ARS | Publication request: Development of a mini-core subset from the USDA Rice Core Collection

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: February 1, 2008
Publication Date: March 1, 2008
Citation: Agrama, H., Yan, W., Fjellstrom, R.G., McClung, A.M. 2008. Development of a mini-core subset from the USDA Rice Core Collection. In: Proceedings of the 32nd Rice Technical Working Group Meetings, February 18-21, 2008, San Diego, CA. 2008. CDROM.

Technical Abstract: Core strategy is an effective tool to extensively describe a large germplasm collection and mini-core strategy further increases the effectiveness in describing the collection on molecular level. The USDA rice core collection including 1,790 entries proved to be representative of the whole collection with 88% certainty, from which a mini-core subset has been developed with Maximizing (M) strategy for exploring allelic diversity. The M strategy is the most powerful function for selecting entries with the most diverse alleles and eliminating redundancy that comes from non-informative alleles, which arise from co-ancestry and certain assertive mating systems in establishing core sets. Twenty nine phenotypic traits and 50 simple sequence repeat (SSR) markers were used to develop the mini-core. The traits include 12 morphological and 2 cooking quality descriptors, 4 micronutrient contents and 11 different disease rating scores. A total of 1,776 entries originated from 113 countries that were characterized for the 29 traits and 50 SSR markers participated in the development. The SSR markers evenly distributed across the 12 rice linkage groups and 605 alleles were detected in the core accessions. The number of alleles produced by SSR ranged from 2 for Rid12, RM338 to 30 for RM474. A set of nested mini-core subsets using advanced M strategy was applied to comparatively analyze captured genetic diversity and mini-core size. The developed mini-core subset successfully captured the existing molecular diversity as well as the morphological diversity present in the core collection. The mini-core subset consists of 176 entries (9.8% of the core collection) from 73 countries in 14 regions and captures 100% of alleles. Due to its greatly reduced size and representing great majority of diversity, the rice mini-core can be economically evaluated extensively for beneficial traits and provides a gateway for enhanced utilization of germplasm for sustainable crop improvement. The mini-core subset will be genotyped with about 200 SSR markers or SNP (single nucleotide polymorphism) markers for characterization of allelic diversity and genetic distance among the Oryza accessions in the USDA collection. Then, it can be more efficiently used by breeders and researchers to exploit valuable genes from the existing collection of rice.