Developing a pipeline for identification, characterization and molecular editing of -regulatory elements: a case study in potato.

Crop breeding requires a balance of tradeoffs among key agronomic traits caused by gene pleiotropy. The molecular manipulation of genes can effectively improve target traits, but this may not reduce gene pleiotropy, potentially leading to undesirable traits or even lethal conditions. However, molecular editing of -regulatory elements (CREs) of target genes may facilitate the dissection of gene pleiotropy to fine-tune gene expression.

Gatifloxacin hydrochloride confers broad-spectrum antibacterial activity against phytopathogenic bacteria.

Bacterial diseases pose significant threats to agriculture and natural ecosystems, causing substantial crop losses and impacting food security. Until now, there has been a less efficient control strategy against some bacterial diseases such as bacterial wilt, caused by . In this study, we screened a library of 58 microorganism-derived natural products for their antibacterial activity against .

Cytokinin-mediated enhancement of potato growth and yield by Verticillium Dahliae effector VDAL under low temperature stress.

The pathogen Verticillium dahliae secreted effector V. dahliae Aspf2-like protein (VDAL) has been found to cause leaf wilting in cotton, but the ectopic expression of VDAL-encoding gene enhances the resistance to V. dahliae in cotton and Arabidopsis.

Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato.

Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene (VInv) and cause reducing sugar accumulation.

Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis.

Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic.

Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs in .

Polyploidization plays important roles in the evolution and breeding of the common wheat. , the D-genome progenitor of the common wheat, provides a valuable pool of resistance genes to multiple diseases. Extensive studies focus on the exploration of these genes for wheat improvement.

Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers.

Polyploid plants typically display advantages on some agronomically important traits over their diploid counterparts. Extensive studies have shown genetic, transcriptomic, and epigenetic dynamics upon polyploidization in multiple plant species. However, few studies have unveiled those alternations imposed only by ploidy level, without any interference from heterozygosity.

Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae).

Background: Analysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species.

Results: Here we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), including Gossypium arboreum, Gossypium raimondii, and Gossypioides kirkii, which differ with respect to chromosome rearrangements.

Chromatin architectural alterations due to null mutation of a major CG methylase in rice.

Associations between 3D chromatin architectures and epigenetic modifications have been characterized in animals. However, any impact of DNA methylation on chromatin architecture in plants is understudied, which is confined to Arabidopsis thaliana. Because plant species differ in genome size, composition, and overall chromatin packing, it is unclear to what extent findings from A.

Quasi-Consensus of Time-Varying Multi-Agent Systems with External Inputs under Deception Attacks.

The quasi-consensus of a class of nonlinear time-varying multi-agent systems suffering from both external inputs and deception attacks is studied in this paper. This is different from a time-varying matrix, which is assumed to be bounded; further reasonable assumptions are supposed. In addition, impulsive deception attacks modeled with Bernoulli variables are considered.

FtMYB18 acts as a negative regulator of anthocyanin/proanthocyanidin biosynthesis in Tartary buckwheat.

FtMYB18 plays a role in the repression of anthocyanins and proanthocyanidins accumulation by strongly down-regulating the CHS and DFR genes in Tartary buckwheat, and the C5 motif plays an important role in this process. Anthocyanins and proanthocyanidins (PAs) are important flavonoids in Tartary buckwheat (Fagopyrum tataricum Gaertn.), which provides various vibrant color and stronge abiotic stress resistance.

Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice.

Recombination plays an integral role in the creation of novel genetic variation in sexually reproducing species. Despite this important role, the determinants and evolution of crossover hotspots have remained poorly understood in plants. Here, we present a comparative analysis of two rice () historical recombination maps from two subspecies ( and ) using 150 resequenced genomes.

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum).

Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato.

Background: Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers.

Results: Using a whole genome sequencing-based approach, we developed two high-density reference-based haplotype maps using diploid potato clones as parents.

Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3.

Centromeres can arise de novo from non-centromeric regions, which are often called "neocentromeres." Neocentromere formation provides the best evidence for the concept that centromere function is not determined by the underlying DNA sequences, but controlled by poorly understood epigenetic mechanisms. Numerous neocentromeres have been reported in several plant and animal species.

Isolation and Proteomics Analysis of Barley Centromeric Chromatin Using PICh.

Identification of proteins that are directly or indirectly associated with a specific DNA sequence is often an important goal in molecular biology research. Proteomics of isolated chromatin fragments (PICh) is a technique used to isolate chromatin that contains homologous DNA sequence to a specific nucleic acid probe. All proteins directly and indirectly associated with the DNA sequences that hybridize to the probe are then identified by proteomics.

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum.

Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement.

Three potato centromeres are associated with distinct haplotypes with or without megabase-sized satellite repeat arrays.

We report discoveries of different haplotypes associated with the centromeres of three potato chromosomes, including haplotypes composed of long arrays of satellite repeats and haplotypes lacking the same repeats. These results are in favor of the hypothesis that satellite repeat-based centromeres may originate from neocentromeres that lack repeats.

High-resolution mapping of open chromatin in the rice genome.

Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa).

Molecular characterization of a wheat -Thinopyrum ponticum partial amphiploid and its derived substitution line for resistance to stripe rust.

Stripe rust (caused by Puccinia striiformis) occurs annually in most wheat-growing areas of the world. Thinopyrum ponticum has provided novel rust resistance genes to protect wheat from this fungal disease. Wheat - Th.