Characterization and genetic differences analysis in adventitious roots development of 38 Populus germplasm resources.

To select poplar clones with excellent adventitious roots development (ARD) and deepen the understanding of its molecular mechanism, a comprehensive evaluation was conducted on 38 Populus germplasm resources with cuttings cultured in the greenhouse. Genetic differences between poplar clones with good ARD and with poor ARD were explored from the perspectives of genomics and transcriptomics. By cluster analysis of the seven adventitious roots (AR) traits, the materials were classified into three clusters, of which cluster I indicated excellent AR developmental capability and promising breeding potential, especially P.×canadensis 'Guariento', P. 'jingtong1', P. deltoides 'Zhongcheng5', P. deltoides 'Zhongcheng2'. At the genomic level, the cross-population composite likelihood ratio (XP-CLR) analysis identified 1944 positive selection regions related to ARD, and variation detection analysis identified 3426 specific SNPs and 687 specific Indels in the clones with good ARD, 3212 specific SNPs and 583 specific Indels in the clones with poor ARD, respectively. Through XP-CLR, variation detection, and weighted gene co-expression network analysis based on transcriptome data, eight major putative genes associated with poplar ARD were primary identified, and a co-expression network of eight genes was constructed, it was discovered that CSD1 and WRKY6 may be important in the ARD. Subsequently, we confirmed that SWEET17 had a non-synonymous mutation at the site of 928,404 in the clones with poor ARD, resulting in an alteration of the amino acid. After exploring phenotypic differences and the genetic variation of adventitious roots development in different poplar clones, this study provides valuable reference information for future poplar breeding and genetic improvement.

Populus cathayana genome and population resequencing provide insights into its evolution and adaptation.

Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.

Combining GS-assisted GWAS and transcriptome analysis to mine candidate genes for nitrogen utilization efficiency in Populus cathayana.

BACKGROUND: Forest trees such as poplar, shrub willow, et al. are essential natural resources for sustainable and renewable energy production, and their wood can reduce dependence on fossil fuels and reduce environmental pollution. However, the productivity of forest trees is often limited by the availability of nitrogen (N), improving nitrogen use efficiency (NUE) is an important way to address it. Currently, NUE genetic resources are scarce in forest tree research, and more genetic resources are urgently needed. RESULTS: Here, we performed genome-wide association studies (GWAS) using the mixed linear model (MLM) to identify genetic loci regulating growth traits in Populus cathayana at two N levels, and attempted to enhance the signal strength of single nucleotide polymorphism (SNP) detection by performing genome selection (GS) assistance GWAS. The results of the two GWAS analyses identified 55 and 40 SNPs that were respectively associated with plant height (PH) and ground diameter (GD), and 92 and 69 candidate genes, including 30 overlapping genes. The prediction accuracy of the GS model (rrBLUP) for phenotype exceeds 0.9. Transcriptome analysis of 13 genotypes under two N levels showed that genes related to carbon and N metabolism, amino acid metabolism, energy metabolism, and signal transduction were differentially expressed in the xylem of P. cathayana under N treatment. Furthermore, we observed strong regional patterns in gene expression levels of P. cathayana, with significant differences between different regions. Among them, P. cathayana in Longquan region exhibited the highest response to N. Finally, through weighted gene co-expression network analysis (WGCNA), we identified a module closely related to the N metabolic process and eight hub genes. CONCLUSIONS: Integrating the GWAS, RNA-seq and WGCNA data, we ultimately identified four key regulatory genes (PtrNAC123, PtrNAC025, Potri.002G233100, and Potri.006G236200) involved in the wood formation process, and they may affect P. cathayana growth and wood formation by regulating nitrogen metabolism. This study will provide strong evidence for N regulation mechanisms, and reliable genetic resources for growth and NUE genetic improvement in poplar.

Polysaccharides of Brassica rapa L. attenuate tumor growth via shifting macrophages to M1-like phenotype.

Macrophages are the major tumor-infiltrating leukocytes, and tumor-associated macrophages (TAM) play a critical role in cancer-related inflammation since they show alternative polarization to M1 (tumor-inhibited macrophages) or M2 (tumor-promoted macrophages) phenotype. Brassica rapa L. (B. rapa) has been clinically proven to have anti-tumor and immunity-enhancing activity, and the polysaccharides of B. rapa (BRP) have been reported to have an immunoregulatory effect on macrophages. In this study, we focus on macrophage polarization to investigate the mechanism of anti-tumor response of BRP in vivo and in vitro. We found that BRP improved the expression of M1 markers, including iNOS, COX-2, HLA-DR, CD11b and M1-related cytokines. The expression of M2 markers Arg-1, CD206 and CD163 induced by IL-4 were inhibited by BRP treatment, resulting in the inhibition of tumor growth both in vivo and in co-culture experiments in vitro. The activation of STAT signaling pathway were significantly regulated by BRP, which are important signals in TAM polarization. Overall, the results indicated that BRP has anti-tumor effect through mediating macrophage polarization.

A coma-free super-high resolution optical spectrometer using 44 high dispersion sub-gratings.

Unlike the single grating Czerny-Turner configuration spectrometers, a super-high spectral resolution optical spectrometer with zero coma aberration is first experimentally demonstrated by using a compound integrated diffraction grating module consisting of 44 high dispersion sub-gratings and a two-dimensional backside-illuminated charge-coupled device array photodetector. The demonstrated super-high resolution spectrometer gives 0.005 nm (5 pm) spectral resolution in ultra-violet range and 0.01 nm spectral resolution in the visible range, as well as a uniform efficiency of diffraction in a broad 200 nm to 1000 nm wavelength region. Our new zero-off-axis spectrometer configuration has the unique merit that enables it to be used for a wide range of spectral sensing and measurement applications.

Ultrahigh-resolution spectrometer based on 19 integrated gratings.

Optical spectrometers play a key role in acquiring rich photonic information in both scientific research and a wide variety of applications. In this work, we present a new spectrometer with an ultrahigh resolution of better than 0.012 nm/pixel in the 170-600 nm spectral region using a grating-integrated module that consists of 19 subgratings without any moving parts. By using two-dimensional (2D) backsideilluminated complementary metal-oxide-semiconductor (BSI-CMOS) array detector technology with 2048 × 2048 pixels, a high data acquisition speed of approximately 25 spectra per second is achieved. The physical photon-sensing size of the detector along the one-dimensional wavelength direction is enhanced by a factor of 19 to approximately 428 mm, or 38912 pixels, to satisfy the requirement of seamless connection between two neighboring subspectral regions without any missing wavelengths throughout the entire spectral region. As tested with a mercury lamp, the system has advanced performance capabilities characterized by the highest k parameter reported to date, being approximately 3.58 × 104, where k = (working wavelength region)/(pixel resolution). Data calibration and analysis as well as a method of reducing background noise more efficiently are also discussed. The results presented in this work will stimulate further research on precision spectrometers based on advanced BSI-CMOS array detectors in the future.