A5084905623- Genetic Mapping and Diversity in Plants and Animals
- GABA and Rice Research
- Rice Cultivation and Yield Improvement
- Plant Molecular Biology Research
- Wheat and Barley Genetics and Pathology
- Genomics and Phylogenetic Studies
- Plant Stress Responses and Tolerance
- Plant-Microbe Interactions and Immunity
- Plant Gene Expression Analysis
- Plant nutrient uptake and metabolism
- Photosynthetic Processes and Mechanisms
- Agricultural Systems and Practices
- Plant pathogens and resistance mechanisms
- Plant tissue culture and regeneration
- Chromosomal and Genetic Variations
- Plant Pathogenic Bacteria Studies
- Research in Cotton Cultivation
- Graphene research and applications
- Plant Micronutrient Interactions and Effects
- Natural Antidiabetic Agents Studies
- Bioenergy crop production and management
- Fullerene Chemistry and Applications
- Polymer Nanocomposite Synthesis and Irradiation
- Plant Pathogens and Resistance
- Plant Reproductive Biology
Institute of Crop Science
2024
Chinese Academy of Agricultural Sciences
2016-2024
National Tsing Hua University
2024
Institute of Crop Sciences
2016-2024
Shenyang Pharmaceutical University
2018-2023
Dalian University of Technology
2023
Agricultural Information Institute
2022
Dalian Maritime University
2018-2021
China Agricultural University
2010-2020
Northeast Agricultural University
2018
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with five major groups previously recognized, but also suggest several unreported subpopulations that correlate geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 small indels over 90,000 structural variations contribute to within- between-population variation....
Abstract Genetic diversity is key to crop improvement. Owing pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence species (known as ‘pan-genome’ 1 ). Multiple high-quality assemblies are an indispensable component pan-genome infrastructure. Barley ( Hordeum vulgare L.) important cereal with long history cultivation that adapted wide range agro-climatic conditions 2 . Here we report construction chromosome-scale for...
A pan-genome is the union of gene sets all individuals a clade or species and it provides new dimension genome complexity with presence/absence variations (PAVs) genes among these genomes. With progress sequencing technologies, study becoming affordable for eukaryotes large-sized The Asian cultivated rice, Oryza sativa L., one major food sources world model organism in plant biology. Recently, 3000 Rice Genome Project (3K RGP) sequenced more than rice genomes mean depth 14.3×, which provided...
JASMONATE ZIM-domain (JAZ) proteins play important roles in plant defence and growth by regulating jasmonate signalling. Through data mining, we discovered that the JAZ7 gene was up-regulated darkness. In dark, jaz7 mutant displayed more severe leaf yellowing, quicker chlorophyll degradation, higher hydrogen peroxide accumulation compared with wild-type (WT) plants. The phenotype of dark-induced senescence could be rescued JAZ7-complemented -overexpression lines. Moreover, double mutants...
Rice (Oryza sativa L.) not only provides insurance covering global food security but also works as a model for plant research. Currently, with overwhelmingly accumulated sequencing data, various databases were constructed different target users, including the Genome Variation Map (Song et al., 2018), RiceVarMap (Zhao 2015), SNP-Seek database (Alexandrov RPAN (Sun 2017) and MBK V1 (Institute of Genetics Developmental Biology, C.A.S., 2018). However, none them is designed to meet increasing...
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton wheat, great model system for heterosis research. Here, we have integrated genome sequences transcriptome data of Gossypium to construct co-expression networks identified functional modules from different species, including 1155 1884 in G. arboreum hirsutum, respectively. We overlayed the gene expression results onto network. further provided network...
Appearance and milling quality are two crucial properties of rice grains affecting its market acceptability. Understanding the genetic base grain could considerably improve high breeding. Here, we carried out an association analysis to identify QTL nine appearance traits using a diverse panel 258 accessions selected from 3K Rice Genome Project evaluated in environments Sanya Shenzhen. Genome-wide analyses 22,488 SNPs identified 72 traits. Combined gene-based haplotype plus functional...
Rice is a very important food staple that feeds more than half the world's population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, molecular mechanisms underlying this are still largely unknown. A common link among different stresses they produce an oxidative burst result increase of reactive oxygen species (ROS). In study, methyl viologen (MV) as ROS agent was applied to...
The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes multiple samples with 3h H2O, NaCl, or PEG treatments in leaf, stem root tissues successfully obtained 123,579 transcripts G. 89,128 which were hits BLAST against known ESTs draft genome raimondii. About 36,961 (including 1,958 possible transcription factor members) identified differential expression...
Abstract Rice is susceptible to salt stress at the seedling stage. To explore molecular mechanisms underlying tolerance, metabolic responses were investigated with a metabolite-profiling technique. Gas chromatography–mass spectrometry was used profile metabolite changes in five rice lines similar genetic background, but obviously diverse growth performances under saline conditions. A total of 84 metabolites detected leaf extracts control and The data revealed that amino acids enriched more...
Abstract Background Bacterial blight (BB), caused by Xanthomonas oryzae pv. ( Xoo ) is one of the most devastating bacterial diseases rice in temperate and tropical regions. Breeding deployment resistant cultivars carrying major resistance R genes has been effective approach for BB management. However, because specific interaction each gene with product corresponding pathogen avirulence or effector gene, new strains that can overcome deployed often emerge rapidly. To deal ever-evolving , it...
As a histone variant, H2A.Z is highly conserved among species and plays significant role in diverse cellular processes. Here, we generated genome-wide maps of Oryza sativa (rice) callus seedling by combining chromatin immunoprecipitation using antibody high-throughput sequencing. We found significantly high peak small distributed at the 5' 3' ends expressed genes, respectively. was also associated with inactive genes both tissues. H3 lysine 4 trimethylation deposition end 27 peaks were...
Abstract Seedling vigour (SV) is important for direct seeding rice ( Oryza sativa L.), especially in a paddy-direct system, but the genetic mechanisms behind related traits remain largely unknown. Here, we used 744 germplasms, having at least two subsets, detection of quantitative trait loci (QTLs) affecting SV-related tiller number, plant height, and aboveground dry weight three sampling stages, 27, 34, 41 d after sowing. A joint map based on GAPIT mrMLM produced satisfying balance between...
Heading date (HD) and panicle length (PL) are important traits that affect rice breeding controlled by pleiotropic genes. Some alleles associated with HD PL from wild relatives might differ those in cultivated rice. In this study, a main effect quantitative trait locus rice, qHD7.2, was identified using chromosomal segment substitution line (CSSL) population. First, qHD7.2 determined to be located near RM172 on chromosome 7 based association analysis of phenotype data six environments 181...
Abstract Background The grain number per panicle (GNP), which is one of three yield components, an important trait for the genetic improvement rice. Although NAL1 and GNP1 genes regulating rice GNP have been cloned, their allelic diversity, functional differences in germplasms, effects combination on remain unclear. Results Based DNA sequences these two 198 cultivated ( Oryza sativa ) 8–10 wild rufipogon 16 14 haplotypes were identified , respectively. gene had strongest indica xian japonica...
Rice SPX domain gene, OsSPX1, plays an important role in the phosphate (Pi) signaling network. Our previous work showed that constitutive overexpression of OsSPX1 tobacco and Arabidopsis plants improved cold tolerance while also decreasing total leaf Pi. In present study, we generated rice antisense sense transgenic lines found down-regulation caused high sensitivity to oxidative stresses seedlings. Compared wild-type OsSPX1-sense lines, more hydrogen peroxide accumulated seedling leaves...
Summary Os SPX 1 , a rice domain gene, involved in the phosphate (Pi)‐sensing mechanism plays an essential role Pi‐signalling network through interaction with PHR 2 . In this study, we focused on potential function of during reproductive phase. Based investigation antisense and sense transgenic lines paddy fields, discovered that down‐regulation caused reduction seed‐setting rate filled grain number. Through examination anthers pollens wild‐type plants by microscopy, found gene led to...
DNA marker profiles play a crucial role in the identification and registration of germplasm, as well distinctness, uniformity, stability (DUS) testing new plant variety protection. However, selecting minimal sets from large-scale SNP dataset can be challenging to distinguish maximum number samples.Here, we developed CoreSNP pipeline using "divide conquer" strategy "greedy" algorithm. The offers adjustable parameters guarantee distinction each sample pair with at least two markers....