Rice is an economically important plant as well as a model organism. The rice genome consists of 35% retrotransposons. Although most of the retrotransposons are inactivated through evolutionary processes, they can be activated under various biotic and abiotic stress conditions. The main objective of this study was to explore the effects of herbicides on retrotransposon activities and the usage of retrotransposons in short-term mutagenicity tests. In this study, bentazone and an MCPA (2-methyl-4-chlorophenoxyacetic acid)-containing herbicide was used. Plant samples were grouped into three classes: control (untreated), 1% and 2% herbicide treatment. Retrotransposon activities were investigated by using the inter-retrotransposon amplified polymorphism (IRAP) marker technique. IRAP analyses were performed for Houba (Tos5/Osr13) retrotransposon. Polymorphism ratios were calculated with the Jaccard similarity index, and the significance of polymorphism was evaluated by one-way analysis of variance (ANOVA). We observed that the polymorphism ratios ranged from 8%-90% for Houba among plant samples. ANOVA showed that these variable ratios were statistically significant. Bentazone and the MCPA-containing herbicide increased the retrotransposon activities, and they might be responsible for DNA mutations. This study indicated valuable data for establishing retrotransposon-based short-term mutagenicity test in rice with suitable retrotransposons such as Houba.

2. Materials and methods 2.1. Plant material and DNA isolation To investigate retrotransposon polymorphisms among individuals, 37 Oryza sativa L. cultivars were used (Table 1). These cultivars were obtained from Trakya Agronomic Research Institute. They included all the major cultivated varieties in Turkey. All cultivars are tolerant or resistant to

We investigated Hopi/Osr27 (gypsy) and Houba/Tos5/Osr13 (copy) retrotransposon movements in 10-day-old roots and leaves of Oryza sativa cvs. Ipsala, Beser and Osmancik-97. Seeds from these three cultivars were germinated between filter papers in Petri dishes for 10 days. Three biologically independent (nonrelated) seeds were germinated for each cultivar. Then, roots and leaves grown from the same rice plant were harvested and used for genomic DNA isolation. Interretrotransposon amplified polymorphismÀpolymerase chain reaction with suitable primers was performed with each DNA template to analyze the movements of Hopi/Osr27 and Houba/Tos5/ Osr13 retrotransposons. Polymorphism ratios were evaluated both among cultivars and among roots and leaves from the same cultivar. The polymorphism ratios ranged from 0% to 17% for Hopi/ Osr27 and from 10% to 87% for Houba/Tos5/Osr13. The obtained results at retrotransposon and varietal levels indicated that the retrotransposon type and genotype dependence are responsible for the occurrence of different variations. Transposable elements are very important for understanding the relationship between cultivars and evolution. Our findings are expected to contribute to the understanding of spontaneous genomic insertion events and their effects on the genetic and epigenetic changes during rice development.

Abstract:Increasing world population needs to enhance agricultural production because of food starvation. Genetically modified organism (GMO) is a way to solve this problem. During gene transfers, DNA is inserted into a plant's genome in a random way. This produces spontaneous genetic changes with movement of transposable elements, and even increases variations. Houba was described as one of the active retrotransposons in rice. The aim of this study was to screen rice samples collected from Turkey, and analyse Houba retrotransposon movements with IRAP technique in transgenic ones and their controls. For this purpose, 71 different rice seeds obtained from different regions of Turkey were used for GMO analysis. All samples were screened by real time PCR to test cauliflower mosaic virus (CaMV) 35S promoter (P-35S) regions, T-NOS (nopaline synthase terminator) regions, figwort mosaic virus (FMV) regions, bar, pat and Cry1ab/ac, and hpt (hygromycin resistance) genes. Hpt gene was identified in 6 samples as a result of real time PCR analysis. These 6 transgenic samples with their controls were used for IRAP-PCR analysis and 0-56% polymorphism ratios were observed in analysed samples. This study is one of the first detailed experimental data of transgenic Oryza sativa L. samples in terms of retrotransposon-based variation.

No abstract