The Rice Biodiversity Center for Africa has genotyped a total of 5,738 O. sativa accessions with 49,685 SNPs of which 25,904 SNPs were polymorphic. Using the SNP genotype data, we have selected a subset of the most genetically diverse 600 O. sativa accessions to represent a mini-core set, which includes 400 indica and 200 japonica accessions. This mini-core represents 54 countries and 6 rice growing ecologies, with 77.3% of them originating within Africa.

Nearly 99% of the SNPs that were polymorphic across the 5,738 accessions were polymorphic in the mini-core set. Genetic distance between pairs of the 5,738 accessions varied from 0.010 to 0.441 and the overall average was 0.256. In the mini-core set, genetic distance varied from 0.050 to 0.445 with an average of 0.300. The proportion of pairs of accessions with a genetic distance exceeding 0.256 (which is the average in all accession) was just 35.6% in the whole set as compared with 77.9% in the mini-core set.