Six Rice Chromosome Segment Substitution Lines Libraries with O. Rufipogon Introgressions.

Chromosome segment substitution lines (CSSLs) are a powerful tool for identifying naturally occurring, favorable alleles in unadapted germplasm. Six CSSL libraries in rice (Oryza sativa) were developed from crosses between three different accessions of the rice progenitor species, O. rufipogon, and the recurrent parents, IR64, an indica variety, and Cybonnet, a tropical japonica variety. The three O. rufipogon (O. nivara) parents were selected from a larger collection of 287 wild accessions to represent geographic, morphological and genetic diversity. Phylogenetic analysis based on 50 SSRs suggested that ‘Khao Pa’ clustered most closely with O. sativa ssp. indica, W1944 with O. sativa ssp. japonica, and IRGC105567 clustered independently of O. sativa. A marker assisted backcrossing (MABC) scheme was used to develop these libraries. Initially, custom-designed 384 SNP BeadXpress arrays were used for genotyping. Subsequently, a 6,000 SNP Infinium array was developed which increased resolution, providing between 1,311 to 1,952 polymorphic genome-wide SNPs per library. Four of the CSSL libraries are being advanced to the BC₄F₃ or BC₅F₃ generation and two are being backcrossed to the BC₄. Once complete, each CSSL library will consist of 63-85 lines, with each line targeting a single wild introgressed region. Collectively, the six CSSL libraries will provide complete coverage of the three divergent O. rufipogon genomes in an elite indica and an elite tropical japonica recurrent parent background, and will be among the most densely genotyped rice CSSL libraries available. These libraries will be used to understand the genetic basis of transgressive variation, investigate allelic series coming from the wild donors, characterize G×G interactions between wild donors and divergent elite cultivated backgrounds, and broaden the gene pool of cultivated rice.