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Genetic Variation and Population Structure of Oryza sativa Accessions in the AfricaRice Collection and Development of the AfricaRice O. sativa Core Collection

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Title Genetic Variation and Population Structure of Oryza sativa Accessions in the AfricaRice Collection and Development of the AfricaRice O. sativa Core Collection
 
Creator Ndjiondjop, M.N.
Gouda, A.C.
Eizenga, G.C.
Warburton, M.L.
Kpeki, S.B.
Wembugu, P.W.
Gnikoua, K.
Tia, D.
Bachabi, F
 
Subject rice
research
 
Description Genetic diversity studies provide an increased understanding of genebank collections and enhance their use for improving global food security. This study explores the genetic variation and population structure of 5,738 rice (Oryza sativa L.) accessions representing 39.6% of the O. sativa collection conserved in the AfricaRice genebank of which 74.0% originated from African countries. These accessions were genotyped with 25,904 polymorphic DArTseq based single nucleotide polymorphisms (SNPs). Genetic distances between pairs of accessions indicate high variability, with 21.0% of pairs being moderately distant and 78.2% highly distant from each other. The genotyped accessions are traditionally grown in six different agro-ecologies from 73 countries. Using neighbor-joining tree, principal component and model-based population structure analyses, the accessions were divided into four genotypic groups representing the two O. sativa subspecies, Japonica (787 accessions) and Indica, which were further divided into landraces (1,879 accessions), and improved cultivars (3,027 accessions), and a fourth small group of admixed accessions. Subclusters identifying a specific agro-ecology (upland, lowland, mangrove swamp) or originating country were noted. Using the maximum length sub-tree method, we selected 10% of the total accessions to form the “AfricaRice O. sativa Core Collection” (AROSCC). The subset of 600 O. sativa accessions captures more than 95% of the SNP polymorphisms in the entire collection. The AROSCC is an important resource to support pre-breeding and rice improvement programs around the world.
 
Date 2023-03
2023-01-16T13:04:30Z
2023-01-16T13:04:30Z
 
Type Journal Article
 
Identifier Ndjiondjop, M.N. Gouda, A.C. Eizenga, G.C. Warburton, M.L. Kpeki, S.B. Wembugu, P.W. Gnikoua, K. Tia, D. Bachabi, F.Genetic Variation and Population Structure of Oryza sativa Accessions in the AfricaRice Collection and Development of the AfricaRice O. sativa Core Collection.Crop Science.2022:csc2.20898.
1435-0653
https://hdl.handle.net/10568/127195
https://doi.org/10.1002/csc2.20898
 
Language en
 
Rights CC-BY-NC-ND-4.0
Open Access
 
Format p. 724-739
 
Publisher Wiley
 
Source Crop Science