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Location: Dale Bumpers National Rice Research Center

Title: Genetic characterization of global rice germplasm for sustainable agriculture

item Yan, Wengui

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 9/5/2011
Publication Date: 1/20/2012
Citation: Yan, W. 2012. Genetic characterization of global rice germplasm for sustainable agriculture. In: Aladjadjiyan, A. editor. Food Production - Approaches, Challenges and Tasks. Rijeka, Croatia: InTech. p. 243-270. Available:

Interpretive Summary: Crop genebanks or germplasm collections store thousands of crop varieties. Each variety has unique genetic traits to be used in fighting diseases and insects, increasing yield and nutritional value and adjusting to environmental changes such as drought, soil salinity, etc. The Germplasm Resources Information Network (GRIN) of the United States manages germplasm of plants, animals, microbes and invertebrates ( Currently, there are 540,935 accessions of plant germplasm for 95,800 taxonomic names, 13,388 species of 2,208 genera along with 1,866,764 inventory records, 1,628,283 germination records, 7,291,757 characteristic records and 201,156 images in the GRIN. Rice is one of the most important food crops because it feeds more than half of the world’s population. Currently, there are more than 18,000 accessions of rice germplasm originated from 116 countries, managed by the GRIN. A core collection is a subset of a large germplasm collection that contains chosen accessions that capture most of the genetic variability within the entire gene bank. The USDA rice core collection consists of 1,794 entries (10% of the whole collection). Using 14 traits, the core was proved to effectively represent the whole collection. Using 72 genome wide SSR markers, genetic differentiation and diversity associated with global distribution are studied. The results show that genetic diversity in the USDA rice collection is sufficient for a sustainable agricultural in the world.

Technical Abstract: The USDA rice core collection, about 10% of the whole collection including more than 18,000 accessions originated from 116 countries, could be effectively used to assess the whole collection with 88% certainty. Genotyping the 1,794 accessions in the core with one indel and 71 SSR genome-wide markers demonstrated that a great majority of genetic variance was due to within instead of among geographic regions, and within instead of among countries. Germplasm accessions obtained from the Southern Asia, Southeast Asia and Africa were highly diversified, while those from North America, and Western and Eastern Europe had the lowest diversity. Different measurements of genetic diversity, including average number of alleles per locus, polymorphic information content (PIC), Nei index, and average number of private alleles per locus, uniformly reached this conclusion. Ancestry analysis proportioned the core collection to 35% indica, 27% temperate japonica, 24% tropical japonica, 10% aus and 4% aromatic. This study of global rice has found significant population stratification generally corresponding to major geographic regions of the world. The USDA rice mini-core contains 217 entries sampled from the core. The sampling was conducted using PowerCore software based on 26 phenotypic traits and 70 molecular markers. Genetic analyses showed that all 962 alleles identified by the 70 markers in the core collection were captured in the mini-core, which maximized allelic richness up to 100%. In conclusion, characterization of the USDA rice world collection for genetic structure, diversity, and differentiation will better serve the global rice community for improvement of cultivars and hybrids because this collection is internationally available, free of charge and without restrictions for research purposes.