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Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the re-sequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species.

Four new indole-terpenoids (1–4) named encindolene A, 18-O-methyl-encindolene A, encindolene B, and encindolene C, as well as three known analogs (5–7), were isolated from the fungus Penicillium sp. HFF16 from the rhizosphere soil of Cynanchum bungei Decne. The structures of compounds including absolute configurations were elucidated by spectroscopic data and electronic circular dichroism (ECD) analysis. Anti-inflammatory activity evaluation revealed that compounds 1–7 inhibit the production of nitric oxide with IC50 values of 79.4, 49.7, 81.3, 40.2, 86.7, 90.1, and 54.4 μM, respectively, and decrease the levels of tumor necrosis factor-α, interleukin-6 contents in lipopolysaccharide-induced RAW264.7 macrophages.

The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP-glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica. CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high-altitude to high-latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.

Rice in cold region is threatened by cold stress frequently, resulting in severe losses of rice production. In the present study, two rice varieties with contrast cold tolerance in the reproductive stage (Longjing25, cold tolerant; Longjing11 cold sensitive) were compared using RNA-seq technique. A total of 14,861 and 12,148 differentially expressed genes (DEGs) were obtained by comparison of LJ25 and LJ11 after 2 days and 4 days of cold stress challenge. Subsequent Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that five significant pathways were specifically enriched in LJ11. Starch and sucrose metabolism was the only one significant pathway (containing 47 DEGs) annotated in both of varieties during two cold treatment periods. By weighted gene co-expression network analysis (WGCNA), 14 co-expression gene modules were calculated, among which turquoise, cyan, and dark green were the most concerned modules, containing 4807, 2682, and 1174 DEGs, respectively. Finally, we analyzed the transcriptional factors (TFs), and TF families of MYB, zinc finger, AP2/ERF-AP2, bHLH, NAC, bZIP, and WRKY were the biggest seven subfamilies. Collectively, our findings provided valuable insights into the molecular and genetic mechanisms responsible for rice’s response to cold stress.

Two new thio-compounds named aspergerthinol A and B (1 and 2) and two new monoterpenes named aspergerthinacids A and B (3 and 4) were isolated from the fungus Aspergillus sp. CYH26 from the rhizosphere soil of Cynanchum bungei Decne. The structures of compounds were elucidated by spectroscopic data and quantum NMR and ECD calculations. Compounds 1 and 2 represented a new family of sulfur containing natural products with a 3-methyl-4H-cyclopenta[b]thiophen-4-one skeleton. Compounds 1–4 showed inhibitory activities against nitric oxide (NO) with IC50 values of 38.0, 19.8, 46.3, and 56.6 μM, respectively.

As one of the abiotic stresses, low temperature severely threatens rice production during its entire growth period, especially during the booting stage. In the present study, transcriptome analysis was performed comparing Longjing (LJ) 25 (chilling-tolerant) and LJ 11 (chilling-sensitive) rice varieties to identify genes associated with chilling tolerance in rice spikelets. A total of 23 845 expressed genes and 13 205 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) enrichment analyses revealed ‘response to cold’ (containing 180 DEGs) as the only category enriched in both varieties during the entire cold treatment period. Through M ap M an analysis, we identified nine and six DEGs related to the Calvin cycle and antioxidant enzymes, respectively, including OsRBCS3 , OsRBCS2 , OsRBCS4 , OsAPX2 and OsCATC , that under chilling stress were markedly downregulated in LJ11 compared with LJ25. Furthermore, we predicted their protein–protein interaction (PPI) network and identified nine hub genes (the threshold of co-expressed gene number ≥ 11) in Cytoscape, including three RuBisCO-related genes with 14 co-expressed genes. Under chilling stress, antioxidant enzyme activities (peroxidase (POD) and catalase (CAT)) were downregulated in LJ11 compared with LJ25. However, the content of malondialdehyde (MDA) was higher in LJ11 compared with LJ25. Collectively, our findings identify low temperature responsive genes that can be effectively used as candidate genes for molecular breeding programmes to increase the chilling tolerance of rice.

Excessive accumulation of free radicals in the body can cause liver damage, aging, cancer, stroke, and myocardial infarction. Anastatin B, a skeletal flavonoid, was reported to have antioxidant and hepatoprotective effects. Anastatin B derivatives, compound 1 and 2, were synthesized by our group previously. In this study, their antioxidant activity and hepatoprotective mechanism were studied using chemical evaluation methods, a cellular model of hydrogen peroxide (H2O2)-induced oxidative damage, and a mouse model of carbon tetrachloride (CCl4)-induced liver injury. Results from the chemical evaluation suggested that both compounds had good antioxidant power and radical scavenging ability in vitro. MTT assay showed that both compounds had cytoprotective activity in H2O2-treated PC12 cells. Moreover, their hepatoprotective activities evaluated using a mouse model of CCl4-induced liver injury that compared with the model group, pretreatment with compound 1 and 2 significantly decreased alanine transaminase (ALT), aspartate transaminase (AST), lactate dehydrogenase (LDH), and malondialdehyde (MDA) levels; reduced the liver tissue damage; and increased glutathione content. However, compound 2 was a more effective hepatoprotectant than compound 1 was. Finally, the amount of TNF-α and cytochrome P450 2E1 (CYP2E1) were significantly downregulated in compound 1 and 2 pretreatment groups. Collectively, our findings demonstrate that both compounds have potential antioxidant activity and hepatoprotective effect in vitro and in vivo. Further chemo-biological study and investigation of the compounds' enzymatic targets are ongoing.

Non-metallic organic tanning agents were used during the leather processing, most of them will be combined with the collagen converted it into leather. But there still some of its components were discarded into the wastewater and caused serious environmental problems. In this study, the structure character of microbial communities in leather wastewater containing non-metallic organic tanning agents and the effect of the leather wastewater on the ecology of the microorganisms were studied with the high-throughput sequencing. The results show that the presence of 1,657, 49 bacterial and fungal OTUs (Operational Taxonomic Unit), at 97% similarity level. Significant differences on microbial community composition in wastewater were observed in systems containing different non-metallic organic tanning agents. The Firmicutes and proteobacteria were dominated bacteria in T1, T3, T8, KB and T6. Ascomycota and Basidiomycota were the most richness fungi in T1, T3, T6, T8 and KB. The relative abundance of dominant bacteria pseudodomonas was significantly positively correlated with TN, NH3, and TOC (0.01

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

Quercetin, luteolin, and epigallocatechin gallate are flavonoids abundant in edible and medicinal plants with beneficial effects on glucose homeostasis. This study explored the action of these flavonoids on glucose disposal in adipocytes. Quercetin, luteolin, and epigallocatechin gallate enhanced glucose consumption with the positive regulation of AMP-activated kinase phosphorylation, and the AMP-activated kinase inhibitor compound C abolished their effects on glucose consumption. Luteolin and epigallocatechin gallate, but not quercetin, increased sirtuin 1 abundance, and their regulation of glucose consumption was also attenuated by co-treatment with sirtuin 1 inhibitor nicotinamide. Quercetin, luteolin, and epigallocatechin gallate suppressed nuclear factor-κB activation by inhibition of p65 phosphorylation with beneficial regulation of adipokine expression, whereas these actions were diminished by coincubation with compound C. The sirtuin 1 inhibitor nicotinamide attenuated the effects of luteolin and EGCG on p65 phosphorylation and adipokine expression without any influence on the activity of quercetin. Results of Western blot and fluorescence microscopy also showed that quercetin, luteolin, and epigallocatechin gallate increased Akt substrate of 160 kDa phosphorylation and promoted 2-deoxy-D-glucose uptake by adipocytes under basal and inflammatory conditions. These findings suggested that quercetin, luteolin, and epigallocatechin gallate inhibited inflammation and promoted glucose disposal in adipocytes with the regulation of AMP-activated kinase and/or sirtuin 1.