title: Isolation of nucleotide binding site-leucine rich repeat and kinase resistance gene analogues from sugarcane (Saccharum spp.).
abstract: BACKGROUND
  Resistance gene analogues (RGAs) have been isolated from many crops and offer potential in breeding for disease resistance through marker-assisted selection, either as closely linked or as perfect markers. Many R-gene sequences contain kinase domains, and indeed kinase genes have been reported as being proximal to R-genes, making kinase analogues an additionally promising target. The first step towards utilizing RGAs as markers for disease resistance is isolation and characterization of the sequences.
  
  
  RESULTS
  Sugarcane clone US01-1158 was identified as resistant to yellow leaf caused by the sugarcane yellow leaf virus (SCYLV) and moderately resistant to rust caused by Puccinia melanocephala Sydow & Sydow. Degenerate primers that had previously proved useful for isolating RGAs and kinase analogues in wheat and soybean were used to amplify DNA from sugarcane (Saccharum spp.) clone US-01-1158. Sequences generated from 1512 positive clones were assembled into 134 contigs of between two and 105 sequences. Comparison of the contig consensuses with the NCBI sequence database using BLASTx showed that 20 had sequence homology to nuclear binding site and leucine rich repeat (NBS-LRR) RGAs, and eight to kinase genes. Alignment of the deduced amino acid sequences with similar sequences from the NCBI database allowed the identification of several conserved domains. The alignment and resulting phenetic tree showed that many of the sequences had greater similarity to sequences from other species than to one another.
  
  
  CONCLUSIONS
  The use of degenerate primers is a useful method for isolating novel sugarcane RGA and kinase gene analogues. Further studies are needed to evaluate the role of these genes in disease resistance.
authors.affiliation: USDA-ARS, Sugarcane Field Station, 12990 US Hwy 441N, Canal Point, 33438 FL, USA. neil.glynn@ars.usda.gov
authors.forename: Neil C
authors.initials: NC
authors.lastname: Glynn
authors.forename: Jack C
authors.initials: JC
authors.lastname: Comstock
authors.forename: Sushma G
authors.initials: SG
authors.lastname: Sood
authors.forename: Phat M
authors.initials: PM
authors.lastname: Dang
authors.forename: Jose X
authors.initials: JX
authors.lastname: Chaparro
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics*; D003001:Cloning, Molecular; D005658:Fungi; D017343:Genes, Plant; D020022:Genetic Predisposition to Disease; D006824:Hybridization, Genetic; D007930:Leucine / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000378:metabolism; D010770:Phosphotransferases / Q000235:genetics*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics*; D010942:Plant Viruses; D031786:Saccharum / Q000235:genetics*
chemical_list: D009711:Nucleotides; D010940:Plant Proteins; D010770:Phosphotransferases; D007930:Leucine