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Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean

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Linkage and genome-wide association analyses using high-throughput SNP genotyping revealed different loci controlling resistance to different isolates of race 65 of Colletotrichum lindemuthianum in common bean.

Abstract

Development of varieties with durable resistance to anthracnose is a major challenge in common bean breeding programs because of the extensive virulence diversity of Colletotrichum lindemuthianum fungus. We used linkage and genome-wide association analyses to tap the genomic regions associated with resistance to different isolates of race 65. Linkage mapping was done using an F2 population derived from the cross between the Mesoamerican common beans BRS Estilo x Ouro Vermelho, inoculated with two different isolates of race 65. Association genetics relied on a diversity common bean panel containing 189 common bean accessions inoculated with five different isolates of race 65 as an attempt to validate the linkage analysis findings and, eventually, identify other genomic regions associated with resistance to race 65. The F2 population and diversity panel were genotyped with the BARCBean6K_3 Illumina BeadChip containing 5398 SNP markers. Both linkage and genome-wide association analyses identified different loci controlling resistance to different isolates of race 65 on linkage group Pv04. Genome-wide association analysis also detected loci on Pv05, Pv10 and Pv11 associated with resistance to race 65. These findings indicate that resistance to race 65 can be overcome by the virulence diversity among different isolates of the same race and could lead to the loss of resistance after cultivar release. We identified 25 resistant common bean cultivars to all five isolates of race 65 in the diversity panel. The accessions should be useful to develop cultivars combining different resistance genes that favor durable resistance to anthracnose in common bean.

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Acknowledgements

The authors are grateful to the following Brazilian funding agencies: Coordenadoria de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and Fundação de Apoio à Pesquisa do Estado de Minas Gerais (FAPEMIG). This research was also supported by the US Department of Agriculture, Agriculture Research Service, USA, and by EMBRAPA–Brazilian Corporation for Agricultural Research.

Funding

This study was funded by Coordenadoria de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (grant number: 88881.131945/2016–01) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grant number: 140589/2015–5).

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Author notes

  1. Oscar P. Hurtado-Gonzales

    Present address: Plant Germplasm Quarantine Program, USDA-APHIS, BARC-East, Beltsville, MD, 20705, USA

Authors and Affiliations

  1. Department of Biology, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil

    Larissa Carvalho Costa, Mariana Andrade Dias & Elaine Aparecida de Souza

  2. Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, São Paulo, Brazil

    Rafael Storto Nalin

  3. Plant Genetics Laboratory, EMBRAPA–Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil

    Márcio Elias Ferreira

  4. Soybean Genomics and Improvement Laboratory, USDA-ARS, BARC-West, Beltsville, MD, 20705, USA

    Qijian Song, Marcial A. Pastor-Corrales & Oscar P. Hurtado-Gonzales

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  1. Larissa Carvalho Costa
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Contributions

Conceived and designed the experiments: LCC RSN MAD MEF QS MAPC OPHG EAS. Performed the experiments: LCC RSN MAD. Analyzed the data: LCC RSN MEF QS EAS. Contributed reagents/materials/analysis tools: LCC RSN MEF QS EAS. Wrote the paper: LCC RSN MAD MEF QS MAPC OPHG EAS.

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Correspondence to Elaine Aparecida de Souza.

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Communicated by Janila Pasupuleti.

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Costa, L.C., Nalin, R.S., Dias, M.A. et al. Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean. Theor Appl Genet 134, 543–556 (2021). https://doi.org/10.1007/s00122-020-03713-x

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