Abstract
Key message
The genetic architecture of resistance to Cercospora janseana was examined, and a single resistance locus was identified. A SNP marker was identified and validated for utilization in U.S. breeding germplasm
Abstract
Cercospora janseana (Racib.) is a fungal pathogen that causes narrow brown leaf spot (NBLS) in rice. Although NBLS is a major disease in the southern United States and variation in resistance among U.S. rice germplasm exists, little is known about the genetic architecture underlying the trait. In this study, a recombinant inbred line population was evaluated for NBLS resistance under natural disease infestation in the field across three years. A single, large-effect QTL, CRSP-2.1, was identified that explained 81.4% of the phenotypic variation. The QTL was defined to a 532 kb physical interval and 13 single nucleotide polymorphisms (SNPs) were identified across the region to characterize the haplotype diversity present in U.S. rice germplasm. A panel of 387 U.S. rice germplasm was genotyped with the 13 haplotype SNPs and phenotyped over two years for NBLS resistance. Fourteen haplotypes were identified, with six haplotypes accounting for 94% of the panel. The susceptible haplotype from the RIL population was the only susceptible haplotype observed in the U.S. germplasm. A single SNP was identified that distinguished the susceptible haplotype from all resistant haplotypes, explaining 52.7% of the phenotypic variation for NBLS resistance. Pedigree analysis and haplotype characterization of historical germplasm demonstrated that the susceptible haplotype was introduced into Southern U.S. germplasm through the California line L-202 into the Louisiana variety Cypress. Cypress was extensively used as a parent over the last 25 years, resulting in the susceptible CRSP-2.1 allele increasing in frequency from zero to 44% in the modern U.S. germplasm panel.
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Data availability
Datasets supporting the results are included as supplemental files.
Abbreviations
- Hap:
-
Haplotype
- SNP:
-
Single nucleotide polymorphism
- Bp:
-
Base pair
- QTL:
-
Quantitative Trait Loci
- RIL:
-
Recombinant Inbred Line
- CRSP:
-
Cercospora janseana
- DTH:
-
Days to 50% Heading
- NBLS:
-
Narrow brown leaf spot
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Acknowledgements
Jovanny Zabaleta, Department of Pediatrics, LSUHSC-New Orleans, processed the Illumina C7AIR array genotype data. Seed of the MY2 mapping population and other historical germplasm were originally obtained from the USDA-GSOR in Stuttgart, AR. Jennifer Dartez for technical contributions in the SNP genotyping. Valerie Dartez for helpful contributions in the manuscript preparation and proofreading. Diane Wang and Susan McCouch for valuable manuscript suggestions and comments. Karen Bearb, Corey Conner, Gavin Guidry, and Brady Williams for field and project support. Raul Guerra assistance with data analysis and R scripts.
Funding
The research project was supported in part by the Louisiana Rice Research Board, the USDA National Institute of Food and Agriculture, and the US National Science Foundation.
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CKA and ANF designed the experiments, coordinated research activities, analyzed the data, and wrote the manuscript. CKA conducted the field phenotyping, managed seed and materials, and conducted literature review. TC developed the MPA/B populations and analyzed the marker data involving the two populations. BA conducted all genotyping, managed the germplasm panel, and edited the manuscript. DEG. rated the RIL population for NBLS and supervised NBLS phenotyping methods. JKR rated the MPA/B populations and edited the manuscript. SDL coordinated field experiments and contributed to the pedigree analysis.
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Communicated by Yunbi Xu.
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Addison, C.K., Angira, B., Cerioli, T. et al. Identification and mapping of a novel resistance gene to the rice pathogen, Cercospora janseana. Theor Appl Genet 134, 2221–2234 (2021). https://doi.org/10.1007/s00122-021-03821-2
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DOI: https://doi.org/10.1007/s00122-021-03821-2