Table 1 Studies investigating multiple rice genomes using different sequencing and genotyping platforms
From: Allele mining and enhanced genetic recombination for rice breeding
Sequencing and genotyping platform | Number of lines | Nature of germplasm | Number of high-quality SNPs discovered | Reference |
|---|---|---|---|---|
Map-based sequencing | 1 | Single japonica variety | NA | International Rice Genome Sequencing Project (2005) |
Perlegen chip array | 20 | OryzaSNP set: diverse collection mostly from japonica and indica, some from aus, deepwater, and aromatic group, actively used in international breeding programs | ~160 k | McNally et al. 2009 |
Affymetrix single nucleotide polymorphism (SNP) array | 413 | Diverse rice varieties from 82 countries | 44,100 | Zhao et al. 2011 |
Illumina GAx resequencing | 1,083 cultivated + 446 wild rice | Cultivated indica and japonica, wild rice O. rufipogon | ~8 million | Huang et al. 2012 |
Illumina GA2 resequencing | 50 | Mostly indica and japonica, O. rufipogon, O. nivara | ~6.5 millon | Xu et al. 2012 |
Illumina GoldenGate BeadArray 768-plex and 384-plex | 180 | Japan improved and landrace accessions (temperate japonica) | 2,688 | Yonemaru et al. 2012 |
Illumina HiSeq2000 | 529 | Parental lines from IRRI breeding program; USDA rice genebank minicore subset | ~6.5 million | |
Illumina GA2 resequencing | 3,000 | Primarily landraces and released varieties | ~30 million | The 3,000 Rice Genomes Project 2014 |
Illumina HiSeq2000 | 54 | 21 elite cultivars from CIAT rice breeding program; 33 elite cultivars from U.S. rice breeding program | ~18 million | Duitama et al. 2015 |