Exploring Wild Relatives of Rice for Aluminum Tolerance Using Chromosome Segment Substitution Lines (CSSLs)

To facilitate mapping, characterization, and utilization of quantitative trait loci from wild relatives of rice, we developed two interspecific populations of chromosome segment substitution lines (CSSLs). Each population was derived from a cross between the recurrent parent “Curinga”, an elite tropical japonica cultivar, and an accession of Oryza meridionalis Ng. (acc. W2112) or O. rufipogon Griff. (acc. IRGC 105491). Using genotyping by sequencing (GBS), the Curinga/O. meridionalis  population was genotyped with 107,445 SNPs and the Curinga/O. rufipogon population was genotyped with 89,577 SNPs. After three generations of backcrossing and one cycle of doubled haploidization, the 32 Curinga/O. meridionalis CSSLs carried 77% of the wild donor genome in targeted introgressions and 7.3% in the background, while the 48 Curinga/O. rufipogon CSSLs carried 97.5% of the donor genome in the target introgressions and 11.5% in the background. Using these populations we identified regions associated with Aluminum (Al) tolerance using a hydroponic/imaging platform. Four of the 80 CSSLs were significantly more tolerant than the Curinga recurrent parent and 12 were significantly more susceptible. Introgressed regions on chromosomes 1, 8 and 10 were putatively associated with Al tolerance. The location and effect of the QTL on chromosome 8 was validated using an F2-derived population created by crossing the tolerant CSSL with Curinga. The interspecific CSSL populations and associated genotypic datasets are valuable for exploring untapped natural variation from wild relatives of rice.