Characterization of Donor Genome Segments of BC2 and BC4 Way Rarem x Oryzica Llanos-5 Progenies Detected by SNP Markers

Plant breeders make a succession of backcrosses to introgress a character from a donor parent into genomic background of a recurrent parent. In several backcrossing, the proportion of a genome tends to return almost fully to recurrent parent, except the small donor genome segment harboring the character of interest. The estimation of the proportion donor segment through backcross generations has been analyzed theoretically using complex mathematical simulations. In this study, the proportion of donor introgression segments were directly analyzed in advanced backcross populations, BC2F7 and BC4F2. The analysis was done by using a set of single nucleotide polymorphism (SNP) markers covering the entire rice genome. Of the 384 SNP markers we found 124 markers which provide polymorphism between recurrent parent, Way Rarem and Oryzica Llanos-5 as donor parent. But only 55 SNP markers could detect Oryzica Llanos-5 alleles in BC2F7 and BC4F2 progenies. The result of this analysis demonstrated that the average of donor segment number was 14.5 in BC2F7 and 12.3 in BC4F2. It was reduced 15% from BC2F7 to BC4F2. The average of donor segment length was 31.2 cM (centiMorgan) in BC2F7 and 8.79 cM in BC4F2. It was decreased 72% during twice backcrossing. The average of donor genome size was 343.95 cM in BC2F7 and 71.35 cM in BC4F2, which means there was 79% decrease from BC2F7 to BC4F2. These results offered a simple method to describe the proportion of target genome segment from donor parent. It was required as one of the main selection criteria in backcross programs.