Background: GRAS proteins are crucial transcription factors, which are plant-specific and participate in various plant biological processes. Thanks to the rapid progress of the whole genome sequencing technologies, the GRAS gene families in different plants have been broadly explored and studied. However, comprehensive research on the soybean (Glycine max) GRAS gene family is relatively lagging. Results: In this study, 117 Glycine max GRAS genes (GmGRAS) were identified. Further phylogenetic analyses showed that the GmGRAS genes could be categorized into nine gene subfamilies: DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR. Gene structure analyses turned out that the GmGRAS genes lacked introns and were relatively conserved. Conserved domains and motif patterns of the GmGRAS members in the same subfamily or clade exhibited similarities. Notably, the expansion of the GmGRAS gene family was driven both by gene tandem and segmental duplication events. Whereas, segmental duplications took the major role in generating new GmGRAS genes. Moreover, the synteny and evolutionary constraints analyses of the GRAS proteins among soybean and distinct species (two monocots and four dicots) provided more detailed evidence for GmGRAS gene evolution. Cis-element analyses indicated that the GmGRAS genes may be responsive to diverse environmental stresses and regulate distinct biological processes. Besides, the expression patterns of the GmGRAS genes were varied in various tissues, during saline and dehydration stresses and during seed germination processes. Conclusions: We conducted a systematic investigation of the GRAS genes in soybean, which may be valuable in paving the way for future GmGRAS gene studies and soybean breeding.

BackgroundThe utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear.ResultsThe comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B.ConclusionsWe concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS.

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Wolbachia is an intracellular bacterium that has aroused intense interest because of its ability to alter the biology of its host in diverse ways. In the two-spotted spider mite, Tetranychus urticae, Wolbachia can induce complex cytoplasmic incompatibility (CI) phenotypes and fitness changes, although little is known about the mechanisms. In the present study, we selected a strain of T. urticae, in which Wolbachia infection was associated with strong CI and enhanced female fecundity, to investigate changes in the transcriptome of T. urticae in Wolbachia-infected vs. uninfected lines. The responses were found to be sex-specific, with the transcription of 251 genes being affected in females and 171 genes being affected in males. Some of the more profoundly affected genes in both sexes were lipocalin genes and genes involved in oxidation reduction, digestion and detoxification. Several of the differentially expressed genes have potential roles in reproduction. Interestingly, unlike certain Wolbachia transinfections in novel hosts, the Wolbachia-host association in the present study showed no clear evidence of host immune priming by Wolbachia, although a few potential immune genes were affected.

BackgroundCytoplasmic male sterility (CMS) provides crucial breeding materials that facilitate hybrid seed production in various crops, and thus plays an important role in the study of hybrid vigor (heterosis), in plants. However, the CMS regulatory network in soybean remains unclear. MicroRNAs (miRNAs) play crucial roles in flower and pollen development by targeting genes that regulate their expression in plants. To identify the miRNAs and their targets that exist in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput sequencing and degradome analysis were conducted in this study.ResultsTwo small RNA libraries were constructed from the flower buds of the soybean CMS line NJCMS1A and its maintainer NJCMS1B. A total of 105 new miRNAs present on the other arm of known pre-miRNAs, 23 new miRNA members, 158 novel miRNAs and 160 high-confidence soybean miRNAs were identified using high-throughput sequencing. Among the identified miRNAs, 101 differentially expressed miRNAs with greater than two-fold changes between NJCMS1A and NJCMS1B were discovered. The different expression levels of selected miRNAs were confirmed by stem-loop quantitative real-time PCR. A degradome analysis showed that 856 targets were predicted to be targeted by 296 miRNAs, including a squamosa promoter-binding protein-like transcription factor family protein, a pentatricopeptide repeat-containing protein, and an auxin response factor, which were previously shown to be involved in floral organ or anther development in plants. Additionally, some targets, including a MADS-box transcription factor, NADP-dependent isocitrate dehydrogenase and NADH-ubiquinone oxidoreductase 24 kDa subunit, were identified, and they may have some relationship with the programmed cell death, reactive oxygen species accumulation and energy deficiencies, which might lead to soybean male sterility.ConclusionsThe present study is the first to use deep sequencing technology to identify miRNAs and their targets in the flower buds of the soybean CMS line NJCMS1A and its maintainer NJCMS1B. The results revealed that the miRNAs might participate in flower and pollen development, which could facilitate our understanding of the molecular mechanisms behind CMS in soybean.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2352-0) contains supplementary material, which is available to authorized users.