ARS | Publication request: RESISTANCE GENE ANALOG POLYMORPHISM (RGAP) MARKERS CO-LOCALIZE WITH DISEASE RESISTANCE GENES AND QTL IN COMMON BEAN

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 21, 2005
Publication Date: January 25, 2005
Citation: Mutlu, N., Miklas, P.N., Coyne, D.P. 2005. Resistance gene analog polymorphism (rgap) markers co-localize with disease resistance genes and qtl in common bean. Molecular Breeding. 17:127-135.

Interpretive Summary: Identifying molecular markers linked with targeted genes can be a laborious task using existing DNA marker technology. Molecular information about plant genes is rapidly expanding which is leading to rapid advancements in the field of plant genomics. Resistance genes have now been cloned and sequenced in many different plant species. Cumulative molecular data indicates that resistance genes are similar across species such that they possess conserved stretches of DNA sequence called motifs. In this study, the kinase and hydrophobic domain motifs of a LLR-NBS disease resistance gene family were used to generate primers for amplification of a new marker in bean. The new marker is called a resistance gene analog polymorphism and is abbreviated with the acronym RGAP. This new marker has an affinity for tagging and mapping disease resistance genes. The RGAP marker techniques can also be applied to other gene families that are conserved across species. RGAP markers will lead to improved tagging, mapping, and marker-assisted selection for disease resistance genes in dry bean and snap bean.

Technical Abstract: Resistance genes containing nucleotide binding site (NBS)-leucine rich repeats (LRR) are the most prevalent types of resistance (R) genes in plants. The objective of this study was to develop PCR based R-gene analog polymorphism (RGAP) markers for common bean (Phaseolus vulgaris L). Twenty degenerate primers were designed from the conserved kinase-1a (GVGKTT) and hydrophobic domains (GLPLAL) of known NBS-LRR type R-genes and from EST databases. Sixty-six of the 100 primer combinations tested yielded polymorphism. Thirty-two RGAP markers were mapped in the BAT 93 X Jalo EEP558 core mapping population for common bean. The markers mapped to 10 of 11 linkage groups with a strong tendency for clustering. In addition, the RGAP markers co-located, on six linkage groups, with fifteen resistance gene analogs (RGAs) that were previously mapped in other populations of common bean. The distance between the priming sites in NBS-LRR type R-genes is around 500 bp. Of the 32 RGAP markers, 19 had sizes larger and 13 less than 500 bp. RGAP markers mapped close to known R-genes on B11, and to QTLs for resistance on B1, B2, B6, B7, B8, B10, and B11. RGAP appears to provide a useful marker technique for tagging and mapping R-genes in segregating common bean populations, discovery of candidate genes underlying resistance QTL, and future cloning of R-genes in common bean.