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PLoS Biol. Novel sequences, structural variations and gene presence variations of Asian cultivated rice. Sun, C. Download references. We thank M. Nature thanks M. Bevan, H. Tang and the other anonymous reviewer s for their contribution to the peer review of this work. Elizabeth B. Wing, Nickolai Alexandrov, Kenneth L. You can also search for this author in PubMed Google Scholar. Zhao, F. Correspondence to Rod A. McNally or Zhikang Li.

Blue curve shows theoretical Hardy—Weinberg equilibrium. The 3, samples capture more than For a given number of samples x axis , the graph shows estimated mean number of new SNPs discovered in the last sample. Raw data for this pipeline is shown in grey boxes and the main output is shown in blue. The numbers of gene families involved in each GO term are shown in blue. Box plots show the median, box edges represent the first and third quartiles and the whiskers extend to 1.

Box plots show the median, box edges represent the first and third quartiles, and the whiskers extend to 1. The colour of the rectangle denotes the number of non-Nipponbare alleles in a genotype. GWAS was performed using filtered and linkage disequilibrium-pruned SNPs for historical trait data on source accessions for grain length and grain width , SNPs and for newly acquired lesion length data for bacterial blight isolate C5 , SNPs.

Major peaks are annotated for known gene loci. Reprints and Permissions. Wang, W. Genomic variation in 3, diverse accessions of Asian cultivated rice. Nature , 43—49 Download citation. Received : 27 November Accepted : 28 February Published : 25 April Issue Date : 03 May Anyone you share the following link with will be able to read this content:.

Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative. Genome Biology BMC Genomics Rice By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. Advanced search. Skip to main content Thank you for visiting nature. Download PDF. Subjects Agricultural genetics Natural variation in plants.

Abstract Here we analyse genetic variation, population structure and diversity among 3, diverse Asian cultivated rice Oryza sativa L.

Main Asian cultivated rice is grown worldwide and comprises the staple food for half of the global population. Genome mapping, size and SNP variation Baseline genome sequencing, analyses, and accession information and metadata for the 3, rice genomes are summarized in Supplementary Data 1 and Supplementary Notes.

Population structure and diversity The 3K-RG accessions were classified into nine subpopulations Fig. Full size image. Utility of the 3K-RG panel We demonstrated the use of the 3K-RG genomes and SNPs for trait mapping analyses for the highly heritable traits of grain length, grain width and bacterial blight resistance Supplementary Notes. Discussion We characterized genetic variation in the 3, sequenced accessions of O.

Methods No statistical methods were used to predetermine sample size. Sequencing data of the 3, Rice Genome project The selection and sequencing of rice accessions have previously been described Determining the effects of SNPs The effects of all bi-allelic SNPs low, medium and high effects on the genome were determined based on the pre-built release 7.

De novo assembly A variation of SOAPdenovo2 56 version r with customized k -mers was used to assemble the rice genomes. Sequencing and de novo assembly of IR 8 and N 22 reference genomes High molecular weight DNA was extracted from young leaves adopting the protocol 58 with minor modifications. Annotation of the pan-genome The gene—transcript annotation of the Nipponbare RefSeq was downloaded from the Rice Annotation Project 64 , and if a protein-coding gene contained multiple transcripts only the transcript with the longest open reading frame was selected as the representative for the gene.

Adjustment of predicted genes We aligned the predicted transcripts against Nipponbare RefSeq to remove potential redundancy. Validation of the non-Nipponbare RefSeq genes We verified the novel genes by multiple approaches.

Determination of core and distributed genes or gene families A core gene or gene family is a gene or gene family present in all rice accessions, and we further defined candidate core genes or gene families as those with loss rates not significantly larger than 0.

Determination of major-group-unbalanced, subpopulation-unbalanced and random genes or gene families Distributed genes or gene families were divided further into major-group-unbalanced, subpopulation-unbalanced and random genes or gene families. Gene and gene-family age Gene ages were inferred with previously described methods Reporting summary Further information on experimental design is available in the Nature Research Reporting Summary linked to this paper. References 1.

Article Google Scholar 2. Google Scholar 6. Article Google Scholar 9. Google Scholar Article Google Scholar PubMed Central Google Scholar Reviewer information Nature thanks M. View author publications. Ethics declarations Competing interests The authors declare no competing interests.

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