The use of rice collections in crop improvement can better be promoted when accessions have been characterized using phenotypic traits and high-density molecular markers. Using 3,834 polymorphic single nucleotide polymorphisms (SNPs) generated via the DArTseq-based genotyping by sequencing (GBS) technology, we previously characterized the genetic variation and population structure of 2,179 Oryza glaberrima accessions and created a mini-core (subset) of 350 accessions (https://www.genesys-pgr.org/subsets/edb035ac-9e4c-4c99-80e9-8c6a9ec4d4e2) that captured 97% of the SNP polymorphism and most of the genetic variation observed in the whole set. For details, please read our open-access research paper from Frontiers in Plant Science https://doi.org/10.3389/fpls.2017.01748.

Currently, we have genotyped a total of 3,130 O. glaberrima accessions with 49,685 SNPs of which 9,990 SNPs were polymorphic. Using combinations of the polymorphic SNPs and trait information from different publications, we have revised the O. glaberrima mini-core set by selecting 350 out of 3,130 accessions. About 98% of the SNPs that were polymorphic across the 3,130 accessions were polymorphic in the revised mini-core set. Genetic distance between pairs of the 3,130 accessions varied from 0.021 to 0.393 and the overall average was 0.217. In the revised mini-core, genetic distance varied from 0.046 to 0.400 with an average of 0.253. The proportion of pairs of accessions with a genetic distance exceeding 0.250 was just 17% in the whole set as compared with 49% in the mini-core set. The revised mini-core consisted of 76 trait donors for multiple traits, including tolerance to abiotic stresses (early-morning flowering and peak spikelet opening time that are associated with heat, anaerobic germination ability, stagnant flooding, drought, and iron toxicity), and biotic stresses (resistance to African gall midge, bacterial leaf blight, and rice yellow mottle virus).

This mini-core represents the different maturity groups (78 early, 194 intermediate, 65 late, and 13 unknown maturity) and originated from 19 countries and 8 rice growing ecologies. Nearly 37% of the accessions in the revised mini-core set (129 of 350) are common with the previous mini-core set (https://www.genesys-pgr.org/subsets/edb035ac-9e4c-4c99-80e9-8c6a9ec4d4e2). More information on subsets of the trait donors is available at https://www.genesys-pgr.org/subsets/v2OkQW9jEGA.