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Isolation and linkage mapping of NBS-LRR resistance gene analogs in red raspberry (Rubus idaeus L.) and classification among 270 Rosaceae NBS-LRR genes

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Abstract

Plant R genes confer resistance to pathogens in a gene-for-gene mode. Seventy-five putative resistance gene analogs (RGAs) containing conserved domains were cloned from Rubus idaeus L. cv. ‘Latham’ using degenerate primers based on RGAs identified in Rosaceae species. The sequences were compared to 195 RGA sequences identified from five Rosaceae family genera. Multiple sequence alignments showed high similarity at multiple nucleotide-binding site (NBS) motifs with homology to Drosophila Toll and mammalian interleukin-1 receptor (TIR) and non-TIR RNBSA-A motifs. The TIR sequences clustered separately from the non-TIR sequences with a bootstrap value of 76%. There were 11 clusters each of TIR and non-TIR type sequences of multiple genera with bootstrap values of more than 50%, including nine with values of more than 75% and seven of more than 90%. Polymorphic sequence characterized amplified region and cleaved amplified polymorphic sequence markers were developed for nine Rubus RGA sequences with eight placed on a red raspberry genetic linkage map. Phylogenetic analysis indicated four of the mapped sequences share sequence similarity to groupTIR I, while three others were spread in non-TIR groups. Of the 75 Rubus RGA sequences analyzed, members were placed in five TIR groups and six 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 process involved in pest resistance development in plants. This information will aid in the understanding of R genes and their proliferation within plant genomes.

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Acknowledgments

This research was supported by a grant from the US Department of Agriculture—National Research Initiative (USDA-NRI) NYG-632526. We are grateful to William Boone for skillful technical work.

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Author notes

  1. Jeremy A. Pattison

    Present address: Virginia Polytechnic Institute and State University, Southern Piedmont AREC, 2375 Darvills Road, Blackstone, VA, 23824, USA

Authors and Affiliations

  1. New York State Agricultural Experiment Station, Cornell University, 630 West North St., Geneva, NY, 14456, USA

    Suren K. Samuelian, Angela M. Baldo, Jeremy A. Pattison & Courtney A. Weber

  2. Center for Viticulture and Small Fruit Research, Florida A&M University, 6505 Mahan Drive, Tallahassee, FL, 32317, USA

    Suren K. Samuelian

  3. USDA-ARS Plant Genetic Resources Unit, 630 W. North St., Geneva, NY, 14456, USA

    Angela M. Baldo

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  1. Suren K. Samuelian
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Correspondence to Courtney A. Weber.

Additional information

Communicated by: J. Davis

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental Table S1

List of all 270 sequences (DOC 423 KB).

S2

Alignment of all 270 amino acid sequences in a format suitable for input into the Phylip phylogenetic inference package (ZIP 23.9 KB)

Supplemental Fig. S3

Detailed tree in color showing all 270 terminal nodes (PDF 46.5 KB)

Supplemental Table S4

Clusters containing multiple genera with a bootstrap of more than 50% and correspondence with other studies (DOC 64 KB)

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Samuelian, S.K., Baldo, A.M., Pattison, J.A. et al. Isolation and linkage mapping of NBS-LRR resistance gene analogs in red raspberry (Rubus idaeus L.) and classification among 270 Rosaceae NBS-LRR genes. Tree Genetics & Genomes 4, 881–896 (2008). https://doi.org/10.1007/s11295-008-0160-2

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  • DOI: https://doi.org/10.1007/s11295-008-0160-2

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