Rice Chromosome Segment Substitution Line Selection Utilizing SNP Markers.

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) are being developed from crosses between three different accessions of the rice progenitor species, O. rufipogon or O. nivara, and the recurrent parents, IR64, an indica variety, and Cybonnet, a tropical japonica variety.  To aid in the development of these libraries, a marker assisted backcrossing scheme is being followed.  Initially, SNP markers selected from genotyping the parents with a 44,000 SNP array, were used to follow the introgression of O. rufipogon/O. nivara segments in the cultivated rice background.  Subsequently, additional SNPs were incorporated into the genotyping and selection scheme to increase the resolution in regions with limited coverage.  Each CSSL library will consist of approximately 60-70 lines in the BC4F2 or BC3F2 generation.  These lines should be ready for field evaluation during the 2013 growing season and will be evaluated for a variety of agronomically interesting traits.  These CSSLs will be used to understand the genetic basis of transgressive variation, investigate allelic series coming from the wild donors, characterize G×G interaction between wild donors and divergent elite cultivated backgrounds, and broaden the gene pool of cultivated rice.