Phenotypic variation and the impact of admixture in the Oryza rufipogon Species Complex (ORSC)

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cg.identifier.doihttps://doi.org/10.3389/fpls.2022.787703en
cg.issn1664-462Xen
cg.journalFrontiers in Plant Scienceen
cg.volume13en
dc.contributor.authorEizenga, Georgia C.en
dc.contributor.authorKim, Hyunjungen
dc.contributor.authorJung, Janelle K. H.en
dc.contributor.authorGreenberg, Anthony J.en
dc.contributor.authorEdwards, Jeremy D.en
dc.contributor.authorNaredo, Maria Elizabeth B.en
dc.contributor.authorBanaticla-Hilario, Maria Celeste N.en
dc.contributor.authorHarrington, Sandra E.en
dc.contributor.authorShi, Yuxinen
dc.contributor.authorKimball, Jennifer A.en
dc.contributor.authorHarper, Lisa A.en
dc.contributor.authorMcNally, Kenneth L.en
dc.contributor.authorMcCouch, Susan R.en
dc.date.accessioned2024-12-19T12:53:23Zen
dc.date.available2024-12-19T12:53:23Zen
dc.identifier.urihttps://hdl.handle.net/10568/164059
dc.titlePhenotypic variation and the impact of admixture in the Oryza rufipogon Species Complex (ORSC)en
dcterms.abstractCrop 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.en
dcterms.accessRightsOpen Access
dcterms.available2022-06-13
dcterms.bibliographicCitationEizenga, Georgia C.; Kim, HyunJung; Jung, Janelle K. H.; Greenberg, Anthony J.; Edwards, Jeremy D.; Naredo, Maria Elizabeth B.; Banaticla-Hilario, Maria Celeste N.; Harrington, Sandra E.; Shi, Yuxin; Kimball, Jennifer A.; Harper, Lisa A.; McNally, Kenneth L. and McCouch, Susan R. 2022. Phenotypic variation and the impact of admixture in the Oryza rufipogon Species Complex (ORSC). Front. Plant Sci., Volume 13en
dcterms.issued2022-06-13
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherFrontiers Mediaen
dcterms.subjectplant scienceen
dcterms.typeJournal Article

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