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

Autor:	Eizenga GC; Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States., Kim H; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States., Jung JKH; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States., Greenberg AJ; Bayesic Research LLC., Ithaca, NY, United States., Edwards JD; Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States., Naredo MEB; International Rice Research Institute, Los Baños, Philippines., Banaticla-Hilario MCN; International Rice Research Institute, Los Baños, Philippines., Harrington SE; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States., Shi Y; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States., Kimball JA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States., Harper LA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States., McNally KL; International Rice Research Institute, Los Baños, Philippines., McCouch SR; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in plant science [Front Plant Sci] 2022 Jun 13; Vol. 13, pp. 787703. Date of Electronic Publication: 2022 Jun 13 (Print Publication: 2022).
DOI:	10.3389/fpls.2022.787703
Abstrakt:	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. Competing Interests: AG is employed by Bayesic Research LLC. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (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.)
Databáze:	MEDLINE
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