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Zheng X, Ratnasekera D, Fan J, Henry RJ, Song BK, Olsen KM, Joshi BK, Banaticla-Hilario MCN, Pusadee T, Melaku AG, Estelle Loko YL, Vilayheuang K, Oppong GK, Poku SA, Wambugu PW, Ge S, Junior AM, Aung OM, Venuprasad R, Kohli A, Zhou W, Qian Q. Global wild rice germplasm resources conservation alliance: World Wild-Rice Wiring. Mol Plant 2024; 17:516-518. [PMID: 38444157 DOI: 10.1016/j.molp.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/07/2024]
Affiliation(s)
- Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing 100081, China; International Rice Research Institute, DAPO Box 7777, Metro Manila 4031, Philippines.
| | - Disna Ratnasekera
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Matara 81000, Sri Lanka
| | - Jiayu Fan
- Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China; Hainan University, Haikou 570228, China
| | - Robert J Henry
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD 4072, Australia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor 47500, Malaysia
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130-4899, USA
| | - Bal Krishna Joshi
- National Agriculture Genetic Resources Center (Genebank), Khumaltar, PO Box 3055, Kathmandu, Nepal
| | - Maria Celeste N Banaticla-Hilario
- Plant Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines
| | - Tonapha Pusadee
- Division of Agronomy, Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Yêyinou Laura Estelle Loko
- National University of Sciences, Technologies, Engineering and Mathematics (UNSTIM), Dassa-Zoumé BP 14, Benin
| | - Koukham Vilayheuang
- National Genebank, Rice and Cash Crops Research Center, NAFRI, Vientiane 0605, Lao PDR
| | - Gavers K Oppong
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden AL5 2JQ, UK; UK Future Food Beacon of Excellence and School of Biosciences and University of Nottingham, Nottingham LE12 5RD, UK
| | - Samuel Aduse Poku
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, Nairobi 00200, Kenya
| | - Song Ge
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Aldo Merotto Junior
- Federal University of Rio Grande do Sul, UFRGS, Porto Alegre 91501-970, RS, Brazil
| | - Ohn Mar Aung
- Department of Agricultural Research, Yezin, Zayarthiri Township, Nay Pyi Taw, Myanmar
| | | | - Ajay Kohli
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Wenbin Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Qian
- Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Yazhouwan National Laboratory, No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Eizenga GC, Kim H, Jung JKH, Greenberg AJ, Edwards JD, Naredo MEB, Banaticla-Hilario MCN, Harrington SE, Shi Y, Kimball JA, Harper LA, McNally KL, McCouch SR. Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex ( ORSC). Front Plant Sci 2022; 13:787703. [PMID: 35769295 PMCID: PMC9235872 DOI: 10.3389/fpls.2022.787703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
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.
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Affiliation(s)
- Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Janelle K. H. Jung
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | | | | | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Jennifer A. Kimball
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Lisa A. Harper
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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Banaticla-Hilario MCN, van den Berg RG, Hamilton NRS, McNally KL. Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon. Ecol Evol 2013; 3:3047-62. [PMID: 24101993 PMCID: PMC3790550 DOI: 10.1002/ece3.689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/17/2013] [Accepted: 06/23/2013] [Indexed: 11/11/2022] Open
Abstract
Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
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Affiliation(s)
- Maria Celeste N Banaticla-Hilario
- T.T. Chang Genetic Resources Center, International Rice Research Institute Los Baños, Laguna, Philippines ; Biosystematics Group, Wageningen University and Research Center Wageningen, The Netherlands
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