used. Melatonin is an effective regulator in promoting plant growth. However, the effects of melatonin and the combination of melatonin and nitrogen on soybeans yields production remain largely unknown.

CRISPR/Cas9-Mediated Targeted Mutagenesis of Enhanced Soybean Resistance Against Leaf-Chewing Insects Through Flavonoids Biosynthesis.

Leaf-chewing insects are important pests that cause yield loss and reduce seed quality in soybeans (). Breeding soybean varieties that are resistant to leaf-chewing insects can minimize the need for insecticide use and reduce yield loss. The marker gene for QTL-M, (LOC100775351) that encodes a UDP-glycosyltransferase (UGT) is the major determinant of resistance against leaf-chewing insects in soybean; it exhibits a loss of function in insect-resistant soybean germplasms.

Whole-Genome Sequencing of 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity.

In the present study, we sequenced the complete genome of 113-2. The genomic characteristics of six selected rhizobial strains (two fast-growing rhizobia, two medium-slow-growing rhizobia and two slow-growing rhizobia) with four different legume hosts were analyzed by comparative genomic analysis. Genomes of 113-2 and USDA110 were found to share a large synteny blocks and a high ANI value, supporting 113-2 as a strain of .

Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis.

Background: Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood.

Results: In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication.

Overexpression of GmMYB14 improves high-density yield and drought tolerance of soybean through regulating plant architecture mediated by the brassinosteroid pathway.

MYB transcription factors (TFs) have been reported to regulate the biosynthesis of secondary metabolites, as well as to mediate plant adaption to abiotic stresses, including drought. However, the roles of MYB TFs in regulating plant architecture and yield potential remain poorly understood. Here, we studied the roles of the dehydration-inducible GmMYB14 gene in regulating plant architecture, high-density yield and drought tolerance through the brassinosteroid (BR) pathway in soybean.

A GATA Transcription Factor from Soybean () Regulates Chlorophyll Biosynthesis and Suppresses Growth in the Transgenic .

Chlorophyll plays an essential role in photosynthetic light harvesting and energy transduction in green tissues of higher plants and is closely related to photosynthesis and crop yield. Identification of transcription factors (TFs) involved in regulating chlorophyll biosynthesis is still limited in soybean (), and the previously identified is suggested to potentially modulate chlorophyll and nitrogen metabolisms, but its complete function is still unknown. In this study, subcellular localization assay showed that GmGATA58 was localized in the nucleus.

Genome-Wide Investigation and Expression Profiling Under Abiotic Stresses of a Soybean Unknown Function (DUF21) and Cystathionine-β-Synthase (CBS) Domain-Containing Protein Family.

Cystathionine-β-synthase (CBS) domain-containing proteins (CDCPs) constitute a large family in plants, and members of this family have been implicated in a variety of biological processes. However, the precise functions and the underlying mechanisms of most members of this family in plants remain to be elucidated. CBSDUF proteins belong to the CDCP superfamily, which contains one domain of unknown function (DUF21) and an N terminus that is adjacent to two intracellular CBS domains.

Identification of soybean drought-tolerant genotypes and loci correlated with agronomic traits contributes new candidate genes for breeding.

Drought tolerance level of 136 soybean genotypes, the correlations among traits were evaluated, and several important drought-tolerant genotypes, traits, SNPs and genes were possibly useful for soybean genetic breeding. Drought is an adverse environmental factor affecting crops growth, development, and yield. Promising genotypes and genes with improved tolerance to drought are probably effective ways to alleviate the situation.

Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean.

WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and the response to abiotic stress. Soybean is one of the most important oil crops worldwide.

CRISPR/Cas9-mediated targeted mutagenesis of GmSPL9 genes alters plant architecture in soybean.

Background: The plant architecture has significant effects on grain yield of various crops, including soybean (Glycine max), but the knowledge on optimization of plant architecture in order to increase yield potential is still limited. Recently, CRISPR/Cas9 system has revolutionized genome editing, and has been widely utilized to edit the genomes of a diverse range of crop plants.

Results: In the present study, we employed the CRISPR/Cas9 system to mutate four genes encoding SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors of the SPL9 family in soybean.

Genome-Wide Identification and Classification of Soybean C2H2 Zinc Finger Proteins and Their Expression Analysis in Legume-Rhizobium Symbiosis.

Root nodule symbiosis (RNS) is one of the most productive and economical systems for nitrogen fixation, and previous studies have shown that several nodule-specific C2H2-zinc finger proteins (ZFPs) play important roles in symbiosis establishment and nodule function. However, C2H2-ZFPs are the most widespread ZFPs in eukaryotes, and a great variation of structure and function exist among the family members. It remains largely unclear whether or not special types of C2H2-ZF genes participate in symbiosis, especially in soybean.

Search for Nodulation and Nodule Development-Related Cystatin Genes in the Genome of Soybean ().

Nodulation, nodule development and senescence directly affects nitrogen fixation efficiency, and previous studies have shown that inhibition of some cysteine proteases delay nodule senescence, so their nature inhibitors, cystatin genes, are very important in nodulation, nodule development, and senescence. Although several cystatins are actively transcribed in soybean nodules, their exact roles and functional diversities in legume have not been well explored in genome-wide survey studies. In this report, we performed a genome-wide survey of cystatin family genes to explore their relationship to nodulation and nodule development in soybean and identified 20 cystatin genes that encode peptides with 97-245 amino acid residues, different isoelectric points (pI) and structure characteristics, and various putative plant regulatory elements in 3000 bp putative promoter fragments upstream of the 20 soybean cystatins in response to different abiotic/biotic stresses, hormone signals, and symbiosis signals.

RNA-Seq Analysis of Differential Gene Expression Responding to Different Rhizobium Strains in Soybean (Glycine max) Roots.

The root nodule symbiosis (RNS) between legume plants and rhizobia is the most efficient and productive source of nitrogen fixation, and has critical importance in agriculture and mesology. Soybean (Glycine max), one of the most important legume crops in the world, establishes a nitrogen-fixing symbiosis with different types of rhizobia, and the efficiency of symbiotic nitrogen fixation in soybean greatly depends on the symbiotic host-specificity. Although, it has been reported that rhizobia use surface polysaccharides, secretion proteins of the type-three secretion systems and nod factors to modulate host range, the host control of nodulation specificity remains poorly understood.

Identification and Comparative Analysis of CBS Domain-Containing Proteins in Soybean (Glycine max) and the Primary Function of GmCBS21 in Enhanced Tolerance to Low Nitrogen Stress.

Nitrogen is an important macronutrient required for plant growth, and is a limiting factor for crop productivity. Improving the nitrogen use efficiency (NUE) is therefore crucial. At present, the NUE mechanism is unclear and information on the genes associated with NUE in soybeans is lacking.

Genome-wide survey of the soybean GATA transcription factor gene family and expression analysis under low nitrogen stress.

GATA transcription factors are transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain and recognize the conserved GATA motif in the promoter sequence of target genes. Previous studies demonstrated that plant GATA factors possess critical functions in developmental control and responses to the environment. To date, the GATA factors in soybean (Glycine max) have yet to be characterized.

Transcript profile of the response of two soybean genotypes to potassium deficiency.

The macronutrient potassium (K) is essential to plant growth and development. Crop yield potential is often affected by lack of soluble K. The molecular regulation mechanism of physiological and biochemical responses to K starvation in soybean roots and shoots is not fully understood.