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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. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.

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. Results Here, we challenged a cultivated soybean accession (C08) and a wild one (W05) with salt treatment and obtained their small RNA transcriptomes at six time points from both root and leaf tissues. In addition to thoroughly analyzing the differentially expressed miRNAs, we also documented the first case of miRNA arm-switching (miR166m), the swapping of dominant miRNA arm expression, in soybean in different tissues. Two arms of miR166m target different genes related to salinity stress (chloroplastic beta-amylase 1 targeted by miR166m-5p and calcium-dependent protein kinase 1 targeted by miR166m-3p), suggesting arm-switching of miR166m play roles in soybean in response to salinity stress. Furthermore, two pairs of miRNA:lncRNA interacting partners (miR166i-5p and lncRNA Gmax_MSTRG.35921.1; and miR394a-3p and lncRNA Gmax_MSTRG.18616.1) were also discovered in reaction to salinity stress. Conclusions This study demonstrates how ncRNA involves in salinity stress responses in soybean by miRNA arm switching and miRNA:lncRNA interactions. The behaviors of ncRNAs revealed in this study will shed new light on molecular regulatory mechanisms of stress responses in plants, and hence provide potential new strategies for crop improvement.

Maize (Zea mays L.), one of the most important cereal crops in the world, is salt-sensitive. It is critical to study the genes associated with salt tolerance, the differential gene expression pattern between salt-tolerant and salt-sensitive lines, and the mechanism of salt tolerance in maize. Two maize inbred lines with different salt sensitivity, NC286 and Huangzao4, were used to reveal early responsive genes under high salinity condition. Suppression subtractive hybridization (SSH) assay was conducted to identify potential genes involved in the early stage of maize seedlings in responses to 200mM NaCl. A custom μparaflo™ microfluidic array (LC science USA) containing Release version 10.1 plant miRNA probes (http://microrna.sanger.ac.uk/) was used to discover salt stress responsive miRNAs using the differences in miRNAs expression between these two maize lines. Cis-elemnet analysis was performed in the promoter regions of these two kinds of salt stress responsive transcriptions. The expression of a total of 141 unique genes was significantly changed under 200mM NaCl salt shock within 24 hours. These genes were involved in a broad spectrum of biochemical, cellular, and physiological processes. They were assigned to 14 categories based on their biological functions. Some of them were previously reported to be associated with biotic and abiotic stresses, and several novel genes detected. A gene model was proposed which showed how these genes could sense and response to the high salinity environment. The promoter regions of these 141 salt responsive genes were analyzed, and salt responsive key cis-elements uncovered. The cis-elements usage bias of the salt responsive mRNAs and non-coding RNAs were of the same. The different expression profiles of the genes, especially the ones involved in salt signal cascades and phytohormones responding, could explain the different salt stress response in the two maize inbred lines. The similar cis-elements usage bias of two kinds of salt responsive transcriptions suggests they may be regulated by the same trans-factors.

The microstructure evolution of Ti-47Al-2Cr-2Nb alloy was investigated on liquid metal cooling type directional solidified apparatus at high temperature gradient. The analysis shows that it is solidified with primary β cells/dendrites, and then α phase is formed through peritectic reaction. Once the columnar grains grow into the steady state, the lamellar orientation inclined with the angle of 45° to the withdrawal direction is more favored than that with parallel to the withdrawal direction. In addition, α phase grain nucleates from β-interdendrite regions, and grows up to the dendritic trunk. If no other α grain hinders its growth, it would occupy the whole dendrite, or it would stop at the dendritic trunk for the weakened motivating drive in the β dendritic core.

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. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement., The identification of genes that control economically important traits is an essential step towards crop improvement. Here the authors sequence the genome of the wild soybean and, through a combined genetic and functional approach, identify a new gene affecting salt tolerance in soybean.