A5015085832- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Cancer Genomics and Diagnostics
- Plant Genetic and Mutation Studies
- Plant Molecular Biology Research
- Genetics and Plant Breeding
- Chromosomal and Genetic Variations
- Plant Disease Resistance and Genetics
- Wheat and Barley Genetics and Pathology
- Animal Genetics and Reproduction
- Rice Cultivation and Yield Improvement
- Plant-Microbe Interactions and Immunity
- GABA and Rice Research
- Photosynthetic Processes and Mechanisms
- Genetic and phenotypic traits in livestock
- Plant Pathogens and Fungal Diseases
- Protist diversity and phylogeny
- Celiac Disease Research and Management
- RNA and protein synthesis mechanisms
- Soybean genetics and cultivation
- Plant Reproductive Biology
- Polysaccharides and Plant Cell Walls
- Plant Pathogenic Bacteria Studies
- Genetic diversity and population structure
- Peanut Plant Research Studies
Henan Agricultural University
2017-2025
Wenzhou University
2025
Huazhong Agricultural University
2012-2022
Griffith University
2019
Harbin Medical University
2015
Beijing Institute of Petrochemical Technology
2011
Wuhan University
2007
Huazhong University of Science and Technology
2007
Tongji Hospital
2007
Abstract Summary Creation of Circos plot is one the most efficient approaches to visualize genomic data. However, installation and use existing tools make are challenging for users lacking coding experiences. To address this issue, we developed an R/Shiny application shinyCircos, a graphical user interface interactive creation plot. shinyCircos can be easily installed either on computers personal or local public servers provide online community. Furthermore, various types plots could...
Abstract Grains from cereals contribute an important source of protein to human food, and grain content (GPC) is determinant nutritional quality in cereals. Here we show that the quantitative trait locus (QTL) qPC1 rice controls GPC by regulating synthesis accumulation glutelins, prolamins, globulins, albumins starch. encodes a putative amino acid transporter OsAAP6 , which functions as positive regulator rice, such higher expression correlated with GPC. greatly enhances root absorption...
Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The provides comprehensive information 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data 1479 accessions. SNP genotypes all accessions were imputed evaluated, resulting in an overall missing rate 0.42% estimated accuracy greater than 99%. SNP/INDEL are available for online query download. Users can search SNPs/INDELs...
Heterosis refers to the superior performance of hybrids relative parents. Utilization heterosis has contributed tremendously increased productivity in many crops for decades. Although there have been a range studies on various aspects heterosis, key understanding biological mechanisms heterotic crop is genetic basis, much which still uncharacterized. In this study, we dissected composition yield and component traits using data replicated field trials an “immortalized F 2 ” population derived...
Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. japonica Despite the fact that accounts for over 70% total production worldwide is genetically much more diverse, a high-quality reference genome has yet to be published. We conducted map-based sequencing lines, Zhenshan 97 (ZS97) Minghui 63 (MH63), which represent major varietal groups subspecies are parents an elite Chinese hybrid. The sequences were assembled into 237 181 (MH63) contigs, with accuracy...
Significance Intensive rice breeding over the past 50 y has produced many high-performing cultivars, but our knowledge of genomic changes associated with such improvement remains limited. By analyzing sequences 1,479 accessions, this study identified efforts, referred to as signatures, involving 7.8% genome. Accumulation selected regions is positively correlated yield improvement. The number in a line may be used for predicting agronomic potential, and loci provide useful targets
We previously developed shinyCircos, an interactive web application for creating Circos diagrams, which has been widely recognized its graphical user interface and ease of use. Here, we introduce shinyCircos-V2.0, upgraded version shinyCircos that includes a new with enhanced usability many features advanced plots. To help users get started provide detailed tutorials example input data sets. The is available online at https://venyao.xyz/shinyCircos/...
Abstract Powdery mildew is a devastating disease that affects wheat yield and quality. Wheat wild relatives represent valuable sources of resistance genes. Cloning characterization these genes will facilitate their incorporation into breeding programs. Here, we report the cloning Pm57 , powdery gene from Aegilops searsii . It encodes tandem kinase protein with putative kinase-pseudokinase domains followed by von Willebrand factor A domain (WTK-vWA), being ortholog Lr9 mediates leaf rust...
Tiller angle is one of the most important components ideal plant architecture that can greatly enhance rice grain yield. Understanding genetic basis tiller and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling using 529 diverse accessions Oryza sativa including 295 indica 156 japonica in two environments. We identified 7 common quantitative trait loci (QTLs), previously...
As a main staple food, rice is also model plant for functional genomic studies of monocots. Decoding every DNA element the genome essential genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in genomics. Systematic characterization and proper deposition gene are vital both crop improvement.We built comprehensive accurate dataset ∼2800 functionally characterized genes ∼5000 members different families by integrating data from...
Complete and highly accurate reference genomes gene annotations are indispensable for basic biological research trait improvement of woody tree species. In this study, we integrated single-molecule sequencing high-throughput chromosome conformation capture techniques to produce a high-quality long-range contiguity chromosome-scale genome assembly the soft-seeded pomegranate cultivar 'Tunisia'. The covers 320.31 Mb (scaffold N50 = 39.96 Mb; contig 4.49 Mb) includes 33 594 protein-coding...
The dispensable genome of a species, consisting the sequences present only in subset individuals, is believed to play important roles phenotypic variation and evolution. However, construction costly labor-intensive at present, so influence genetic functional genomic studies has not been fully explored. We construct rice through metagenome-like de novo assembly strategy based on low-coverage (1–3×) sequencing data 1483 cultivated (Oryza sativa L.) accessions. Thousands protein-coding genes...
Nuclear factor-Y (NF-Y) transcription factors are important regulators of several essential biological processes, including embryogenesis, drought resistance, meristem maintenance, and photoperiod-dependent flowering in Arabidopsis. However, the regulatory mechanisms NF-Ys maize (Zea mays) not well understood yet. In this study, we identified an NF-Y factor, ZmNF-YA3. Genome-wide analysis showed that ZmNF-YA3 bound to >6000 sites genome, 2259 which associated with genic sequences. was found...
CCT domain-containing genes generally control flowering in plants. Currently, only six of the 41 family have been confirmed to rice. To efficiently identify more heading date-related from family, we compared positions date QTLs and found that 25 were located QTL regions. Association mapping showed a total 19 associated with date. Five seven within regions two four outside regulate by transformation. None non-associated regulates Obviously, combination candidate gene-based association linkage...
Abstract Development of interactive web applications to deposit, visualize and analyze biological datasets is a major subject bioinformatics. R programming language for data science, which also one the most popular languages used in analysis However, building was great challenge users before Shiny package developed by RStudio company 2012. By compiling code into HTML, CSS JavaScript code, has made it incredibly easy build large community bioinformatics even non-programmers. Over 470 have...
Low temperature is an environmental stress factor that always been applied in research on improving crop growth, productivity, and quality of crops. Polyunsaturated fatty acids (PUFAs) play important role cold tolerance, so its genetic manipulation the PUFA contents crops has led to modification sensitivity. In this study, we over-expressed ω-3 acid desaturase from Glycine max (GmFAD3A) drove by a maize ubiquitin promoter rice. Compared wild type (ZH11), ectopic expression GmFAD3A increased...
As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built funRiceGenes database including ~ 2800 5000 members different gene families. Since being published, accessed by more than 54,400 users over 540,000 pageviews. The continuously updated newly cloned published literature, based on progress functional genomics studies. Up to Nov 2021, 4100 6000 families were collected in...
Fusarium verticillioides (F. verticillioides) is a widely distributed phytopathogen that incites multiple destructive diseases in maize, posing grave threat to corn yields and quality worldwide. However, there are few reports of resistance genes F. verticillioides. Here, we reveal combination two single nucleotide polymorphisms (SNPs) corresponding ZmWAX2 gene associates with quantitative variations maize through genome-wide association study. A lack compromises verticillioides-caused seed...
Abstract Noncanonical peptides (NCPs) are a class of generated from regions previously thought as noncoding, such introns, 5′ UTRs, 3′ and intergenic regions. In recent years, the significance diverse functions NCPs have come to light, yet systematic comprehensive NCP database remains absent. Here, we developed NCPbook (https://ncp.wiki/ncpbook/), evidence-supported NCPs, which aims provide resource for efficient exploration, analysis, manipulation NCPs. incorporates data public databases...
Mitogen-activated protein (MAP) kinase cascades, with each cascade consisting of a MAP (MAPKKK), (MAPKK), and (MAPK), play important roles in dicot plant responses to pathogen infection. However, no single has been identified rice, the functions cascades rice - interactions are unknown.To explore contribution response Xanthomonas oryzae pv. (Xoo), which causes bacterial blight, one devastating diseases worldwide, we performed comprehensive expression analysis genes. We transcriptionally...
Heterotrimeric Heme Activator Protein (HAP) family genes are involved in the regulation of flowering plants. It is not clear how many HAP regulate heading date rice. In this study, we identified 35 genes, including seven newly and performed gene duplication candidate gene-based association analyses. Analyses showed that segmental tandem main mechanisms duplication. Expression profiling functional identification indicated probably diversifies functions genes. A nucleotide diversity analysis...
In the present study, complete mitogenome of Clavaria fumosa, was sequenced, assembled, and compared. The C. fumosa is 256,807 bp in length largest mitogenomes among all Basidiomycota reported. Comparative mitogenomic analysis indicated that contained most introns intronic ORFs fungal mitogenomes. Large intergenic regions, accumulation repeat sequences plasmid-derived genes together promoted size expansion mitogenome. addition, rps3 gene found subjected to positive selection between some...