ArticlePloS one2015
Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it, 75 citations in OpenAlex.
- Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach.G3 (Bethesda, Md.) · 2023Pooled it
- A yield-reducing introgression linked to sd1 in rice.The plant genome · 2026Article
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- Genome-Wide Identification and Expression Profiling of Potato (International journal of molecular sciences · 2024Article
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- A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.AoB PLANTS · 2023Article
- Genomic and Bioinformatic Resources for Perennial Fruit Species.Current genomics · 2022Review
- Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice.Frontiers in plant science · 2022Article
- Whole-Genome Sequencing of KMR3 andFrontiers in plant science · 2022Article
- Scripting Analyses of Genomes in Ensembl Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.BMC bioinformatics · 2021Article
- Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice.Rice (New York, N.Y.) · 2021Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations.BMC genomics · 2020Article
- Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.PLoS genetics · 2020Article
- Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective.Rice (New York, N.Y.) · 2019Review
- TASUKE+: a web-based platform for exploring genome-wide association studies results and large-scale resequencing data.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Haplotype Characterization of the sd1 Semidwarf Gene in United States Rice.The plant genome · 2019Article
- 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice.Rice (New York, N.Y.) · 2019Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.