Discerning the influence of admixture on the genotypic and phenotypic characterization of 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; MCNALLY, KENNETH - International Rice Research Institute; MCCOUCH, SUSAN - Cornell University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/20/2022
Publication Date: 1/1/2023
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., McNally, K.L., McCouch, S.R. 2023. Discerning the influence of admixture on the genotypic and phenotypic characterization of the Oryza rufipogon species complex (ORSC). Plant and Animal Genome 30 Conference, San Diego, California. January 13-18, 2023.

Interpretive Summary:

Technical Abstract: Wild relatives of crop plants are a critical genepool for expanding the diversity of modern cultivars and improving adaption to climate change. The Oryza rufipogon Species Complex (ORSC) is the 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 and 2) 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 like those reported by genebanks. Over 100 of these ORSC accessions also were 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 and mating habit and were largely consistent with genebank species designations. The phenotypic group “P1” contained accessions that were predominantly classified as O. rufipogon, perennial and largely out-crossing. The P4 group contained predominantly O. nivara accessions that were characterized as annual and largely inbreeding. From these groups, 42 “core” O. rufipogon and 25 “core” O. nivara accessions were identified for domestication studies. The third group (P2/P3) included 20% of the collection of which 51.2% were classified as “Oryza spp.”. This group was characterized by levels of O. sativa admixture comprising more than 50% of the genome making it potentially useful as a “pre-breeding” pool to incorporate novel variation into elite breeding lines. Furthermore, selected ORSC donors, previously used to develop introgression lines in in elite O. sativa cultivars, were examined to ascertain their phenotypic and genotypic groupings. The population structure of this collection of ORSC accessions was compared to a previously analyzed collection of 435 ORSC accessions from China using a set of 55,213 SNPs that were shared between the two datasets. This comparison revealed shared genotypic groups that were represented in different proportions in these two different studies and confirmed the confounding effect of admixture with O. sativa when exploring the genetic structure and phenotypic variation of the Oryza rufipogon Species Complex.