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Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean

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The Co - x anthracnose R gene of common bean was fine-mapped into a 58 kb region at one end of chromosome 1, where no canonical NB-LRR-encoding genes are present in G19833 genome sequence.

Abstract

Anthracnose, caused by the phytopathogenic fungus Colletotrichum lindemuthianum, is one of the most damaging diseases of common bean, Phaseolus vulgaris. Various resistance (R) genes, named Co-, conferring race-specific resistance to different strains of C. lindemuthianum have been identified. The Andean cultivar JaloEEP558 was reported to carry Co-x on chromosome 1, conferring resistance to the highly virulent strain 100. To fine map Co-x, 181 recombinant inbred lines derived from the cross between JaloEEP558 and BAT93 were genotyped with polymerase chain reaction (PCR)-based markers developed using the genome sequence of the Andean genotype G19833. Analysis of RILs carrying key recombination events positioned Co-x at one end of chromosome 1 to a 58 kb region of the G19833 genome sequence. Annotation of this target region revealed eight genes: three phosphoinositide-specific phospholipases C (PI-PLC), one zinc finger protein and four kinases, suggesting that Co-x is not a classical nucleotide-binding leucine-rich encoding gene. In addition, we identified and characterized the seven members of common bean PI-PLC gene family distributed into two clusters located at the ends of chromosomes 1 and 8. Co-x is not a member of Co-1 allelic series since these two genes are separated by at least 190 kb. Comparative analysis between soybean and common bean revealed that the Co-x syntenic region, located at one end of Glycine max chromosome 18, carries Rhg1, a major QTL contributing to soybean cyst nematode resistance. The PCR-based markers generated in this study should be useful in marker-assisted selection for pyramiding Co-x with other R genes.

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Acknowledgments

The research was supported by INRA, CNRS, IFR87 and IDEEV.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

All experiments described in this manuscript comply with the current laws of the country in which they were performed.

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Authors and Affiliations

  1. CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), Rue Noetzlin, 91405, Orsay, France

    Manon M. S. Richard, Stéphanie Pflieger, Mireille Sévignac, Vincent Thareau, Sophie Blanchet & Valérie Geffroy

  2. Univ Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France

    Stéphanie Pflieger

  3. Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics, and Genomics, University of Georgia, Athens, GA, 30602, USA

    Yupeng Li & Scott A. Jackson

  4. INRA, Unité Mixte de Recherche de Génétique Végétale, IDEEV FR3284, Université Paris Sud, Ferme du Moulon, 91190, Gif-sur-Yvette, France

    Valérie Geffroy

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  1. Manon M. S. Richard
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  2. Stéphanie Pflieger
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Correspondence to Valérie Geffroy.

Additional information

Communicated by David A. Lightfoot.

Electronic supplementary material

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122_2014_2328_MOESM1_ESM.pdf

Fig. S1 Fine mapping of Co-x and annotation of target region. a Physical map of Co-x region and graphical genotypes of RILs in which recombination occured between markers M5 and CV542014. Light grey and dark grey bars represent genomic regions derived from BAT93 and JaloEEP558, respectively. Phenotypes of resistance (R) and suceptibility (S) of RILs to C. lindemuthianum strain 100 are indicated below. For each RIL, a black arrow indicates the genetic interval carrying the inferred recombination breakpoint, represented by light/dark grey hatched motif. Location and name of markers are indicated on the left, in black when they are polymorphic and in grey when they are not polymorphic. b Annotation of the Co-x 58-kb target region between markers P05 and K06 in G19833. Predicted candidate genes for Co-x resistance are indicated by black or hatched arrows, for full-length and truncated genes, respectively. Loci names according to www.phytozome.net and putative gene function are indicated on the right. Location and name of markers are indicated on the right, in black when they are polymorphic and in grey when they are not polymorphic. (PDF 183 kb)

122_2014_2328_MOESM2_ESM.pdf

Fig. S2 Multiple sequence alignment of P. vulgaris PI-PLC gene products. The conserved PI-PLC-X, PI-PLC-Y and C2 domains are indicated below the alignment. (PDF 100 kb)

122_2014_2328_MOESM3_ESM.pptx

Fig. S3 Semi-quantitative RT-PCR analysis of the expression pattern of Co-x candidate genes during infection kinetics on JaloEEP558, at 24, 48, 72 and 96 h post infection (hpi), with an avirulent strain (strain 100) and a virulent strain (strain C531) of Colletotrichum lindemuthianum. Ubiquitine was used as an internal control to standardize cDNA input. (PPTX 1807 kb)

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Richard, M.M.S., Pflieger, S., Sévignac, M. et al. Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean. Theor Appl Genet 127, 1653–1666 (2014). https://doi.org/10.1007/s00122-014-2328-5

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