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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #411372
Research Project: Broadening and Strengthening the Genetic Base of Rice for Adaptation to a Changing Climate, Crop Production Systems, and Markets

Location: Dale Bumpers National Rice Research Center

Title: Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq

Author
item GOUDA, ARNAUD - Africa Rice Center (AFRICARICE)
item SANGARE, JEAN - Mali Institute D'Economie
item WAMBUGU, PETERSON - Kenya Agricultural Research Institute
item Huggins, Trevis
item NDJIONDJOP, MARIE NOELLE - Africa Rice Center (AFRICARICE)

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/26/2024
Publication Date: 11/4/2024
Citation: Gouda, A., Sangare, J., Wambugu, P., Huggins, T.D., Ndjiondjop, M. 2024. Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq. Crop Science. https://doi.org/10.1002/csc2.21395.
DOI: https://doi.org/10.1002/csc2.21395

Interpretive Summary: Rice germplasm collections are treasure chests of phenotypic and genetic diversity that can be utilized to improve rice yields, grain quality, disease resistance and abiotic stresses. A lack of phenotypic and genotypic information limits the use of the genetic diversity. Exploring and understanding this variation will facilitate the use of these germplasm for crop improvement now and for generations to come. The largest collection of African rice is housed in the AfricaRice genebank and plays a key role in the conservation and characterization of this untapped genetic diversity. The AfricaRice collection contains about 22,797 accessions of which 64% (14,480) are African Oryza sativa and 14% (3,130) Oryza glaberrima. A set of 9,013 accessions from four Oryza species believed to be O. sativa, O. glaberrima, O. barthii, and O. longistaminata were genotyped with 27,718 genetic markers to assess genetic diversity and verify species. Cluster analyses separated the 9,013 accessions into six groups of O. glaberrima, O. barthii, O. longistaminata, O. sativa ssp. japonica and two O. sativa ssp. indica, improved/advanced cultivars and traditional/landraces. Genetic analyses showed that the set of 9,013 accessions are unique and highly diverse. Hence, the rich genetic variation present within these accessions can be used by rice breeders and researchers to improve crop productivity, preserve agricultural sustainability, and increase crop value worldwide. The genetic markers will also enhance characterization and efficiency of curation of this distinctive and valuable rice germplasm collection.

Technical Abstract: Genebanks play a key role in conserving world-wide crop genetic diversity maintained in ex situ collections. These collections can be used by current and future plant breeders and researchers to improve crop value and productivity. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. The collection contains about 22,797 accessions of which about 18,900 (83%) were collected from Africa. Sixty-four percent of the collection is African Oryza sativa (14,480) and 14% (3,130) is African rice, Oryza glaberrima. A subset of 9,013 accessions believed to be Oryza barthii, Oryza glaberrima, Oryza longistaminata, Oryza sativa ssp. indica and Oryza sativa ssp. japonica was selected and comprehensively characterized. This subset was assessed for genetic diversity and population structure using genotyping-by-sequencing (GBS) through DArTseq analysis. SNP calling analysis identified 27,718 high-quality single nucleotide polymorphism (SNP) markers after the genotypic data was filtered. Neighbor-joining tree, principal component and Bayesian population structure analyses clustered the 9,013 accessions into six groups, based roughly on their taxonomic and biological status. The accessions clustered in groups associated with the Oryza species O. glaberrima, O. barthii, O. longistaminata, O. japonica, and two O. indica, improved-indica, and traditional-indica. According to the analyses, this subset is extensively genetically diverse with an average genetic distance of 0.267 (range 0.001 – 0.469). The analysis also indicated that 45.1% of pairs of accessions were highly distant and 40.1% moderately distant from each other. Molecular diversity indices indicated that O. indica accessions, proportion of polymorphic sites (Ps) = 0.911 and nucleotide diversity (p) = 0.147, were more diverse than the other Oryza species and O. longistaminata accessions were the least diverse, Ps = 0.251 and p = 0.045. Additionally, according to AMOVA analysis, the highest level of diversity was observed for ecology classification within populations, 89% and the lowest was for species classification. These results provide a better understanding of the genetic diversity present in 9,013 rice accessions maintained in the AfricaRice genebank and are a valuable tool for pre breeding, breeding, and further genetic applications for rice improvement and sustainability.