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Genotyping-by-Sequencing enabled mapping and marker development for the By-2 potyvirus resistance allele in Common bean.

Hart, J. P., & Griffiths, P. D. (2015). The Plant Genome doi:10.3835/plantgenome2014.09.0058

Paper summary

Use of genotyping-by-sequencing (GBS) and genome-wide association study (GWAS) for the first time in common bean to identify SNPs (single nucleotide polymorphisms) associated with Bean yellow mosaic virus resistance (mediated by By-2). Following SNP discovery, informative SNPs were converted into KASP genotyping assays to produce a robust set of allele-specific molecular markers for rapid and cost-effective marker-assisted selection (MAS) for By-2 in common bean crop lines.

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Highlights of the paper

  • SNP discovery in Common bean using GBS and GWAS
  • Conversion of GBS data to KASP allele-specific molecular marker assays
  • KASP assays validated to enable rapid and cost-effective MAS for By-2.


There is an urgent need for cultivars resistant to Bean yellow mosaic virus, a devastating crop pest in Common bean conditioned by the dominant resistance allele By-2. The current absence of commercial cultivars with resistance to prevalent viruses such as this leaves the valuable snap bean crop vulnerable to yield losses.
In this paper, GBS was used to discover potentially informative SNPs in a set of recombinant inbred lines derived from an introgression program. This approach delivered a set of highly informative SNPs linked to the resistance phenotype which could then be used for marker-assisted selection as part of commercial crop improvement programmes. This study illustrates the utility of KASP to complement GBS and GWAS for precision breeding.

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Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean. Bello, M. H., Moghaddam, S. M., Massoudi, M., McClean, P. E., Cregan, P. B., & Miklas, P. N. (2014). BMC genomics, 15(1), 903.

Common bean is a great example of the benefits of using MAS to generate improved crop lines carrying major disease resistance genes.
This paper demonstrates the utility of a novel, in silico BSA approach to initial SNP discovery, using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNPs at a specific targeted genomic region. Informative SNPs at known resistance loci are then targeted for conversion to co dominant KASP and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study.