Development of Inter-Specific Chromosome Segment Substitution Libraries (CSSL) in Rice

Six libraries of inter-specific Chromosome Segment Substitution Lines (CSSLs) of rice are being developed as pre-breeding materials and genetic stocks. Three accessions of O. rufipogon were selected as donors, based on phylogenetic, geographical and morphological divergence, and crossed with two recurrent parents, Cybonnet, a high yielding US tropical japonica cultivar, and IR64, an elite IRRI indica known for its good grain quality.  Each CSSL carries a single 4-5 Mb target introgression, along with 0-3 spurious donor segments in the genetic background and there are 70-80 BC3-BC5 CSSLs in each library. Genotyping for foreground and background selection was performed using either an Illumina 384-SNP OPA or Genotyping-by-Sequencing (GBS) based on 384-plex bar-coded libraries. We compare the efficiency and resolution of the two genotyping assays for CSSL construction. When completed, these CSSLs will be used to screen for wild introgressions conferring a variety of agronomically important traits and to expand the pool of genetic variation available to breeders in elite breeding backgrounds.