SRA

The germplasm set of 533 O. sativa accessions consisted of both landraces and elite varieties, including 192 accessions from a core/mini core collection of Oryza sativa L. in China (Zhang et al. 2011), 132 parental lines used in the International Rice Molecular Breeding Program (Yu et al. 2003), 148 accessions from a mini-core subset of the USDA rice gene bank (Agrama et al. 2009), 15 accessions used for SNP discovery in the OryzaSNP project (McNally et al. 2009), and 46 additional accessions from the Rice Germplasm Center at IRRI. Total DNA was isolated from leaf tissues of each plant using the CTAB method. Paired-end sequencing libraries with insert sizes of 450~500 bp were constructed for each accession according to Illumina''s standard instructions. Paired-end 90-bp reads were obtained using the Illumina HiSeq 2000 platform and the raw sequences were further processed to remove adapter pollutions and low quality reads (base quality of more than 50% bases<=5), yielding more than 1 Gb for each accession. The library construction, sequencing and sequence cleaning were carried out by BGI-Shenzhen, China.