Genomic variation for 104 rice elite cultivars, landraces and wild relatives

Genomic variation obtained from analysis of high throughput sequencing (HTS) illumina data for 94 varieties of Oryza sativa and 10 wild relatives from O. rufipogon and O. nivara. The 94 O. sativa varieties include 21 latin american elite cultivars from the CIAT rice breeding program, 33 north american elite cultivars from USDA, as well as 40 landraces and 10 wild relatives sequenced and previously analyzed (doi: 10.1038/nbt.2050). Raw sequencing data was analyzed using the NGSEP pipeline (http://sourceforge.net/projects/ngsep/). Details of the analysis and the main research outcomes obtained from these data can be found here (doi: 10.1371/journal.pone.0124617). SNPs and small indels for the 104 varieties are provided as a single VCF file, whereas predictions of copy number variation (CNVs), large indels and inversions are provided as one file per sample in GFF format.

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Author Duitama, Jorge
Last Updated September 10, 2026, 18:01 (UTC)
Published April 8, 2026, 06:49 (UTC)
Citation Duitama, Jorge 2015. Genomic variation for 104 rice elite cultivars, landraces and wild relatives. CyVerse Data Commons. DOI 10.7946/P21595
contributor Farmer, Andrew, Oard, James, Tohme, Joe
de_created_date 2015-02-11T04:02:30Z
de_modified_date 2020-02-20T22:05:33Z
identifierType DOI
publisher iPlant Collaborative Data Commons
relatedIdentifier 10.5061/dryad.8hg32
resourceType rice genomic data