A graph-based genome and pan-genome variation of the model plant Setaria.

Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.

Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant.

Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C4 model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.

[Identification of circulating type II pre-dendritic cells (pDC2) and its clinical significance in chronic hepatitis B virus infection].

OBJECTIVE: To investigate the characteristics of circulating type II pre-dendritic cells (pDC2) and evaluate its role in patients with chronic hepatitis B virus infection. METHODS: The quantitative alterations of pDC2 in 27 chronic HBV-infected patients as treated group and 15 healthy individuals as a control group were analyzed by using flow cytometry based on the comparison of CD4+/CD8+ ratios of T lymphocyte subsets between the two groups. The IFN-alpha-producing ability of pDC2 after incubation was determined by ELISA. RESULTS: The percentage of pDC2 (0.096 +/- 0.086) from the peripheral blood in chronic HBV-infected patients were significantly lower than that (0.304 +/- 0.093) from the normal controls (P less than 0.001) while the CD4+/CD8+ ratios were higher than those in normal controls (P less than 0.01). The values of IFN-alpha-producing function and IL-12 of circulating pDC2 in chronic HBV-infected patients group were significantly lower than those in healthy subjects (P < 0.001). The percentage of pDC2 and CD4+/CD8+ ratios were higher in the patients positive for HBV DNA in sera than those in patients negative for HBV DNA in sera (P < 0.01). CONCLUSION: The decreased number of circulating pDC2 and IFN-alpha-producing function from peripheral blood in patients with chronic hepatitis B virus infection may result in the decline of host immune response, which may partially contribute to the disease progress of HBV infection and existence of viral genomic DNA in patient's sera.

[Antiviral effect of human CTLs activated by HBsAg stimulated dendritic cells in vitro].

OBJECTIVE: To investigate the ability of human dendritic cells (DCs) inducing specific T lymphocyte response and inhibit the expression of HBeAg and HBsAg in 2.2.15 cell culture supernatant. METHODS: DCs were prepared from peripheral blood mononuclear cells induced with granulocyte macrophage colony-stimulating factor(GM-CSF) and interleukin 4. DCs was impulsed with pure HBsAg before DCs maturation and cocultured with self-blood T lymphocyte, while DCs without pure HBsAg stimulated group, T lymphocyte group and only T lymphocyte group were prepared as control group. The culture supernatant of 2.2.15 cell with stimulated T lymphocytes was collected on day 1, day 3, day 5 and day 7, respectively. The expressed levels of HBeAg and HBsAg were detected by ELISA method. RESULTS: DCs after antigen stimulation had a strong ability to present antigen and induce immune activation, DCs after loading with antigen in normal control and chronic hepatitis patients group had stronger stimulative ability for T lymphocytes proliferation than that of DCs without loading with antigen and only T lymphocyte group(P less than 0.01). The stimulating ability of DCs had a positive correlation to the dosage of loaded antigen; CTLs produced as a result of DCs stimulation had a specific inhibitive effect on the expression of HBeAg in 2.2.15 cell supernatant,but not on the expression of HbsAg. CONCLUSION: Human dendritic cells stimulated with HBsAg in vitro can efficiently present antigen and stimulate the production of specific CTLs to HBV, which can efficiently inhibit the expression of HBeAg in 2.2.15 cell supernatant- DC vaccine may become an antiviral therapy strategy for chronic hepatitis B virus infected patients in future.