Phenotypic variation and the impact of admixture in 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 - 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; MCNALLY, KENNETH - International Rice Research Institute; MCCOUCH, SUSAN - Cornell University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2022
Publication Date: 6/13/2022
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., Kimball, J.A., Harper, L.A., Mcnally, K.L., McCouch, S.R. 2022. Phenotypic variation and the impact of admixture in the Oryza rufipogon Species Complex (ORSC). Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.787703.
DOI: https://doi.org/10.3389/fpls.2022.787703

Interpretive Summary: The wild species that crop plants were derived from potentially harbor useful characteristics including tolerance to extremes in climate and plant pests that were lost during domestication. Cultivated rice, Oryza sativa, was domesticated from either of the wild ancestral species, O. rufipogon or O. nivara. Understanding the relationships between different accessions of these wild Oryza species collected from diverse locations and environments would enable rice geneticists and breeders to make selections among diverse O. nivara and/or O. rufipogon accessions in genebanks for introgressing novel genes into new cultivated rice varieties. To this end a “statistical tool” named a “Mixture Model” was developed to group together the wild Oryza species accessions having similar phenotypes (traits). Next, the Mixture Model was tested with a collection of 222 accessions which were previously grouped by genotypes. The phenotypic groups were similar to those based on genotype, thus validating that the Mixture Model can group these ancestral Oryza species based on phenotype. This Mixture Model will aid genebanks in grouping the ancestral Oryza species accessions in their collections by utilizing the phenotypic data already available, thus enhancing the value of the collection. Additionally, having both the genotypic and phenotypic groups will allow genebank managers to determine if accessions are misclassified and have the incorrect species name. The Mixture Model also can be used to group accessions of other crop species based on phenotype, which will enable those requesting accessions in the collection to better select accessions for crop improvement.

Technical Abstract: Crop wild relatives represent valuable reservoirs of novel variation for breeding, but their populations are threatened in declining natural habitats, are sparsely represented in genebanks, and most are poorly characterized. Here we focus on the wild progenitor of Asian rice (Oryza sativa L.), often referred to as the Oryza rufipogon species complex (ORSC). A collection of 240 diverse ORSC accessions, previously characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 43 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 for 14 traits at Ithaca, New York and for 18 traits at Stuttgart, Arkansas, USA. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained four phenotype-based group assignments. We used concordance between the previously reported six genotypic populations and four phenotype-based groups to identify a suite of phenotypic traits that can reliably differentiate the ORSC populations. We further identified traits, whether measured in the tropics or temperate regions, that can discriminate groups and facilitate genebank management of ORSC collections. Phenotypic groups are loosely associated with life history (perenniality versus annuality) and mating habit (self-versus cross-pollinated), and harbor differing levels of introgression from O. sativa.