RAD-seq of Oryza spp: leaf tissue
Leaf tissue was collected at the seedling stage and DNA was extracted using the CTAB (cetyltrimethylammonium bromide) method with minor modifications (Fulton et al., 1995). Restriction site-associated DNA sequencing (RAD-seq) libraries were prepared according to Clark et al. (2014) based on the method of Poland et al. (2012). In brief, DNA from each individual was digested with the restriction enzymes PstI-HF and MspI followed by ligation to barcoded adapters; then, the samples were pooled, and fragments 200-500 bp were selected and amplified by polymerase chain reaction (PCR). Libraries were sequenced on an Illumina Hi-Seq 2000 for 100 bp single-end reads at the Roy J. Carver Biotechnology Center at the University of Illinois.