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Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC)
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 A...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235872/ https://www.ncbi.nlm.nih.gov/pubmed/35769295 http://dx.doi.org/10.3389/fpls.2022.787703 |
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author | Eizenga, 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. McCouch, Susan R. |
author_facet | Eizenga, 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. McCouch, Susan R. |
author_sort | Eizenga, Georgia C. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9235872 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-92358722022-06-28 Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) Eizenga, 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. McCouch, Susan R. Front Plant Sci Plant Science 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. Frontiers Media S.A. 2022-06-13 /pmc/articles/PMC9235872/ /pubmed/35769295 http://dx.doi.org/10.3389/fpls.2022.787703 Text en 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. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Eizenga, 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. McCouch, Susan R. Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) |
title | Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) |
title_full | Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) |
title_fullStr | Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) |
title_full_unstemmed | Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) |
title_short | Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex (ORSC) |
title_sort | phenotypic variation and the impact of admixture in the oryza rufipogon species complex (orsc) |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235872/ https://www.ncbi.nlm.nih.gov/pubmed/35769295 http://dx.doi.org/10.3389/fpls.2022.787703 |
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