Isolation and analysis of resistance gene homologues in sweetpotato

The majority of functionally characterized plant disease resistance genes are of the nucleotide-binding site (NBS)-LRR gene family, encoding proteins with a central NBS domain, a carboxy-terminal leucine-rich repeat domain, and a variable N-terminal region with or without homology to the Toll interleukin 1-like receptor (TIR) domain, referred to as TIR and non-TIR resistance gene homologues (RGH), respectively. Degenerate primers designed from conserved motifs within the NBS sequence were used to amplify, clone and sequence NBS-RGH from the sweetpotato genome. Two hundred and twenty-five distinct sweetpotato NBS sequences with similarity to known RGH genes were identified. Additional 50 sweetpotato RGHs were mined from the public genomic sequence database. Thus, a total of 275 RGH sequences were obtained using both PCR-based method and data-mining approach, from which 237 were non-TIR sequences organized into 35 singletons and 35 groups after reduced to 90% nucleotide identity, and 38 were TIR sequences divided into three primary phylogenetic clades. A bias of non-TIR vs. TIR was observed not only in genomic RGH sequences, but also in expressed sequence tags-RGH sequences. A subset of sweetpotato non-TIR RGH genes contained a conserved intron within the NBS sequences. The exploration of RGH diversity enables resistance gene evolutionary study and may facilitate the isolation of new and functional alleles. These new RGH sequences provided a resource of candidate genes and molecular markers for disease resistance research in sweetpotato.

[1]  M. Egnin,et al.  Factors enhancingAgrobacterium tumefaciens-mediated gene transfer in peanut (Arachis hypogaea L.) , 1998, In Vitro Cellular & Developmental Biology - Plant.

[2]  B. Roe,et al.  Identification and Characterization of Nucleotide-Binding Site-Leucine-Rich Repeat Genes in the Model Plant Medicago truncatula1[W][OA] , 2007, Plant Physiology.

[3]  Sheng Lin,et al.  Diversity and evolutionary relationship of nucleotide binding site-encoding disease-resistance gene analogues in sweet potato (Ipomoea batatas Lam.) , 2007, Journal of Biosciences.

[4]  Jing Zhao,et al.  Mapping of genome-wide resistance gene analogs (RGAs) in maize (Zea mays L.) , 2007, Theoretical and Applied Genetics.

[5]  Jonathan D. G. Jones,et al.  The plant immune system , 2006, Nature.

[6]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[7]  C. Town.  Annotating the genome of Medicago truncatula. , 2006, Current opinion in plant biology.

[8]  J. Drenth,et al.  Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance. , 2005, Genome.

[9]  A. Monfort,et al.  Analysis of the melon genome in regions encompassing TIR-NBS-LRR resistance genes , 2005, Molecular Genetics and Genomics.

[10]  Blake C Meyers,et al.  Multiple Genetic Processes Result in Heterogeneous Rates of Evolution within the Major Cluster Disease Resistance Genes in Lettucew⃞ , 2004, The Plant Cell Online.

[11]  A. Castagnaro,et al.  Isolation and diversity analysis of resistance gene analogues (RGAs) from cultivated and wild strawberries , 2004, Molecular Genetics and Genomics.

[12]  Jian-Qun Chen,et al.  Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes , 2004, Molecular Genetics and Genomics.

[13]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[14]  Blake C. Meyers,et al.  Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. , 2003, The Plant Cell Online.

[15]  P. Langridge,et al.  Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping , 2003, Molecular Genetics and Genomics.

[16]  J. Leach,et al.  Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. , 2002, Genome research.

[17]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[18]  Steven B Cannon,et al.  Phylogeny and genomic organization of the TIR and non-tIR NBS-LRR resistance gene family in Medicago truncatula. , 2002, Molecular plant-microbe interactions : MPMI.

[19]  Barry G. Hall,et al.  Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists , 2001 .

[20]  R. Fluhr,et al.  Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes , 2000, Journal of Molecular Evolution.

[21]  B. Sobral,et al.  Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide‐binding superfamily , 1999 .

[22]  H. Leung,et al.  Genome scanning for resistance-gene analogs in rice, barley, and wheat by high-resolution electrophoresis , 1998, Theoretical and Applied Genetics.

[23]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[24]  D. Leister,et al.  A PCR–based approach for isolating pathogen resistance genes from potato with potential for wide application in plants , 1996, Nature Genetics.

[25]  Y. G. Yu,et al.  Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[26]  R. Shoemaker,et al.  Resistance gene analogs are conserved and clustered in soybean. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[27]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.