Exploring relationships between phenotypic groups and genotypic subpopulations in ancestral rice, the Oryza rufipogon Species Complex (ORSC)

Authors: Eizenga, Georgia; KIM, HYUN-JUNG - Cornell University; JUNG, JANELLE - Cornell University; MCNALLY, KENNETH - International Rice Research Institute; GREENBERG, ANTHONY - Bayesic Research; Edwards, Jeremy; NAREDO, ELIZABETH - International Rice Research Institute; BANATICLA-HILARIO, CELESTE - International Rice Research Institute; HARRINGTON, SANDRA - Cornell University; SHI, YUXIN - Cornell University; KIMBALL, JENNIFER - University Of Minnesota; HARPER, LISA - Cornell University; MCCOUCH, SUSAN - Cornell University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/7/2022
Publication Date: 1/7/2022
Citation: Eizenga, G.C., Kim, H., Jung, J., McNally, K.L., Greenberg, A.J., Edwards, J., Naredo, E.B., Banaticla-Hilario, C.N., Harrington, S.E., Shi, Y., Kimball, J.A., Harper, L.A., McCouch, S.R. 2022. Exploring relationships between phenotypic groups and genotypic subpopulations in ancestral rice, the Oryza rufipogon Species Complex (ORSC). Abstract. Plant and Animal Genome Conference. San Diego, California. January 8-12, 2022.

Interpretive Summary:

Technical Abstract: The wild progenitors of Asian cultivated rice (Oryza sativa L.), O. rufipogon and O. nivara, often referred to as the Oryza rufipogon species complex (ORSC), are a valuable reservoir of novel variation for breeding. A collection of 240 diverse ORSC accessions from the International Rice Germplasm Collection, previously characterized by genotyping-by-sequencing (GBS) with 113,739 SNPs, was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as passport data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse at Ithaca, New York (16 traits) and Stuttgart, Arkansas, USA (18 traits). We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data (32 traits) and ascertained three phenotype-based group assignments. We used concordance between the previously reported six genotypic subpopulations based on GBS and newly reported phenotype-based groups to identify a suite of 16 phenotypic traits that can reliably differentiate the ORSC populations. Furthermore, we identified traits, whether measured in tropical or temperate regions, that discriminated the three groups, thus facilitating genebank management of ORSC collections. These phenotypic groups are associated with species designation, life history and mating habit. Two of the phenotypic groups are consistent with traditional species designations, while one, comprising 20% of our collection, harbored highly admixed accessions with >35% introgression from O. sativa and confounds previous species classification.