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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #393360
Research Project: Management of Priority Legume, Oilseed, Vegetable, Forage Grass, Sugar, Ornamental, and Medicinal Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

Title: Genetic variation and population structure of Oryza sativa accessions in the AfricaRice collection and development of the AfricaRice O. sativa Core Collection

Author
item NDJIONDJOP, MARIE NOELLE - Africa Rice Center (AFRICARICE)
item GOUDA, ARNAUD - Africa Rice Center (AFRICARICE)
item Eizenga, Georgia
item Warburton, Marilyn
item BIENVENU KPEKI, SÈDJRO - Africa Rice Center (AFRICARICE)
item WAMBUGU, P - Kenya Agricultural And Livestock Research Organization
item GNIKOUA, K - Africa Rice Center (AFRICARICE)
item DRO TIA, DANIEL - Africa Rice Center (AFRICARICE)
item BACHABI, FATIMATA - Africa Rice Center (AFRICARICE)

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2022
Publication Date: 2/22/2023
Citation: Ndjiondjop, M., Gouda, A.C., Eizenga, G.C., Warburton, M.L., Bienvenu Kpeki, S., Wambugu, P.W., Gnikoua, K., Dro Tia, D., Bachabi, F. 2023. Genetic variation and population structure of Oryza sativa accessions in the AfricaRice collection and development of the AfricaRice O. sativa Core Collection. Crop Science. 63(2):724-739. https://doi.org/10.1002/csc2.20898.
DOI: https://doi.org/10.1002/csc2.20898

Interpretive Summary: The crop diversity that is conserved in genebanks is important to global food security. Genetic diversity studies provide increased understanding of genebank collections and help to enhance their use. This study looked at the DNA marker variation of 5,738 rice samples from the AfricaRice genebank and determined that the samples were related as three broad groups. A subset of the collection (a core collection) was identified that breeders can use to find all the genetic diversity present in the entire collection, but will only have to look at 600 total samples, which will make seeking important new traits more efficient.

Technical Abstract: The crop diversity that is conserved in genebanks is important to global food security. Genetic diversity studies provide increased understanding of genebank collections and help to enhance their use. This study investigated the genetic variation and population structure of 5,738 Oryza sativa L. accessions conserved at the AfricaRice genebank using DArTseq based single nucleotide polymorphisms (SNPs). There were 25,904 polymorphic SNPs within the genotyped accessions. Genetic distances between accessions were highly variable, with 21.0% of the accession pairs being moderately distant while 78.2% were highly distant. Using cluster, principal component and model-based population structure analyses, the 5,738 accessions were divided into three groups, corresponding to indica, japonica, and a mixture of accessions. Using the maximum length sub-tree method, we propose a subset of 600 accessions to act as the core subset of the O. sativa collection for the AfricaRice genebank. These accessions account for ~10% of the genotyped collection and captured more than 95% of the SNP polymorphisms in the entire collection. The assembled core collection forms an important resource that will play a vital role in supporting rice improvement.