title: Isolation and diversity analysis of resistance gene homologues from switchgrass.
abstract: Resistance gene homologs (RGHs) were isolated from the switchgrass variety Alamo by a combination of polymerase chain reaction and expressed sequence tag (EST) database mining. Fifty-eight RGHs were isolated by polymerase chain reaction and 295 RGHs were identified in 424,545 switchgrass ESTs. Four nucleotide binding site--leucine-rich repeat RGHs were selected to investigate RGH haplotypic diversity in seven switchgrass varieties chosen for their representation of a broad range of the switchgrass germplasm. Lowland and upland ecotypes were found to be less similar, even from nearby populations, than were more distant populations with similar growth environments. Most (83.5%) of the variability in these four RGHs was found to be attributable to the within-population component. The difference in nucleotide diversity between and within populations was observed to be small, whereas this diversity is maintained to similar degrees at both population and ecotype levels. The results also revealed that the analyzed RGHs were under positive selection in the studied switchgrass accessions. Intragenic recombination was detected in switchgrass RGHs, thereby demonstrating an active genetic process that has the potential to generate new resistance genes with new specificities that might act against newly-arising pathogen races.
authors.affiliation: Department of Genetics, The University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Qihui
authors.initials: Q
authors.lastname: Zhu
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Shavannor M
authors.initials: SM
authors.lastname: Smith
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D003001:Cloning, Molecular; D016000:Cluster Analysis; D017124:Conserved Sequence / Q000235:genetics; D030561:Databases, Nucleic Acid; D060467:Disease Resistance / Q000235:genetics*; D060146:Ecotype; D020224:Expressed Sequence Tags; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D008897:Panicum / Q000235:genetics* / Q000276:immunology*; D010802:Phylogeny; D025341:Principal Component Analysis; D011995:Recombination, Genetic / Q000235:genetics; D012641:Selection, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: D009711:Nucleotides
keywords: NBS-LRR; bioenergy crop; genetic diversity; population structure; resistance gene homologue (RGH); switchgrass