Allele-specific CAPS markers based on point mutations in resistance alleles at the pvr1 locus encoding eIF4E in Capsicum
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Marker-assisted selection has been widely implemented in crop breeding and can be especially useful in cases where the traits of interest show recessive or polygenic inheritance and/or are difficult or impossible to select directly. Most indirect selection is based on DNA polymorphism linked to the target trait, resulting in error when the polymorphism recombines away from the mutation responsible for the trait and/or when the linkage between the mutation and the polymorphism is not conserved in all relevant genetic backgrounds. In this paper, we report the generation and use of molecular markers that define loci for selection using cleaved amplified polymorphic sequences (CAPS). These CAPS markers are based on nucleotide polymorphisms in the resistance gene that are perfectly correlated with disease resistance, the trait of interest. As a consequence, the possibility that the marker will not be linked to the trait in all backgrounds or that the marker will recombine away from the trait is eliminated. We have generated CAPS markers for three recessive viral resistance alleles used widely in pepper breeding, pvr1, pvr11, and pvr12. These markers are based on single nucleotide polymorphisms (SNPs) within the coding region of the pvr1 locus encoding an eIF4E homolog on chromosome 3. These three markers define a system of indirect selection for potyvirus resistance in Capsicum based on genomic sequence. We demonstrate the utility of this marker system using commercially significant germplasm representing two Capsicum species. Application of these markers to Capsicum improvement is discussed.
KeywordsPepper Potyvirus eIF4E Disease resistance Marker-assisted selection
We thank G. Moriarty, M. Falise and M. Kreitinger for technical assistance. We thank Carole Caranta and Susan McCouch for useful discussion and Helen Griffiths, Kari Perez and Jason Cavatorta for critical review of this paper. This work was supported in part by USDA NRICGP Plant Genome Award No. 94-37300-0333, USDA IFAFS Award No. 2001-52100-113347 and NSF Plant Genome Award No. 0218166. I. Yeam was supported in part by a fellowship from the Kwanjeong Educational Foundation. J.D. Frantz was supported in part by a USDA National Needs Fellowship in Plant Biotechnology.
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