title: Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display.
abstract: CACTA is a class 2 transposon, that is very abundantly present in plant genomes. Using Rim2/Hipa CACTA transposon display (hereafter Rim2/Hipa-TD), we analyzed several A-genome diploid Oryza species that have a high distribution of the CACTA motifs. High levels of polymorphism were detected within and between the Oryza species. The African taxa, O. glaberrima and O. barthii, both showed lower levels of polymorphism than the Asian taxa, O. sativa, O. rufipogon, and O. nivara. However, O. longistaminata, another African taxon, showed levels of polymorphism that were similar to the Asian taxa. The Latin American taxon, O. glumaepatula, and the Australian taxon, O. meridionalis, exhibited intermediate levels of polymorphism between those of the Asian and African taxa. The lowest level of polymorphism was observed in O. glaberrima (32.1%) and the highest level of polymorphism was observed in O. rufipogon (95.7%). The phylogenetic tree revealed three major groups at the genetic similarity level of 0.409. The first group consisted of three Asian taxa, O. sativa, O. rufipogon and O. nivara. The second group consisted of three African taxa, O. glaberrima, O. barthii, O. longistaminata, and an American taxon, O. glumaepatula. The third group contained an Australian taxon, O. meridionalis. The clustering patterns of these species matched well with their geographical origins. Rim2/Hipa-TD appears to be a useful marker system for studying the genetic diversity and species relationships among the AA diploid Oryza species.
authors.affiliation: Plant Biotechnology Program, Division of Biotechnology, Kangwon National University, Chunchon, Korea.
authors.forename: Soon-Jae
authors.initials: SJ
authors.lastname: Kwon
authors.forename: Ju Kyong
authors.initials: JK
authors.lastname: Lee
authors.forename: Sung-Won
authors.initials: SW
authors.lastname: Hong
authors.forename: Yong-Jin
authors.initials: YJ
authors.lastname: Park
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: McNally
authors.forename: Nam-Soo
authors.initials: NS
authors.lastname: Kim
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D004251:DNA Transposable Elements / Q000502:physiology*; D004171:Diploidy; D020869:Gene Expression Profiling / Q000379:methods; D049810:Genetic Speciation; D014644:Genetic Variation; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011110:Polymorphism, Genetic; D013045:Species Specificity; D019895:Transposases / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins; C484284:Rim2 protein, Oryza sativa; D019895:Transposases