Name Description Type Publication
Whole Genome Assembly and Annotation of R498

A high quality reference genome would enable discovery of genome structure and genetic variation. Here we report an integrative method to generate a 390.3-megabase assembly covering over 99% of the indica rice genome Shuhui498 with 7 of the 12 chromosomes complete and the rest 5 each containing only one gap in its centromeric region.

We predicted 38,714 high confidence protein coding genes in R498 through an evidence-based gene prediction pipeline by combining known proteins, experimentally... read more

Annotation of a genome. Du H, Yu Y, Ma Y, et al. Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications. 2017;8:15324
The Whole African Rice Genome resequencing project

The Whole African Rice Genome resequencing project is a collaboration between Genoscope, CIRAD and IRD (UMR DIADE). In this project, a focus have been done on 300 cultivated African Rice (O. glaberrima) and 100 wild relative (O. barthii). A SNP analysis have been performed and results have been used for evolution study, new gene discovery, QTL cloning, forward/reverse genetics and allele identification. This work was supported by a grant from the France Genomique French National infrastructure and... read more

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Cubry et al. Current Biology, Volume 28, Issue 14, 23 July 2018, Pages 2274-2282.e6

Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

This GWAS project for root traits is a collaboration between IRD (UMR DIADE) and LMI RICE (Vietnam). A panel of 180 Vietnamese rice varieties originating from provinces from North to South Vietnaman and from different agrosystems characterized by contrasted water regimes were used to perform a genome-wide association study for different root parameters.

Genome-wide association study experiments. Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam. Phung et al. 2016. BMC Plant Biology, 2016, Volume 16, Number 1, Page 1
Whole Genome Assembly and Annotation of Oryza sativa Kitaake Annotation of a genome. Li G, Jain R, Chern M, et al. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. The Plant Cell. 2017;29(6):1218-1231.
Whole Genome Assembly and Annotation of N22
This data package contains processed data from the International Oryza Map Alignment Project (IOMAP) covering annotation and comparative genomics in 13 species of the Oryzeae tribe in relation to the following reference genome assemblies; Oryza sativa vg. indica [IR 8], Oryza sativa vg. aus [N 22], Oryza sativa vg. japonica [IRGSP-1.0], Oryza sativa vg. indiac [93-11], Oryza nivara, Oryza rufipogon, Oryza barthii, Oryza glaberrima, Oryza glumaepatula, Oryza meridionalis, Oryza punctata, Oryza... read more
Annotation of a genome. JC Stein, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics volume 50, pages 285–296 (2018)
Whole Genome Assembly and Annotation of MH63

The Rice Information GateWay (RIGW) 2.0 was updated with the near-complete reference genome assemblies of MH63. MH63 contained 19 contigs (387.42 Mb), and seven (i.e. Chr03/Chr04/ Chr05/Chr06/Chr08/Chr10/Chr12) were assembled into single contigs.

Annotation of a genome. Zhang J, Chen L-L, Xing F, et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(35):E5163-E5171. doi:10.1073/pnas.1611012113.
Whole Genome Assembly and Annotation of IR8
This data package contains processed data from the International Oryza Map Alignment Project (IOMAP) covering annotation and comparative genomics in 13 species of the Oryzeae tribe in relation to the following reference genome assemblies; Oryza sativa vg. indica [IR 8], Oryza sativa vg. aus [N 22], Oryza sativa vg. japonica [IRGSP-1.0], Oryza sativa vg. indiac [93-11], Oryza nivara, Oryza rufipogon, Oryza barthii, Oryza glaberrima, Oryza glumaepatula, Oryza meridionalis, Oryza punctata, Oryza... read more
Annotation of a genome. JC Stein, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics volume 50, pages 285–296 (2018)
Genome wide association study of panicle morphological traits in O. sativa

The GWAS project of panicle morphological traits is a collaboration between IRD (UMR DIADE) and LMI RICE (Vietnam). A panel of 159 vietnamese landraces was used in association with a detail phenotyping of panicle traiats at mature stage using P-TRAP software (AL Tam et al 2013) over two years (2014 and 2015)

Genome-wide association study experiments. Ta KN, Khong NG, Ha TL, et al. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits. BMC Plant Biol. 2018;18(1):282
Whole Genome Assembly and Annotation of ZS97 Annotation of a genome. Zhang J, Chen L-L, Xing F, et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(35):E5163-E5171. doi:10.1073/pnas.1611012113.
Whole Genome Assembly and Annotation of Oryza glaberrima (ENA)

As part of the OMAP project a large insert BAC library has been developed for O. glaberrima to 5X coverage and clone end sequences were developed as one of the steps in generating the genome sequence for this organism. This project has been extended to determine the genome sequence.

Annotation of a genome. The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology, Volume 16, Issue 2, May 2013, Pages 147 - 156. Julie Jacquemin, Dharminder Bhatia, Kuldeep Singh, Rod A Wing

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