Maximizing the potential of African O. sativa Rice through the creation of an Africa Rice O. sativa Core Collection (AROSCC)

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: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/21/2022
Publication Date: 1/1/2023
Citation: Eizenga, G.C., Ndjiondjop, M., Warburton, M.L., Gouda, A.C., Kpeki, S.B., Wambugu, P.W., Gnikoua, K., Tia, D.D. 2023. Maximizing the potential of African O. sativa Rice through the creation of an Africa Rice O. sativa Core Collection (AROSCC). Plant and Animal Genome 30 Conference, San Diego, California. January 13-18, 2023.

Interpretive Summary:

Technical Abstract: Rice (Oryza sativa L.) is grown in 40 of the 54 countries in Africa and is a staple food in West Africa and Madagascar. Africa has a rich diversity of Oryza genetic resources, including both cultivated rice species, O. sativa and O. glaberrima Steud., also called African rice because it is indigenous to the African continent. The AfricaRice genebank holds nearly 22,000 Oryza accessions, with phenotypic traits and passport (origin) information available in public databases (https://www.genesys-pgr.org/). Previously, a mini-core collection of 350 O. glaberrima accessions selected to maximize genetic variation was established from 2,179 accessions genotyped with 3,834 SNP markers. The genebank also 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. From these O. sativa accessions, 5,738 were selected to genotype with DArTseq-based SNP markers; of these, 4,242 (73.9%) of the genotyped accessions originated from African countries. The objectives of this study were to use 25,904 polymorphic SNP markers 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 genetic distances between pairs of accessions indicated high variability, with 78.2% of the pairs being 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. Indica further sub-divided into “traditional cultivars/landraces” (1,879 accessions) and “advanced breeding lines/improved cultivars” (3,027 accessions). A fourth small group of admixed accessions was also identified. Subclusters identifying a specific agro-ecology (upland, lowland, mangrove swamp, hydromorphic or floating) and originating country, were noted. To form the “AfricaRice O. sativa Core Collection” (AROSCC), 600 genotyped accessions were selected using the maximum length sub-tree method. This subset captures >95% of the SNP polymorphisms in the entire collection and the percentage of accession pairs that were highly distant from each other increased to 92.3%. The AROSCC includes 400 Indica (AROSCC-indica) and 200 Japonica (AROSCC-japonica) accessions. 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 total accessions, respectively. The African continent was most heavily represented in both the 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.