Comparative genome assemblies reveal distinct allelic and structural variation at blast resistance loci in rice CT21375-F4-4and Moroberekan
5 affiliations
- 1Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA.
- 2Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
- 3CIAT, Crops for Nutrition and Health, Cali, Colombia.
- 4Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- 5CIRAD, Montpellier, France.
Abstract
Rice blast, caused by Magnaporthe oryzae, remains a major constraint to rice (Oryza sativa L.) production, and durable resistance will require broader use of genetic diversity beyond commonly studied elite cultivars. We present chromosome-scale genome assemblies of two agronomically significant but genetically divergent rice cultivars: CT21375-F4-4 (hereafter, CT21) and Moroberekan. Despite their genetic divergence, both cultivars show consistently strong resistance to blast under multiyear field conditions. We combined field phenotyping with genome-wide protein-to-genome alignment, predicted proteome comparisons, nucleotide-binding leucine-rich repeat (NLR) annotation, and locus-specific analyses of cloned blast resistance genes to examine resistance-associated genomic variation in these cultivars. The cultivars contained similar numbers and overall subtype compositions of NLR loci, but differed markedly in their correspondence to characterized blast resistance genes. CT21 contained multiple exact or near-exact matches to cloned blast resistance genes and alleles, whereas Moroberekan contained fewer exact matches and was characterized predominantly by high-identity but divergent homologs, suggesting the presence of divergent alleles or resistance architectures that are not well represented by the cloned gene repertoire. Locus-specific analyses further confirmed that high sequence similarity alone does not reliably predict resistance function, and revealed structural variation, including duplication within the Pish NLR cluster in CT21. These results demonstrate that comparable blast resistance phenotypes can occur in cultivars with distinct allelic and structural architectures at known resistance loci. The assemblies and comparative framework developed here provide resources for identifying resistance diversity that may be overlooked by reference gene or marker-based analyses and for prioritizing candidate loci for functional validation and rice improvement.
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BibTeX
@article{martin2026comparative,
title = {{Comparative genome assemblies reveal distinct allelic and structural variation at blast resistance loci in rice CT21375-F4-4and Moroberekan}},
author = {Federico Martin and Jorge Duitama and Manuel Narvaez and Alvaro L Perez-Quintero and Constanza Quintero and Kamal Neupane and Duvan S Bonilla and Camila Rebolledo Cid and M Fernanda Alvarez and Gloria M Mosquera and Jan E Leach},
journal = {Plant Genome},
year = {2026},
month = oct,
doi = {10.1002/tpg2.70328},
url = {https://hal.science/hal-05841564v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Comparative genome assemblies reveal distinct allelic and structural variation at blast resistance loci in rice CT21375-F4-4and Moroberekan
AU - Federico Martin
AU - Jorge Duitama
AU - Manuel Narvaez
AU - Alvaro L Perez-Quintero
AU - Constanza Quintero
AU - Kamal Neupane
AU - Duvan S Bonilla
AU - Camila Rebolledo Cid
AU - M Fernanda Alvarez
AU - Gloria M Mosquera
AU - Jan E Leach
PY - 2026
DA - 2026/10/19
JO - Plant Genome
DO - 10.1002/tpg2.70328
UR - https://hal.science/hal-05841564v1
AB - Rice blast, caused by Magnaporthe oryzae, remains a major constraint to rice (Oryza sativa L.) production, and durable resistance will require broader use of genetic diversity beyond commonly studied elite cultivars. We present chromosome-scale genome assemblies of two agronomically significant but genetically divergent rice cultivars: CT21375-F4-4 (hereafter, CT21) and Moroberekan. Despite their genetic divergence, both cultivars show consistently strong resistance to blast under multiyear field conditions. We combined field phenotyping with genome-wide protein-to-genome alignment, predicted proteome comparisons, nucleotide-binding leucine-rich repeat (NLR) annotation, and locus-specific analyses of cloned blast resistance genes to examine resistance-associated genomic variation in these cultivars. The cultivars contained similar numbers and overall subtype compositions of NLR loci, but differed markedly in their correspondence to characterized blast resistance genes. CT21 contained multiple exact or near-exact matches to cloned blast resistance genes and alleles, whereas Moroberekan contained fewer exact matches and was characterized predominantly by high-identity but divergent homologs, suggesting the presence of divergent alleles or resistance architectures that are not well represented by the cloned gene repertoire. Locus-specific analyses further confirmed that high sequence similarity alone does not reliably predict resistance function, and revealed structural variation, including duplication within the Pish NLR cluster in CT21. These results demonstrate that comparable blast resistance phenotypes can occur in cultivars with distinct allelic and structural architectures at known resistance loci. The assemblies and comparative framework developed here provide resources for identifying resistance diversity that may be overlooked by reference gene or marker-based analyses and for prioritizing candidate loci for functional validation and rice improvement.
SN - 1940-3372
SN - 1940-3372
ER -