The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira1,2,14,
- Eshan Sharma3,14,
- Shradha Saraf2,14,
- Guy Naamati2,
- Parul Gupta4,
- Justin Elser4,
- Dmytro Chebotarov5,
- Kapeel Chougule6,
- Zhenyuan Lu6,
- Sharon Wei6,
- Andrew Olson6,
- Ian Tsang7,8,
- Disha Lodha2,
- Yong Zhou9,
- Zhichao Yu10,
- Wen Zhao10,
- Jianwei Zhang10,
- Sandeep Amberkar3,
- Kawinnat Sue-Ob3,
- Zhi Sun11,
- Maria Martin2,
- Kenneth L. McNally5,
- Doreen Ware6,12,
- Eric W. Deutsch11,
- Dario Copetti13,
- Rod A. Wing9,13,
- Pankaj Jaiswal4,
- Sarah Dyer2 and
- Andrew R. Jones3
- 1Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei–Consejo Superior de Investigaciones Científicas, 50059, Zaragoza, Spain;
- 2European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom;
- 3University of Liverpool, Institute of Systems, Molecular and Integrative Biology, Liverpool L69 7ZB, United Kingdom;
- 4Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- 5International Rice Research Institute (IRRI), Los Baños, 4031 Laguna, Philippines;
- 6Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 7NIAB, Cambridge CB3 0LE, United Kingdom;
- 8University of Nottingham, Department of Plant Science, Nottingham LE12 5RD, United Kingdom;
- 9Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
- 10National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
- 11Institute for Systems Biology, Seattle, Washington 98109, USA;
- 12USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, New York 14853, USA;
- 13Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona 85721, USA
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↵14 These authors contributed equally to this work.
Abstract
The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent the japonica, indica, aus, and aromatic varietal groups. The RPRP has been consistently annotated and supported by extensive experimental data, and here, we report the computational assignment, characterization, and dissemination of stably identified pangenes, collectively called the PanOryza data set. We identify 25,178 core pangenes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains, and AlphaFold structures, whereas cultivar-specific genes are enriched for domains under selective breeding pressure, such as for disease resistance. We identify more than 5000 genes absent in the IRGSP rice reference genome and present in at least two other Oryza cultivars. We demonstrate the utility of this resource through various examples of pangenes and their protein domains. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware “reference guide” across rice genomes, advancing both basic and applied research.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.280790.125.
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Freely available online through the Genome Research Open Access option.
- Received April 16, 2025.
- Accepted September 29, 2025.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
