ArticlePlant & cell physiology2011
Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing.
Article in Plant & cell physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Population structure and genetic diversity of a coffee germplasm collection in China revealed by RAD-seq.Frontiers in plant science · 2025Article
- Genome-Wide Identification and Characterization of SNPs and InDels ofPlants (Basel, Switzerland) · 2024Article
- A Cluster ofPlants (Basel, Switzerland) · 2024Article
- Genetic Diversity Analysis and Core Germplasm Construction ofPlants (Basel, Switzerland) · 2024Article
- Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi.Rice (New York, N.Y.) · 2023Article
- DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials.Rice (New York, N.Y.) · 2022Article
- A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations ofFrontiers in plant science · 2022Article
- Genomic Variation in KoreanGenes · 2021Article
- Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution.Communications biology · 2021Article
- Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.BMC genomics · 2021Article
- Translation of continuous artificial selection on phenotype into genotype during rice breeding programs.Breeding science · 2021Article
- Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress.Scientific reports · 2020Article
- Mapping and Functional Characterization ofFrontiers in plant science · 2020Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
- Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance.Scientific reports · 2018Article
- Role of genomics in promoting the utilization of plant genetic resources in genebanks.Briefings in functional genomics · 2018Review
- Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines.Plant molecular biology reporter · 2018Article
- Exploiting the Genomic Diversity of Rice (Frontiers in plant science · 2018Article
- Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.).BMC genomics · 2017Article
- Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits inFrontiers in plant science · 2017Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7% of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi (http://www.nodai-genome.org/oryza_sativa_en.html).
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