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Salt stress is a major abiotic stress with detrimental effects on plants. Sucrose, the main product of photosynthesis in plants, is used as a source of energy for the development of Chinese rose (Rosa chinensis). Hua Xianzi, a variety of Chinese rose, was investigated in this study. Phenotypic traits such as digital biomass, greenness average, leaf angle and leaf area, as well as physiological characters such as proline (Pro), malondialdehyde (MDA), H2O2, O2- and antioxidant enzymes such as SOD (Superoxide Dismutase), POD (Peroxidase), CAT (Catalase) and APX (Ascorbate Peroxidase), changed significantly in response to salt stress (150 mmol/L NaCl for 72 h). The physiological changes were examined based on photosynthetic and fluorescence indicators. Salt stress increased the concentration of glucose, fructose and sucrose, upregulated the expression of Rc-SS1, Rc-SS2, Rc-SPS1, Rc-SPS2, Rc-αA1, Rc-αA2, Rc-αA3, Rc-βA1 and Rc-βA3 genes. Finally, it decreased the starch content in leaves. This study revealed that salt stress disrupted the equilibrium of sucrose metabolism in leaves. This finding provides the basis for further research into the mechanism of salt tolerance adaption.

To investigate whether mutations in the minichromosome maintenance complex component (MCM) family genes were present in patients with polycystic ovary syndrome (PCOS) of Chinese descent. A total of 365 Chinese patients with PCOS and 860 women without PCOS as control who underwent with assisted reproductive technology were enrolled. Genomic DNA was extracted from the peripheral blood of these patients for PCR and Sanger sequencing. The potential damage of these mutations/rare variants was analyzed through evolutionary conservation analysis and bioinformatic programs. Twenty-nine missense or nonsense mutations/rare variants in the MCM genes were identified in 365 patients with PCOS (7.9%, 29/365), all these mutations/rare variants were predicted to be ‘disease causing’ by SIFT and PolyPhen2 programs. Among those, four mutations were reported here for the first time, p.S7C (c.20C > G) in MCM2 (NM_004526.3), p.K350R (c.1049A > G) in MCM5 (NM_006739.3), p.K283N (c.849G > T) in MCM10 (NM_182751.2), and p.S1708F (c.5123C > T) in MCM3AP (NM_003906.4). All of these novel mutations were not found in our 860 control women, or also absent in public databases. In addition, the evolutionary conservation analysis results suggested that these novel mutations caused highly conserved amino acid substitutions among 10 vertebrate species. This study identified a high frequency of potential pathogenic rare variants/mutations in MCM family genes in Chinese women with PCOS, which further expands the genotype spectrum in PCOS.

Additional file 1: Table S1. The sequence assembly analysis for shotgunmetagenomic sequencing. Table S2. The differential KEGG pathways amongthree weaning periods. Table S3. The differential CAZy family amongthree weaning periods. Table S4. The differential metabolites amongthree weaning periods.

Background Intrahepatic cholestasis of pregnancy (ICP) is characterized by pruritus and cholestasis in late pregnancy and results in adverse pregnancy outcomes, including preterm delivery and birth weight, which are affected by the genetic and environmental background. However, until now, the genetic architecture of ICP has remained largely unclear. Methods Twenty-six clinical data points were recorded for 151 Chinese ICP patients. The data generated from whole-exome sequencing (WES) using the BGISEQ-500 platform were further analyzed by Burrows-Wheeler Aligner (BWA) software, Genome Analysis Toolkit (GATK), ANNOVAR tool, etc. R packages were used to conduct t-test, Fisher’s test and receiver operating characteristic (ROC) curve analyses. Results We identified eighteen possible pathogenic loci associated with ICP disease in known genes, covering ABCB4, ABCB11, ATP8B1 and TJP2. The loci Lys386Gln, Gly527Gln and Trp708Ter in ABCB4, Leu589Met, Gln605Pro and Gln1194Ter in ABCB11, and Arg189Ser in TJP2 were novel discoveries. In addition, WES analysis indicated that the gene ANO8 involved in the transport of bile salts is newly identified as associated with ICP. The functional network of the ANO8 gene confirmed this finding. ANO8 contained 8 rare missense mutations that were found in eight patients among the 151 cases and were absent from 1029 controls. Out of the eight SNPs, 3 were known, and the remaining five are newly identified. These variants have a low frequency, ranging from 0.000008 to 0.00001 in the ExAC, gnomAD – Genomes and TOPMED databases. Bioinformatics analysis showed that the sites and their corresponding amino acids were both highly conserved among vertebrates. Moreover, the influences of all the mutations on protein function were predicted to be damaging by the SIFT tool. Combining clinical data, it was found that the mutation group (93.36 µmol/L) had significantly (P = 0.038) higher total bile acid (TBA) levels than the wild-type group (40.81 µmol/L). Conclusions To the best of our knowledge, this is the first study to employ WES technology to detect genetic loci for ICP. Our results provide new insights into the genetic basis of ICP and will benefit the final identification of the underlying mutations.

The use of male sterile lines is one of the ideal means in hybrid seed production. Despite the widespread application of Ogura cytoplasmic male sterile (CMS) lines, the molecular mechanisms remain largely unknown. In this study, histological analyses of floral buds from a CMS line 40MA and its corresponding maintainer line 40MB were conducted, which indicate that microspore abortion was initiated shortly after the tetrad stage. RNA sequencing was performed to analyze the transcriptomes of floral buds from the tetrad stage and the early microspore stages of these two lines. More than 39 million clean reads were generated for each library, and the portions mapped to the reference genome were all above 70.60%. To further analyze the differentially expressed genes (DEGs), the samples were grouped into four pairs, of which the pair of 40MA and 40MB at the early microspore stage showed the most DEGs (5100 members). According to the abnormal appearance of the tapetum cells in 40MA, a series of tapetum development related genes were screened and analyzed. In addition, a total of 623 genes with differential expressions in the tetrad stage, but not in the early microspore stage between the two lines were filtered as the microspore abortion initiation related candidates. Twelve genes were selected to validate the sequencing result by quantitative RT-PCR. In this study, we identified a number of candidate genes involved in the initiation of microspore degeneration, which may provide a new perspective to unravel the molecular mechanism of Ogura CMS.

High-throughput small RNA sequencing and degradome analysis were used in this study to thoroughly investigate the role of miRNA-mediated regulatory network in tuberous root development of radish. Samples from the early seedling stage (RE) and the cortex splitting stage (RL) were used for the construction of six small RNA libraries and one degradome library. A total of 518 known and 976 novel miRNAs were identified, of which, 338 known and 18 novel miRNAs were expressed in all six libraries, respectively. A total of 52 known and 57 novel miRNAs were identified to be significantly differentially expressed between RE and RL, and 195 mRNAs were verified to be the targets of 194 miRNAs by degradome sequencing. According to the degradome analysis, 11 differentially expressed miRNAs had miRNA-mRNA targets, and 13 targets were identified for these 11 miRNAs. Of the 13 miRNA-mRNA targets, 4 genes (RSG11079.t1, RSG11844.t1, RSG16775.t1, and RSG42419.t1) were involved in hormone-mediated signaling pathway, 2 gens (RSG11079.t1 and RSG16775.t1) were related to post-embryonic root development, and 1 gene (RSG23799.t1) was involved in anatomical structure morphogenesis, according to the GO function analysis for biological process. Target Genes participated in these processes are important candidates for further studies. This study provides valuable information for a better understanding of the molecular mechanisms involved in radish tuberous root formation and development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1330-z) contains supplementary material, which is available to authorized users.

Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during vernalization. More than 36 million clean reads were generated for each sample and the portions mapped to the reference genome were all above 67.0%. Our results show that the differentially expressed genes (DEGs) between room temperature and the early stage of vernalization (4,845) are the most in all treatments pairs. A series of vernalization related genes, including two FLOWERING LOCUS C (FLC) genes, were screened according to the annotations. A total of 775 genes were also filtered as the vernalization related candidates based on their expression profiles. Cold stress responsive genes were also analyzed to further confirm the sequencing result. Several key genes in vernalization or cold stress response were validated by quantitative RT-PCR (RT-qPCR). This study identified a number of genes that may be involved in vernalization, which are useful for other functional genomics research in radish.

We report the identification of McpS as the specific chemoreceptor for 6 tricarboxylic acid (TCA) cycle intermediates and butyrate in Pseudomonas putida. The analysis of the bacterial mutant deficient in mcpS and complementation assays demonstrate that McpS is the only chemoreceptor of TCA cycle intermediates in the strain under study. TCA cycle intermediates are abundantly present in root exudates, and taxis toward these compounds is proposed to facilitate the access to carbon sources. McpS has an unusually large ligand-binding domain (LBD) that is un-annotated in InterPro and is predicted to contain 6 helices. The ligand profile of McpS was determined by isothermal titration calorimetry of purified recombinant LBD (McpS-LBD). McpS recognizes TCA cycle intermediates but does not bind very close structural homologues and derivatives like maleate, aspartate, or tricarballylate. This implies that functional similarity of ligands, such as being part of the same pathway, and not structural similarity is the primary element, which has driven the evolution of receptor specificity. The magnitude of chemotactic responses toward these 7 chemoattractants, as determined by qualitative and quantitative chemotaxis assays, differed largely. Ligands that cause a strong chemotactic response (malate, succinate, and fumarate) were found by differential scanning calorimetry to increase significantly the midpoint of protein unfolding (T(m)) and unfolding enthalpy (DeltaH) of McpS-LBD. Equilibrium sedimentation studies show that malate, the chemoattractant that causes the strongest chemotactic response, stabilizes the dimeric state of McpS-LBD. In this respect clear parallels exist to the Tar receptor and other eukaryotic receptors, which are discussed.