Insights from the phenotypic and genotypic characterization of accessions belonging to the Oryza rufipogon Species Complex (ORSC)

Authors: Eizenga, Georgia; KIM, HYUN-JUNG - Cornell University; JUNG, JANELLE - Cornell University; GREENBERG, ANTHONY - Bayesic Research; Edwards, Jeremy; NAREDO, ELIZABETH - University Of The Philippines Los Banos; BANATICLA-HILARIO, CELESTE - University Of The Philippines Los Banos; HARRINGTON, SANDRA - Cornell University; SHI, YUXIN - Cornell University; McClung, Anna; MCNALLY, KENNETH - International Rice Research Institute; MCCOUCH, SUSAN - Cornell University

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., Kim, H., Jung, J., Greenberg, A.J., Edwards, J., Naredo, E.B., Banaticla-Hilario, C.N., Harrington, S.E., Shi, Y., McClung, A.M., McNally, K.L., McCouch, S.R. 2024. Insights from the phenotypic and genotypic characterization of accessions belonging to the Oryza rufipogon Species Complex (ORSC). Proceedings of 39th Rice Technical Working Group meeting, Hot Springs, Arkansas, Feb 20-23, 2023. p. 61-62.

Interpretive Summary:

Technical Abstract: Crop wild relatives are a valuable reservoir of variation for crop improvement, but they are poorly represented in genebanks, their natural habitats are threatened, and most are poorly characterized. This study focuses on the Oryza rufipogon Species Complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC includes perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on morphological, geographical, and/or ecological habitats. The objectives of this study were to 1) understand the relationship between ORSC genotypic subpopulations and phenotypic groups, 2) review ORSC accessions that have been targeted for rice improvement in Arkansas, USA, and 3) clarify the relationship between the genotypic subpopulations identified by two different collections of ORSC accessions. To probe the relationship between genotypic subpopulations and phenotypic groups, a collection of 240 diverse ORSC accessions previously evaluated using genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute (IRRI) in the Philippines. These included highly heritable traits similar to those reported by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, USA. A Bayesian Gaussian mixture model was implemented to infer accession groups from a subset of these phenotypic data and three phenotype-based group assignments (P1, P2/P3, P4) were ascertained. Concurrence between the genotypic subpopulations and phenotypic groups was used to identify a suite of phenotypic traits that could reliably differentiate the ORSC genetic subpopulations. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated) and were largely consistent with genebank species designations. The phenotypic group identified as “P1” contained accessions that were predominantly classified as O. rufipogon, perennial and largely out-crossing. A second group (P4) contained predominantly O. nivara accessions that were characterized as annual and largely inbreeding. The third group (P2/P3) included 20% of the collection and 51.2% of the accessions classified as “Oryza spp.”. This third group was characterized by levels of O. sativa admixture comprising more than 50% of the genome. Nine ORSC accessions from this collection were used to develop mapping populations. Three accessions were selected as donors to develop six interspecific libraries of chromosome segment substitution lines (CSSLs) that are currently being distributed through the Genetic Stocks-Oryza Collection for breeding and basic genetics studies. The three wild donors included an O. rufipogon from Indonesia categorized as P1, an O. nivara from Laos classified as P4, and an O. rufipogon from China belonging to P1. These wild donors were crossed into two elite varieties, Cybonnet, a U.S. tropical japonica and IR64, an indica developed at IRRI. In addition, advanced backcross (ABC) populations were developed using five different wild ORSC donors and used to identify major QTL for sheath blight and blast resistance, as well as seedling vigor. All five of these ORSC donors phenotypically belonged to P4. Finally, ORSC accession, IRGC105491, a highly admixed accession belonging to P2/P3 was used to develop five ABC populations using diverse, elite O. sativa recurrent parents adapted for cultivation in different geographies and ecosystems. In the USA, introgressions in the tropical japonica variety, ‘Jefferson’, resulted in the commercial re