title: Molecular analysis of utility of a retrotransposon, p-SINE1-r2 in the Asian wild rice and weedy rice populations.
abstract: The distribution of a retrotransposon, p-SINE1-r2 located at the waxy locus was analyzed by the PCR assay in the perennial wild rice (Oryza rufipogon) which inhabited in four isolated and six disturbed populations and in the weedy rice population. The level of clonality of the wild rice species was determined in populations subject to level of water supply and another disturbance. The results showed that all four isolated populations carried the genotype (-/-) and (-/+), while three genotypes (-/-), (-/+) and (+/+) was found on the six populations which grown near by rice fields. This finding was strongly supported the idea that the original wild rice populations of O. rufipogon exhibited prominent genotype (-/-) and (-/+) and mainly propagated by vegetative reproduction and the allele (+) which found in the wild rice plant with the genotype (+/+) may originated from gene flow from cultivated rice to wild rice. Weedy rice accessions used in this study showed the three genotypes based on this DNA locus. The distribution of this DNA locus in wild rice and weedy rice populations were deviated from the Hardy-Weinberg equilibrium. The perennial wild rice populations were annually under season drought (March to May of the year in Thailand, Laos and Cambodia), they tended to have small size clones with relatively high clonal diversity (i.e., number of genotypes), except for the population from Cambodia, which carried only the genotype (-/+). Although DNA maker used to detect genetic variation at population levels is too small, but this locus is very sensitive enough to be a useful indicator for genetic variation at the population level.
authors: Rice Genetics Research Unit, Department of Biotechnology, Faculty of Technology, Mahasarakham University, Khamriang Sub-District, Kantarawichai District, Maha Sarakham Province 4400, Thailand.
authors: Preecha
authors: P
authors: Prathepha
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D017753:Ecosystem; D014644:Genetic Variation; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D011110:Polymorphism, Genetic; D018626:Retroelements
chemical_list: D018744:DNA, Plant; D018626:Retroelements