ArticleScientific reports2018
Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 26 citations in OpenAlex.
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- Characteristics analysis ofPlant signaling & behavior · 2023Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice.International journal of molecular sciences · 2022Article
- Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines.Frontiers in plant science · 2022Article
- Field Screen and Genotyping ofInsects · 2021Article
- Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress.Scientific reports · 2020Article
- A Novel Mutation of theInternational journal of molecular sciences · 2020Article
- Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture.International journal of molecular sciences · 2020Article
- Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Parallel reaction monitoring revealed tolerance to drought proteins in weedy rice (Oryza sativa f. spontanea).Scientific reports · 2020Article
- Comprehensive Analysis of the Chitinase Gene Family in Cucumber (International journal of molecular sciences · 2019Article
- Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress.Genes · 2019Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to japonica and indica subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.
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