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Title: Isolation and Linkage Mapping of NBS-LRR Resistance Gene Analogs in Red Raspberry (Rubus idaeus L.) and Classification Among 269 Rosaceae NGS-LRR Genes

Author
item SAMUELIAN, SUREN
item Baldo, Angela
item PATTISON, JEREMY
item WEBER, COURTNEY

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2008
Publication Date: 6/10/2008
Citation: Samuelian, S.K., Baldo, A.M., Pattison, J.A., Weber, C. 2008. Isolation and Linkage Mapping of NBS-LRR Resistance Gene Analogs in Red Raspberry (Rubus idaeus L.) and Classification Among 269 Rosaceae NGS-LRR Genes. Electronic Online First Article http://www.springerlink.com/content/n423jnx741586448.

Interpretive Summary: Plant resistance (R) genes are responsible for providing defense against pathogens in a gene-for-gene mode. R genes are widely distributed in plant genomes, with as many as 200 estimated in Arabidopsis thaliana, alone. The presence of conserved protein motifs in these genes have made it possible to use universal PCR primers for isolation of resistance gene analogs (RGAs) from many plant species. There are already available nearly 200 of these genes in the Rosaceae family (strawberry, apple, peach, almond, pear, and ornamental rose), but there has to date been no comprehensive catalog or classification of the RGAs in the family as a whole. This study adds 75 sequences from red raspberry to the list and provides the necessary groundwork for understanding how the RGAs in Rosaceae are related, and which groups in the gene family have already been linked to disease resistance. This groundwork paves the way for using RGAs to characterize genetic diversity and predict genetic resistance to disease in the wild and cultivated Rosaceous crops curated at the Geneva clonal repository (apple and tart cherry).

Technical Abstract: Plant R genes are known to confer resistance to a variety of pathogens in a gene-for-gene mode. Seventy-five putative resistance gene analogs (RGAs) containing conserved domains were cloned and sequenced from the red raspberry (Rubus idaeus L.) cultivar ‘Latham’ using degenerate primers based on RGAs identified in other Rosaceae species. The resulting sequences were aligned and compared in context to 194 RGA sequences identified from five genera in the Rosaceae family. Multiple alignments showed high similarity at multiple nucleotide binding site. (NBS) motifs with clearly visible homology to Drosophila Toll and mammalian interleukin-1 receptor (TIR) and non-TIR RNSA-A motifs. The TIR sequences clustered separately from the non-TIR sequences with a bootstrap value of 76%. In total there were 11 clusters of each TIR and non-TIR type sequences of multiple 25 genera with bootstrap values over 50%, including nine with values over 75% and seven with values over 90%. Polymorphic sequence characterized amplified region (SCAR) and cleaved amplified polymorphic sequence (CAPS) markers were developed for 9 Rubus RGA sequences with 8 placed on a genetic linkage map of red raspberry used for quantitative trait loci (QTL) analysis for resistance to Phytophthora root rot. Four of the mapped sequences clustered near the TIR I group while three others were spread in non-TIR groups. Of the 75 Rubus RGA sequences analyzed, members were placed in 5 TIR groups and 6 non-TIR groups. These group classifications closely matched those in 12 of 13 studies from which these sequences were derived. The analysis of related DNA sequences within plant families elucidates the evolutionary relationship and processes involved in the development of pest resistance in plants. This information will provide a better understanding of R genes and their proliferation within plant genomes.