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As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, understanding the response mechanisms to low N (LN) stress is essential for the regulation of NUE in wheat. In this study, LN stress significantly accelerated wheat root growth, but inhibited shoot growth. Further transcriptome analysis showed that 8468 differentially expressed genes (DEGs) responded to LN stress. The roots and shoots displayed opposite response patterns, of which the majority of DEGs in roots were up-regulated (66.15%; 2955/4467), but the majority of DEGs in shoots were down-regulated (71.62%; 3274/4565). GO and KEGG analyses showed that nitrate reductase activity, nitrate assimilation, and N metabolism were significantly enriched in both the roots and shoots. Transcription factor (TF) and protein kinase analysis showed that genes such as MYB-related (38/38 genes) may function in a tissue-specific manner to respond to LN stress. Moreover, 20 out of 107 N signaling homologous genes were differentially expressed in wheat. A total of 47 transcriptome datasets were used for weighted gene co-expression network analysis (17,840 genes), and five TFs were identified as the potential hub regulatory genes involved in the response to LN stress in wheat. Our findings provide insight into the functional mechanisms in response to LN stress and five candidate regulatory genes in wheat. These results will provide a basis for further research on promoting NUE in wheat. [ABSTRACT FROM AUTHOR]

Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo‐Tolerance and grain Length 1 (TTL1), from the super pan‐genomic and transcriptomic data. Loss‐of‐function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into TTL1 as a novel potential target for the development of high‐yield and thermotolerant rice varieties. [ABSTRACT FROM AUTHOR]

Fusarium graminearum (F. graminearum) is the main pathogen of Fusarium head blight (FHB) in wheat, barley, and corn. Deoxynivalenol (DON), produced by F. graminearum, is the most prevalent toxin associated with FHB. The wheat defense compound putrescine can promote DON production during F. graminearum infection. However, the underlying mechanisms of putrescine-induced DON synthesis are not well-studied. To investigate the effect of putrescine on the global transcriptional regulation of F. graminearum, we treated F. graminearum with putrescine and performed RNA deep sequencing. We found that putrescine can largely affect the transcriptome of F. graminearum. Gene ontology (GO) and KEGG enrichment analysis revealed that having a large amount of DEGs was associated with ribosome biogenesis, carboxylic acid metabolism, glycolysis/gluconeogenesis, and amino acid metabolism pathways. Co-expression analysis showed that 327 genes had similar expression patterns to FgTRI genes and were assigned to the same module. In addition, three transcription factor genes were identified as hub genes in this module, indicating that they may play important roles in DON synthesis. These results provide important clues for further analysis of the molecular mechanisms of putrescine-induced DON synthesis and will facilitate the study of the pathogenic mechanisms of FHB. [ABSTRACT FROM AUTHOR]

The extensive phenotypic diversity within natural populations of Arabidopsis is associated with differences in gene expression. Transcript levels can be considered as inheritable quantitative traits, and used to map expression quantitative trait loci (eQTL) in genome‐wide association studies (GWASs). In order to identify putative genetic determinants for variations in gene expression, we used publicly available genomic and transcript variation data from 665 Arabidopsis accessions and applied the single nucleotide polymorphism‐set (Sequence) Kernel Association Test (SKAT) method for the identification of eQTL. Moreover, we used the penalized orthogonal‐components regression (POCRE) method to increase the power of statistical tests. Then, gene annotations were used as test units to identify genes that are associated with natural variations in transcript accumulation, which correspond to candidate regulators, some of which may have a broad impact on gene expression. Besides increasing the chances to identify real associations, the analysis using POCRE and SKAT significantly reduced the computational cost required to analyze large datasets. As a proof of concept, we used this approach to identify eQTL that represent novel candidate regulators of immune responses. The versatility of this approach allows its application to any process that is subjected to natural variation among Arabidopsis accessions. [ABSTRACT FROM AUTHOR]

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference. [ABSTRACT FROM AUTHOR]

RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants. RdDM mediates the transcriptional silencing of many endogenous genomic loci, most of which are transposon related. A forward genetics screen identified DTF1 (DNA-binding transcription factor 1) as a new component for RdDM in Arabidopsis. Loss-of-function mutations in DTF1 release the transcriptional silencing of RdDM target loci and reduce the accumulation of 24-nt small interfering RNAs (siRNAs) from some of the targets. Interestingly, in the dtf1 mutant plants, the release of transcriptional gene silencing at solo-LTR is accompanied by decreased siRNA accumulation but not by reduced DNA methylation. These results suggest that DTF1 is an atypical component of RdDM and has both DNA methylation-dependent and -independent roles in transcriptional gene silencing. We suggest that besides DNA methylation, siRNAs may cause some other uncharacterized epigenetic modifications that lead to transcriptional gene silencing. [ABSTRACT FROM AUTHOR]

Backtracking Search Algorithm (BSA) is a younger population-based evolutionary algorithm and widely researched. Due to the introduction of historical population and no guidance toward to the best individual, BSA does not adequately use the information in the current population, which leads to a slow convergence speed and poor exploitation ability of BSA. To address these drawbacks, a novel backtracking search algorithm with reflection mutation based on sine cosine is proposed, named RSCBSA. The best individual found so far is employed to improve convergence speed, while sine and cosine math models are introduced to enhance population diversity. To sufficiently use the information in the historical population and current population, four individuals are selected from the historical or current population randomly to construct an unit simplex, and the center of the unit simplex can enhance exploitation ability of RSCBSA. Comprehensive experimental results and analyses show that RSCBSA is competitive enough with other state-of-the-art meta-heuristic algorithms. [ABSTRACT FROM AUTHOR]

Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions. [ABSTRACT FROM AUTHOR]

Focusing on problems of blurred detection boundary, small target miss detection, and more pseudo changes in high-resolution remote sensing image change detection, a change detection algorithm based on Siamese neural networks is proposed. Siam-FAUnet can implement end-to-end change detection tasks. Firstly, the improved VGG16 is utilized as an encoder to extract the image features. Secondly, the atrous spatial pyramid pooling module is used to increase the receptive field of the model to make full use of the global information of the image and obtain the multi-scale contextual information of the image. The flow alignment module is used to fuse the low-level features in the encoder to the decoder and solve the problem of semantic misalignment caused by the direct concatenation of features when the features are fused, so as to obtain the change region of the image. The experiments are trained and tested using publicly available CDD and SZTAKI datasets. The results show that the evaluation metrics of the Siam-FAUnet model are improved compared to the baseline model, in which the F1-score is improved by 4.00% on the CDD and by 7.32% and 2.62% on the sub-datasets of SZTAKI (SZADA and TISZADOB), respectively; compared to other state-of-the-art methods, the Siam-FAUnet model has improved in both evaluation metrics, indicating that the model has a good detection performance. [ABSTRACT FROM AUTHOR]

A Ti/β-TCP composite porous scaffold with a hierarchical pore structure composed of 3D printed interconnected macroscopic pores and sintered microscopic pores was prepared by direct ink writing (DIW) 3D printing technology. This method can control the extrusion of composite ink at room temperature and produce a 3D scaffold using layer-by-layer deposition. We studied the effects of the β-TCP powder particle size, β-TCP/Ti powder ratio and solid loading on the rheological properties of the ink and optimised the DIW printing process parameters. After sintering, the compressive strength and elastic modulus of the composite scaffold reached 45 MPa and 1 GPa, which is close to the strength of human cancellous bone. The cell culture experiment confirmed that the composite scaffold had better biological properties than the pure titanium scaffold. The composite scaffold has satisfactory mechanical and biological properties, meeting the requirements for orthopaedic implants. [ABSTRACT FROM AUTHOR]

In this paper, the basic ant colony optimization procedure is further developed by the idea of crowded factors in fish swarm optimization which can improve the global search ability to solve the Vehicle Routing Problem, or the VRP model. Experimental simulation shows that fish swarm ant colony optimization can solve VRP model effectively, quickly find the optimal solution, and improve the basic ant colony optimization ability and efficiency. [ABSTRACT FROM AUTHOR]