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Saturation of genomic region implicated in resistance to Fusarium oxysporum f. sp. ciceris race 5 in chickpea

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Abstract

Fusarium oxysporum f. sp. ciceris (Foc) is the major soilborne fungus affecting chickpea and race 5 (Foc5) is the most important in the Mediterranean basin. A gene controlling resistant reaction to Foc5 has been located on LG2 of the chickpea genetic map forming a cluster with resistance genes to other Foc races. The sequence-tagged microsatellite site (STMS) marker TA59 is tightly linked to this genomic region. In the current study, our aim was to look for candidate genes related to resistance to Foc5 starting from the physical position of TA59 and taking advantage of the whole chickpea genome sequence information. We selected a set of markers, covering a region of around 25 Mbp that were genotyped in near-isogenic lines and recombinant inbred lines. Joining data of different plant materials, it was possible to define an area of approximately 820 Kbp. One of the 26 genes annotated in the selected region (LOC101511605) could be considered a candidate gene for its possible implication in resistance reactions. Single-nucleotide polymorphism (SNP) markers selected in the target region were used to screen a collection of 32 genotypes differing in their reactions to Foc5. A cluster analysis showed four main groups, three of them grouping the resistant genotypes and the fourth one, the susceptible lines. The comparison between the haplotypes of representative accessions for each cluster allowed the identification of six SNPs coincident among resistant lines and different from the susceptible lines. These SNPs could be used in marker-assisted selection.

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Acknowledgements

Caballo C. acknowledges her Ph.D. fellowship INIA-CCAA. The author thankfully acknowledges the computer resources, technical expertise, and assistance provided by the SCBI (Supercomputing and Bioinformatics) center of the University of Malaga.

Author contribution statement

GJ, RJ, and MT conceived and designed the experiment. CC and ME performed the experiments. WC provided re-sequencing data and analysis. RJ and MT contributed materials and phenotypic analysis. JG designed the statistical analysis performed by CC. CC, ME, GJ, RJ, and MT wrote the manuscript that was reviewed by WC.

Funding

This work has been supported by INIA project RTA2017-00041-00-00 (co-financed by the European Union through the ERDF2014–2020 “Programa Operativo de Crecimiento Inteligente”) and PP.AVA.AVA201601.17.

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Authors and Affiliations

  1. Área de Genómica y Biotecnología, IFAPA, 14080, Córdoba, Spain

    C. Caballo & J. Rubio

  2. Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany

    E. Madrid

  3. ETSIAM-Dpto. Genética, Universidad de Córdoba, Campus de Rabanales, 14071, Córdoba, Spain

    J. Gil & T. Millan

  4. Grain Legume Genetics and Physiology Research Unit, USDA-ARS, Washington State University, Pullman, WA, 99164, USA

    W. Chen

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  1. C. Caballo
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  2. E. Madrid
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  3. J. Gil
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  5. J. Rubio
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Correspondence to C. Caballo.

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Key message

We report fine mapping to define an area related whit Foc5 including a putative candidate gene. Six SNPs coincident in resistant lines were proposed to be used in MAS.

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Caballo, C., Madrid, E., Gil, J. et al. Saturation of genomic region implicated in resistance to Fusarium oxysporum f. sp. ciceris race 5 in chickpea. Mol Breeding 39, 16 (2019). https://doi.org/10.1007/s11032-019-0932-4

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