Exploring the genetic variation among Oryza sativa accessions in the AfricaRice genebank collection

Authors: Eizenga, Georgia; NDJIONDJOP, MARIE NOELLE - Africa Rice Center (AFRICARICE); Warburton, Marilyn; GOUDA, ARNAUD - Africa Rice Center (AFRICARICE); KPEKI, SEDJRO - Africa Rice Center (AFRICARICE); WAMBUGU, PETERSON - Kenya Agricultural And Livestock Research Organization; GNIKOUA, KARLIN - Africa Rice Center (AFRICARICE); TIA, DANIEL - Africa Rice Center (AFRICARICE)

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/11/2023
Publication Date: 1/30/2024
Citation: Eizenga, G.C., Ndjiondjop, M., Warburton, M.L., Gouda, A.C., Kpeki, S.B., Wambugu, P.W., Gnikoua, K., Tia, D.D. 2024. Exploring the genetic variation among Oryza sativa accessions in the AfricaRice genebank collection. Proceedings of 39th Rice Technical Working Group meeting, Hot Springs, Arkansas, Feb 20-23, 2023. p. 77-78.

Interpretive Summary:

Technical Abstract: Rice (Oryza sativa L.) is grown in 40 of the 54 African countries, acting not only as a source of income for more than 35 million farmers, but also as a staple food in West Africa and Madagascar. In Africa, rice is grown in three main environments: upland, rainfed lowland and irrigated lowland ecologies. About 4% of rice is cultivated in other ecologies, including in mangrove swamps, hydromorphic fringes (the fringes of rainfed lowlands) and as floating rice. The AfricaRice genebank holds 14,480 O. sativa accessions, of which 8,994 accessions have been characterized using 24 phenotypic descriptors under field conditions and 27 grain physicochemical characteristics. This information is available in Genesys (https://www.genesys-pgr.org/datasets/v2OkQW9jEGA) along with passport data. Genotypic characterization of genebank collections can complement phenotypic data and provide an increased understanding of the relationships between accessions and their potential genetic value. This study explores the genetic variation and population structure of 5,738 O. sativa accessions that were previously phenotyped, and which represent 39.6% of the O. sativa accessions conserved in the AfricaRice genebank. Of these genotyped accessions, 4,242 (73.9%) originated from African countries. The genotyping revealed 25,904 polymorphic DArTseq-based single nucleotide polymorphisms (SNPs), which were used to (i) investigate the genetic variation, relatedness and subpopulation structure of the genotyped accessions and (ii) create an AfricaRice O. sativa Core Collection (AROSCC) that captures most of the genetic variation for future basic genetics and breeding studies. The genotypic data revealed the genetic distances between pairs of accessions, which indicated high variability, with 21.0% of pairs being moderately distant and 78.2% highly distant from each other. Based on 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 was further divided into “traditional cultivars/landraces” (1,879 accessions) or “advanced breeding lines/improved cultivars” (3,027 accessions), and a fourth small group of admixed accessions. Subclusters identifying specific agro-ecology (upland, lowland, mangrove swamp, hydromorphic or floating), originating country or continent, were noted. To form the “AfricaRice O. sativa Core Collection” (AROSCC), 600 (10.5%) of the genotyped and phenotyped O. sativa accessions were selected using the maximum length sub-tree method. This subset captures more than 95% of the SNP polymorphisms in the entire collection. The percentage of accession pairs that were highly distant from each other increased from 78.2% to 92.3% in this core collection, indicating the AROSCC has avoided most of the similar pairs of accessions. The AROSCC includes 400 Indica (AROSCC-indica) and 200 Japonica (AROSCC-japonica) accessions, representing 7.96% and 27.97%, respectively, of each genotyped subspecies and 18 Indica accessions classified as “Admixed” based on the neighbor-joining tree analysis. The most prevalent germplasm type in both the AROSCC-indica and AROSCC-japonica accessions were the more variable traditional cultivars and landraces, which included 218 and 134 accessions of the 400 and 200 total accessions, respectively. The African continent was most heavily represented in both AROSCC-indica and japonica accessions with 306 and 148 African accessions, respectively. The AROSCC is a well characterized and important resource to support pre-breeding and rice improvement programs around the world.