BackgroundSoybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited.ResultsIn this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development.ConclusionsOur results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean.

BackgroundMicroRNAs (miRNAs) play important regulatory roles in development and stress response in plants. Wild soybean (Glycine soja) has undergone long-term natural selection and may have evolved special mechanisms to survive stress conditions as a result. However, little information about miRNAs especially miRNAs responsive to aluminum (Al) stress is available in wild soybean.ResultsTwo small RNA libraries and two degradome libraries were constructed from the roots of Al-treated and Al-free G. soja seedlings. For miRNA identification, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries, respectively, were generated, and 97 known miRNAs and 31 novel miRNAs were identified. In addition, 49 p3 or p5 strands of known miRNAs were found. Among all the identified miRNAs, the expressions of 30 miRNAs were responsive to Al stress. Through degradome sequencing, 86 genes were identified as targets of the known miRNAs and five genes were found to be the targets of the novel miRNAs obtained in this study. Gene ontology (GO) annotations of target transcripts indicated that 52 target genes cleaved by conserved miRNA families might play roles in the regulation of transcription. Additionally, some genes, such as those for the auxin response factor (ARF), domain-containing disease resistance protein (NB-ARC), leucine-rich repeat and toll/interleukin-1 receptor-like protein (LRR-TIR) domain protein, cation transporting ATPase, Myb transcription factors, and the no apical meristem (NAM) protein, that are known to be responsive to stress, were found to be cleaved under Al stress conditions.ConclusionsA number of miRNAs and their targets were detected in wild soybean. Some of them that were responsive to biotic and abiotic stresses were regulated by Al stress. These findings provide valuable information to understand the function of miRNAs in Al tolerance.

Wild soybean is a typical short-day plant that begins flowering when the days are shorter than its critical photoperiod. Soybean was domesticated in the temperate region of East Asia at the relatively high latitude, and the breeding and release of soybean varieties have historically centered on mid-and high-latitude temperate regions. Low-latitude areas with tropical and subtropical climates were previously considered unsuitable for soybean production because most temperate soybean varieties exhibited precocious flowering and early maturity and suffered from low yields. The discovery and introduction of the long juvenile trait into soybean varieties in the 1970s (Hartwig and Kiihl, 1979) fundamentally changed global soybean production in a way that has had an enormous influence on commodity markets. This trait delays flowering and thereby ensures sufficient vegetative growth prior to the developmental transition to reproductive growth. The long juvenile trait thus solved the early maturation and low yield problems that had hitherto prevented economically viable soybean production in lowlatitude regions (Destro et al., 2001). The United States and Brazil pioneered the introduction of the long juvenile trait in low-latitude soybean breeding programs. Brazil has expanded its soybean production enormously, from 1 million hectares in 1970 (Brown, 2004) to over 33 million hectares in 2016 (http:// gain.fas.usda.gov/Recent%20GAIN%20Publications/Oilseeds %20and%20Products%20Update_Brasilia_Brazil_12-1-2016. pdf).

Recently, we showed that secretion of citrate in an aluminium (Al) tolerant cultivar soybean (Glycine max) (cv. Suzunari) is a specific response to Al stress [Yang et al. (2000) Physiol Plant 110: 72–77]. Here we investigated the intrinsic mechanisms behind the secretion of citrate induced by Al. The amount of citrate secreted during the 24‐h Al treatment period increased with increasing concentration of Al (0–70 μM). We analysed citrate secretion basically under 3 conditions: (1) by varying light‐exposure, (2) with intact or excised shoots and (3) by using a divided chamber technique. Further, the content of organic acids in the tissue and the activity of enzymes involved in organic acid metabolism were analysed and evaluated. The results indicate that high rate of citrate secretion in soybean requires a 4‐h induction period. Al had a continuous effect on the citrate secretion when Al was removed from the treatment solution. Citrate secretion increased steadily under exposure to continuous light. However, when the shoots were excised the citrate secretion rate dropped to 3–6 times that of their control counterparts. Results of root manipulation experiments revealed that citrate secretion required the direct contact of Al. In other words, only the Al‐treated root portions secreted citrate. All these observations suggest that the shoots play a role in Al‐induced citrate secretion. Although shoots may not supply citrate for the secretion upon Al treatment, it seems that they may provide the carbon source and/or energy for citrate synthesis in the root. On the other hand, the root organic acid content (1‐cm apex) indicated that malate might contribute to citrate secretion by keeping the balance between citrate synthesis and release in the root apices. Quantification of enzymes involved in organic acid metabolism showed only a 16% increase in citrate synthase activity upon Al treatments (6 h) with no differences in other enzymes. Hence, we could not rule out completely the potential contribution of citrate from shoots and the results are discussed in the light of shoots contributing either energy or citrate itself for enhanced citrate secretion in the Al‐tolerant plant roots.