Transcriptomes of soybean roots and nodules inoculated with Sinorhizobium fredii with NopP and NopI variants.

The major crop, soybean, forms root nodules with symbiotic rhizobia, providing energy and carbon to the bacteria in exchange for bioavailable nitrogen. The relationship is host-specific and highly host-regulated to maximize energy efficiency. Symbiotic nitrogen fixation (SNF) is greener than synthetic fertilizer for replenishing soil fertility, contributing to yield increase.

Effect of Multi-Element Microalloying on the Structure and Properties of High Chromium Cast Iron.

High chromium cast iron (HCCI) has been widely used as wear-resistant material in the industry. Alloying is an effective way to improve the microstructure and mechanical properties of HCCI. This paper added multi-component V-Fe-Ti-Nb-C-Zr-B alloy (VFC) to HCCI, showing a significant synergistic solution-strengthening effect.

Process Optimization of Dual-Liquid Casting and Interfacial Strength-Toughness of the Produced LAS/HCCI Bimetal.

The pouring time interval is the decisive factor of dual-liquid casting for bimetallic productions. Traditionally, the pouring time interval is fully determined by the operator's experience and on-site observation. Thus, the quality of bimetallic castings is unstable.

QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits.

The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean.

Wildsoydb DataHub: a platform for accessing soybean multiomic datasets across multiple reference genomes.

The Wildsoydb DataHub is an integrated interface for biologists and breeders to access soybean genomic resources easily, allowing them to fully utilize the results of genomic research.

ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data.

Motivation: Synteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region.

Identification of the accessible chromatin regions in six tissues in the soybean.

Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues.

Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean.

Background: Soybean is a major legume crop with high nutritional and environmental values suitable for sustainable agriculture. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are important regulators of gene functions in eukaryotes. However, the interactions between these two types of ncRNAs in the context of plant physiology, especially in response to salinity stress, are poorly understood.

Galactolipid and Phospholipid Profile and Proteome Alterations in Soybean Leaves at the Onset of Salt Stress.

Salinity is a major environmental factor that constrains soybean yield and grain quality. Given our past observations using the salt-sensitive soybean ( [L.] Merr.

An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts.

ChIP-seq is widely used for mapping the transcription factor (TF) binding sites throughout the genome in vivo. In this study, we adopted and modified ChIPmentation, a fast, robust, low-input requirement ChIP-seq method, to a transient expression system using soybean protoplasts to expedite the exploration of TF binding sites. To test this new protocol, we expressed a tagged version of a C2H2-type zinc finger TF, JAGGED1 (GmJAG1), in soybean protoplasts and successfully identified its binding sites in the soybean genome.

Calculation on surface energy and electronic properties of CoS.

Density functional theory was employed to investigate the (111), (200), (210), (211) and (220) surfaces of CoS. The surface energies were calculated with a sulfur environment using first-principle-based thermodynamics. It is founded that surfaces with metal atoms at their outermost layer have higher energy.

Understanding the Composition, Biosynthesis, Accumulation and Transport of Flavonoids in Crops for the Promotion of Crops as Healthy Sources of Flavonoids for Human Consumption.

Flavonoids are a class of polyphenolic compounds that naturally occur in plants. Sub-groups of flavonoids include flavone, flavonol, flavanone, flavanonol, anthocyanidin, flavanol and isoflavone. The various modifications on flavonoid molecules further increase the diversity of flavonoids.

ABAS1 from soybean is a 1R-subtype MYB transcriptional repressor that enhances ABA sensitivity.

Transcription factors (TFs) help plants respond to environmental stresses by regulating gene expression. Up till now, studies on the MYB family of TFs have mainly focused on the highly abundant R2R3-subtype. While the less well-known 1R-subtype has been generally shown to enhance abscisic acid (ABA) sensitivity by acting as transcriptional activators, the mechanisms of their functions are unclear.

Reference-Based Identification of Long Noncoding RNAs in Plants with Strand-Specific RNA-Sequencing Data.

Long noncoding RNAs (lncRNAs) have been shown to play important roles in various organisms, including plant species. Several tools and pipelines have emerged for lncRNA identification, including reference-based transcriptome assembly pipelines and various coding potential calculating tools. In this protocol, we have integrated some of the most updated computational tools and described the procedures step-by-step for identifying lncRNAs from plant strand-specific RNA-sequencing datasets.

A reference-grade wild soybean genome.

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.

Transcriptomic reprogramming in soybean seedlings under salt stress.

To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole-transcriptome sequencing on the leaf and root of soybean seedlings subjected to salt treatment in a time-course experiment (0, 1, 2, 4, 24, and 48 hr). This time series dataset enabled us to identify important hubs and connections of gene expressions. We highlighted the analysis on phytohormone signaling pathways and their possible crosstalks.

Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress.

The F-box family is one of the largest gene families in plants that regulate diverse life processes, including salt responses. However, the knowledge of the soybean F-box genes and their roles in salt tolerance remains limited. Here, we conducted a genome-wide survey of the soybean F-box family, and their expression analysis in response to salinity via in silico analysis of online RNA-sequencing (RNA-seq) data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) to predict their potential functions.

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.

Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance.