DOI: 10.5061/dryad.8hg32
title: Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

description: 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.
description: Structural variants
 WGSOryza_CIAT_LSU_USDA_NCGRStructural variation
 identified for the 104 varieties analyzed in this study in GFF format (one
 file per sample). Genomic coordinates are relative to
 IRGSP1.0.WGSOryza_CIAT_LSU_USDA_NCGR_SV.tar.gzWGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr1_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 1 from basepairs 1 to 15000000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr2_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 2 from basepairs 1 to 15000000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr3_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 3 from basepairs 1 to 15000000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr1_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 1 from basepairs 15,000,000 to 30,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr1_2.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 1 from basepairs 30,000,000 to 43,270,923WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr2_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 2 from basepairs 15,000,000 to 30,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr2_2.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 2 from basepairs 30,000,000 to 35,937,250WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr3_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 3 from basepairs 15,000,000 to 30,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr3_2.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 3 from basepairs 30,000,000 to 36,413,819WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr5_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 5 from basepairs 1 to 15,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr5_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 5 from basepairs 15,000,000 to 29,958,434WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr6_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 6 from basepairs 1 to 16,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr6_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 6 from basepairs 16,000,000 to 31,248,787WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr7_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 7 from basepairs 1 to 15,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr7_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 7 from basepairs 15,000,000 to 29,697,621WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr8_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 8 from basepairs 1 to 12,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr8_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 8 from basepairs 12,000,000 to 24,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr8_2.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 8 from basepairs 24,000,000 to 28,443,022WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 1 to 10,000,000.WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 10,000,000 to 20,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_2.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 20,000,000 to 30,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_3.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 30,000,000 to 35,502,694WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr9_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 9 from basepairs 1 to 12,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr9_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 9 from basepairs 12,000,000 to 23,012,720WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr10_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 10 from basepairs 1 to 12,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr10_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 10 from basepairs 12,000,000 to 23,207,287WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr11_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 11 from basepairs 1 to 15,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr11_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 11 from basepairs 15,000,000 to 29,021,106WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr12_0.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 12 from basepairs 1 to 12,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr12_1.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 12 from basepairs 12,000,000 to 24,000,000WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr12_2.vcfSNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 12 from basepairs 24,000,000 to 27,531,856