The most important objectives of soybean (Glycine max (L.) Merr.) breeding are to increase oil content and to improve oil quality. Although the biochemical processes of oil accumulation in oilseeds are very clear, knowledge of their underlying genetic mechanisms and regulation is limited. We performed RNA-Seq of soybean seeds from six accessions with high, medium and low seed oil contents. Through comparative genome analysis, promoter-enrichment study, and protein–protein interaction (PPI) analysis, 80 lipid-metabolism-related genes and 31 transcription factors were detected. The pathways of fatty acid elongation, desaturation and export from plastid (P = 2.53E-4), and triacylglycerol biosynthesis (P = 2.31E-8), were significantly over-represented in accessions with high total oil content. Further, in an integration analysis of RNA-Seq and a genome-wide association study (GWAS) database, 62 candidate genes were found to be associated with seed oil content, 73 with oleic acid content, and 83 with linolenic acid content. Of these, 60 genes were found to be involved mainly in metabolism of lipids (25), carbohydrates (24), and amino acids (11). Thirty are known oil-synthesis-related genes; LOX1, CYP93D1 and GPT2 for oil content, SAD and FAD2 for oleic acid, and FAD2, CYP89A6 and GPT2 for linolenic acid were detected twice. There were 22 genes found to be associated with at least two oil-related traits, and of 154 pairs of PPIs, two genes for each pair of 95 PPIs (62%) were found to be associated with various oil-related traits, indicating the genetic foundations of oil-related traits. Three transcription factor genes were found to be associated with oil-related traits: HRE2 (Glyma.10G016500), ERF12 (Glyma.13G236600) and WRKY6 (Glyma.15G110300). This study provides an efficient strategy for further discovery of mechanisms of oil composition and accumulation.

Our study shows that the expression of AtCBF3 and AtCOR15A improved the chilling tolerance in transgenic eggplant. In an attempt to improve chilling tolerance of eggplant (Solanum melongena L) plants, Arabidopsis C-repeat binding factor 3 (AtCBF3) and cold-regulated 15A (AtCOR15A) genes both driven by an Arabidopsis RESPONSIVE TO DESSICATION 29A promoter (AtRD29A) were transferred into the plants of eggplant cultivar Sanyueqie. Two independent homozygous transgenic lines were tested for their cold tolerance. The leaves of the transgenic plants in both lines withered much slower and slighter than the wild-type plants after exposure to cold stress treatment at 2 ± 1 °C. The gene expression of AtCBF3 and AtCOR15A was significantly increased as well as the proline content and the levels of catalase and peroxidase activities, while the relative electrical conductivity and the malondialdehyde content were remarkably decreased in the transgenic plants compared with the wild type at 4 ± 0.5 °C. The results showed that the expression of the exogenous AtCBF3 and AtCOR15A could promote the cold adaptation process to protect eggplant plants from chilling stress.

A plastidic ATP/ADP transporter (AATP) is responsible for importing ATP from the cytosol into plastids. Increasing the ATP supply is a potential way to facilitate anabolic synthesis in heterotrophic plastids of plants. In this work, a gene encoding the AATP protein, named , was successfully isolated from tomato. Expression of was induced by exogenous sucrose treatment in tomato. The coding region of was cloned into a binary vector under the control of 35S promoter and then transformed into to obtain transgenic plants. Constitutive expression of significantly increased the starch accumulation in the transgenic plants. Real-time quantitative PCR (qRT-PCR) analysis showed that constitutive expression of up-regulated the expression of phosphoglucomutase (), ADP-glucose pyrophosphorylase (), granule-bound starch synthase ( and ), soluble starch synthases (, , and ) and starch branching enzyme ( and ) genes involved in starch biosynthesis in the transgenic plants. Meanwhile, enzymatic analyses indicated that the major enzymes (AGPase, GBSS, SSS and SBE) involved in the starch biosynthesis exhibited higher activities in the transgenic plants compared to the wild-type (WT). These findings suggest that may improve starch content of by up-regulating the expression of the related genes and increasing the activities of the major enzymes invovled in starch biosynthesis. The manipulation of expression might be used for increasing starch accumulation of plants in the future.

Quantitative real-time reverse-transcriptase PCR (qRT-PCR) has been frequently used for detecting gene expression. To obtain reliable results, selection of suitable reference genes is a fundamental and necessary step. Garlic (Allium sativum), a member from Alliaceae family, has been used both as a food flavoring and as a traditional medicine. In the present study, garlic plants were exposed to salt stress (200 mM NaCl) for 0, 1, 4 and 12 h, and garlic roots, bulbs, and leaves were harvested for subsequent analysis. The expression stability of eight candidate reference genes, eukaryotic translation initiation factor 4α (eIF-4α), actin (ACTIN), tubulin β-7 (TUB7), TAP42-interacting protein of 41 kDa (TIP41), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), SAND family protein (SAND), elongation factor 1 alpha (EF-1α), and protein phosphatase 2A (PP2A) were evaluated by geNorm, NormFinder, and BestKeeper. All genes tested displayed variable expression profiles under salt stress. In the leaf and root group, ACTIN was the best reference gene for normalizing gene expression. In garlic clove, ACTIN and SAND were the least variable, and were suitable for gene expression studies under salt stress; these two genes also performed well in all samples tested. Based on our results, we recommend that it is essential to use specific reference genes in different situations to obtain accurate results. Using a combination of multiple stable reference genes, such as ACTIN and SAND, to normalize gene expression is encouraged. The results from the study will be beneficial for accurate determination of gene expression in garlic and other plants.

Laccase, as a copper-containing polyphenol oxidase, primarily functions in the process of lignin, anthocyanin biosynthesis, and various abiotic/biotic stresses. In this study, forty-eight laccase members were identified in the eggplant genome. Only forty-two laccase genes from eggplant (SmLACs) were anchored unevenly in 12 chromosomes, the other six SmLACs were mapped on unanchored scaffolds. Phylogenetic analysis indicated that only twenty-five SmLACs were divided into six different groups on the basis of groups reported in Arabidopsis. Gene structure analysis revealed that the number of exons ranged from one to 13. Motif analysis revealed that SmLACs included six conserved motifs. In aspects of gene duplication analysis, twenty-one SmLACs were collinear with LAC genes from Arabidopsis, tomato or rice. Cis-regulatory elements analysis indicated many SmLACs may be involved in eggplant morphogenesis, flavonoid biosynthesis, diverse stresses and growth/development processes. Expression analysis further confirmed that a few SmLACs may function in vegetative and reproductive organs at different developmental stages and also in response to one or multiple stresses. This study would help to further understand and enrich the physiological function of the SmLAC gene family in eggplant, and may provide high-quality genetic resources for eggplant genetics and breeding.