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pssRNAit-a web server for designing effective and specific plant siRNAs with genome-wide off-target assessment
Bioinformatics plant RNAi siRNA efficacy off-target gene silencing VIGS syntasiRNA
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2024/1/12
We report an advanced web server named pssRNAit (plant specific small non-coding RNAi tool) that can be used to design a pool of small interfering RNAs (siRNAs) for highly effective, specific, and non...
Unraveling the 3D Genome Architecture in Plants: Present and Future
3D genomic methods plant 3D genome dynamic chromatin organization liquid-liquid phase separation RNA-chromatin interaction
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2023/12/19
The eukaryotic genome has a hierarchical three-dimensional organization with functional implications in DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists ha...
Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis
ABFs Land plants Phylogenetic relationship Expression analysis TaABFs Drought stress
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2023/12/15
Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known abou...
Genome-wide analysis and expression profile of the bZIP gene family in poplar
Poplar bZIP gene family Tissue-differential expression Salt stress Co-expression analysis
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2023/12/8
The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological pr...
MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns
MYB transcription factors PavMYB genes Phylogenetic analysis Expression pattern Dormancy
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2023/11/30
MYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been ...
Functional divergence of Populus MYB158 and MYB189 gene pair created by whole genome duplication
duplicate gene functional divergence MYB transcription factor regulatory networks secondary cell wall biosynthesis whole genome duplication
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2023/11/28
Whole genome duplication (WGD) provides new genetic material for genome evolution. After a WGD event, some duplicates are lost, while other duplicates still persist and evolve diverse functions. A par...
Targeted introduction of heritable point mutations into the plant mitochondrial genome
plant mitochondrial genome heritable ALEN-GDM mtDNA genome editing CRISPR-Cas
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2023/11/28
The development of technologies for the genetic manipulation of mitochondrial genomes remains a major challenge. Here we report a method for the targeted introduction of mutations into plant mitochond...
The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences
Adiantum capillus-veneris evolution of seed plants origin of euphyllophytes defences
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2023/11/16
Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the ev...
Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice
rice shoot length genome-wide association study OsCPS1 selection
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2023/4/21
High seedling vigor can improve the ability to compete against weeds and flooding at the seedling stage and is essential for the direct seeding of rice. Early shoot length is an important performance ...
Genome-wide association study of pericarp color in rice using different germplasm and phenotyping methods reveals different genetic architectures
rice pericarp color quantitative trait locus candidate gene genome-wide association study
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2023/4/21
Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. Howev...
The asparagus genome sheds light on the origin and evolution of a young Y chromosome
雄性双倍体 芦笋 石刁柏 基因组测序
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2023/3/31
该成果为江西省农业科学院牵头，与美国乔治亚大学和华大基因等联合，对雄性双倍体（YY）芦笋（石刁柏）进行全基因组测序，利用Illumina（二代）+PacBio（三代）+BioNano（基因组拼接系统）等多种技术手段组装，得到芦笋（石刁柏）基因组大小约为1.3Gb，有27,656个蛋白编码基因被预测。通过对石刁柏参考基因组的比较组学及实验分析发现，单独但相互关联的基因负责性别决定。性染色体在细胞遗传...
The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis
XTH Gene Family Genome-Wide Identification Schima superba
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2023/6/2
Xyloglucan endotransglucosylase/hydrolase (XTH), belonging to glycoside hydrolase family 16, is one of the key enzymes in plant cell wall remodeling. Schima superba is an important timber and fireproo...
Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice
AM-relaxed Cas9 nucleases cytosine base editor adenine base editor off-target effect whole-genome sequencing genome editing rice
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2023/7/20
PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely unexplore...
Genome-wide quantitative trait loci reveal the genetic basis of cotton fiber quality and yield-related traits in a G.hirsutum recombinant inbred line population
0-153 sGK9708 棉花产量 品质性状
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2024/5/17
利用0-153和sGK9708为亲本构建的RIL群体为材料，通过全基因组QTL挖掘明确了棉花产量及品质性状的相关性及其与QTL簇加性效应方向的关系，初步揭示了棉花产量纤维品质性状负相关形成的遗传基础，为进一步利用标记辅助选择、基因组编辑等技术同步改良棉花纤维品质和产量提供了重要的基因资源和位点信息。该研究以0-153*SGK9708为亲本构建的含有196个重组自交系群体为材料，在黄河流域及西北内陆...
Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome wide association study, QTL seq and transcriptome sequencing in cotton
棉花 抗黄萎病性状 关联群体 遗传分离群体
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2024/4/16
构建了棉花抗黄萎病性状的关联群体和遗传分离群体，联合利用全基因组关联分析(GWAS)、QTL- Seq和转录组测序开展了棉花抗黄萎病基因发掘与KASP标记开发研究,获得了5个主效抗黄萎病QTL的候选基因区间，开发出10个可以用于陆地棉抗病性标记辅助选择育种的KASP标记，同时鉴定出8个抗黄萎病候选基因，这些基因主要参与植物基础免疫反应及广谱抗病性，推测基础免疫反应相关基因在抗、感品种间的gDNA&...