Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC)

Georgia C. Eizenga, Hyun Jung Kim, Janelle K.H. Jung, Anthony J. Greenberg, Jeremy D. Edwards, Maria Elizabeth B. Naredo, Maria Celeste N. Banaticla-Hilario, Sandra E. Harrington, Yuxin Shi, Jennifer A. Kimball, Lisa A. Harper, Kenneth L. McNally, Susan R. McCouch

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises 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 non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by 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, Philippines. These traits included heritable phenotypes often recorded as characterization data 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, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions 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, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a “pre-breeding” pool for breeders attempting to incorporate novel variation into elite breeding lines.

Original languageEnglish (US)
Article number787703
JournalFrontiers in Plant Science
Volume13
DOIs
StatePublished - Jun 13 2022

Bibliographical note

Funding Information:
This study was funded in part by the National Science Foundation with grants to SRM and GCE (NSF-PGRP nos. 0606461 and 1026555). Mention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by the US Department of Agriculture and does not imply its approval to the exclusion of other products that also can be suitable. The USDA is an equal opportunity provider and employer.

Funding Information:
This study was funded in part by the National Science Foundation with grants to SRM and GCE (NSF-PGRP nos. 0606461 and 1026555). Mention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by the US Department of Agriculture and does not imply its approval to the exclusion of other products that also can be suitable. The USDA is an equal opportunity provider and employer.

Publisher Copyright:
Copyright © 2022 At least a portion of this work is authored by Georgia C. Eizenga and Jeremy D. Edwards on behalf of the U.S. Government and as regards Dr. Eizenga, Dr Edwards and the U.S. Government, is not subject to copyright protection in the United States. Foreign and other copyrights may apply.

Keywords

  • Bayesian Gaussian mixture models
  • crop wild relatives
  • genebank accessions
  • Oryza nivara
  • Oryza rufipogon
  • Oryza rufipogon species complex
  • Oryza sativa
  • rice

PubMed: MeSH publication types

  • Journal Article

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