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Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus

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Abstract

Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is the main disease affecting soybean in Brazil. This study aimed at investigating and mapping the resistance of the PI 594756 to P. pachyrhizi, by using Bulked Segregant Analysis (BSA). The PI 594756 and the susceptible PI 594891 were crossed and the resulting F2 and F2:3 populations (208 and 1770 plants, respectively) were tested against ASR. Also, these PIs and differential varieties were tested against a panel of monosporic isolates. Plants presenting tan lesions were classified as susceptible (S) while plants presenting reddish-brown (RB) lesions were classified as resistant. DNA bulks were genotyped with Infinium BeadChips and the genomic region identified was further analyzed in the F2 individuals with target GBS (tGBS). PI 594,56 presented a unique resistance profile compared to the differential varieties. The resistance was monogenic dominant; however, it was classified as incompletely dominant when quantitatively studied. Genetic and QTL mapping placed the PI 594756 gene between the genomic region located at 55,863,741 and 56,123,516 bp of chromosome 18. This position is slightly upstream mapping positions of Rpp1 (PI 200492) and Rpp1-b (PI 594538A). Finally, we performed a haplotype analysis in a whole genomic sequencing-SNP database composed of Brazilian historical germplasm and sources of Rpp genes. We found SNPs that successfully differentiated the new PI 594756 allele from Rpp1 and Rpp1-b sources. The haplotype identified can be used as a tool for marker-assisted selection (MAS).

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Data availability

All phenotypic and genotypic data is provided in the supplementary material. Re-sequencing data is part of a Genome Wide Association Study still not published. Nonetheless, it can be partially available through direct contact to the corresponding author Dra. Francismar C. Marcelino-Guimarães by email: francismar.marcelino@embrapa.br.

Code availability

Codes used in the study are available in the corresponding references and also through direct contact to the corresponding author Dra. Francismar C. Marcelino-Guimarães by email: francismar.marcelino@embrapa.br.

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Acknowledgements

We would like to acknowledge Adriana Santos, Ana Maria Avelino, Allan Flausino, Marcia Kuwaraha, and Rogério Omura at Embrapa Soybean for providing technical support in greenhouse assays and genotyping support in the Laboratory of Plant Biotechnology and Laboratory of Molecular Genetics and Marker Assisted Selection. We would also like to acknowledge David Silva and Rafaella Bissi for helping in the phenotyping assays.

Funding

This work was funded by Brazilian Agricultural Research Corporation (EMBRAPA) (20.18.01.010.00.00) and National Council for the Improvement of Higher Education (CAPES) – Finance code 001 for a scholarship to Luciane Barros.

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Contributions

Luciane Barros conducted and reported all mapping experiments and helped in writing the manuscript. Bruna Avelino helped in conducting all mapping experiments and the comparative testing of the level of resistance against pure pathotypes. Danielle Silva provided oversight for experiments, interpreted the results, and helped in writing the manuscript. Everton Ferreira designed the line graphs and helped in mapping and haplotype analysis. Carlos Arias provided crosses and populations, and revised the manuscript. Fernanda Castanho conducted the comparative testing of the level of resistance against pure pathotypes. Marcio Ferreira provided SoySNP6K Infinium Chips results. Valeria Lopes-Caitar processed the re-sequencing data to variant calling file. Silvana Marin oversighted SSR analyses. Ricardo Abdelnoor revised the manuscript and English language adequacy. Ivani Lopes helped in statistical interpretation and English language adequacy. Francismar Guimarães designed the project, supervised the study, approved funding, helped in writing and edited the manuscript.

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Correspondence to Francismar C. Marcelino-Guimarães.

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Barros, L.G., Avelino, B.B., da Silva, D.C.G. et al. Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus. Mol Breeding 43, 12 (2023). https://doi.org/10.1007/s11032-023-01358-4

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  • DOI: https://doi.org/10.1007/s11032-023-01358-4

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