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A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean

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Clover yellow vein virus (ClYVV) is capable of causing severe damage to common bean (Phaseolus vulgaris L.) production worldwide. The snap bean market class is particularly vulnerable because infection may lead to distortion and necrosis of the fresh green pods and rejection of the harvest. Three putatively independent recessive genes (cyv, desc, bc-3) have been reported to condition resistance to ClYVV; however, their allelic relationships have not been resolved. We identified, evaluated, and characterized the phenotypic and molecular genetic variation present in 21 informative common bean genotypes for resistance to ClYVV. Allelism testing phenotypes from multiple populations provided clear evidence that the three genes were a series of recessive alleles at the Bc-3 locus that condition unique potyvirus strain- and species-specific resistance spectra. Candidate gene analysis revealed complete association between the recessive resistance alleles and unique patterns of predicted amino acid substitutions in P. vulgaris eukaryotic translation initiation factor 4E (PveIF4E). This led to the discovery and characterization of two novel PveIF4E alleles associated with resistance to ClYVV, PveIF4E 3, and PveIF4E 4. We developed KASPar allele-specific SNP genotyping assays and demonstrated their ability to accurately detect and differentiate all of the PveIF4E haplotypes present in the germplasm, allelism testing, and in three separate segregating populations. The results contribute to an enhanced understanding and accessibility of the important potyvirus resistance conditioned by recessive alleles at Bc-3. The KASPar assays should be useful to further enable germplasm exploration, allelic discrimination, and marker-assisted introgression of bc-3 alleles in common bean.

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The authors wish to thank James Kelly, Phil Miklas, Elise Vendeuvre, and Molly Welsh for provision of bean germplasm. A special thanks is due to Jason Cavatorta for his initial assistance with preliminary research and Michael Mazourek for providing laboratory space. We acknowledge the technical assistance of Matt Wavrick, and Sarah Durkee. We also thank two anonymous reviewers whose suggestions helped to improve the manuscript. This research was supported through funding from the New York State Vegetable Research Association. John Hart was provided with support from Pioneer Hi-Bred Intl. through Cornell University’s Department of Plant Breeding and Genetics, a Cornell Graduate School Fellowship, and the Bullis Fellowship of the NYSAES.

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Correspondence to Phillip D. Griffiths.

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The GenBank accession numbers for the sequences reported in this paper are KC417354-KC417372.

Communicated by B. Hulke.

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Hart, J.P., Griffiths, P.D. A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean. Theor Appl Genet 126, 2849–2863 (2013).

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  • Common Bean
  • Allelism Testing
  • Bean Common Mosaic Virus
  • Snap Bean
  • Recessive Resistance