The presence of potentially toxic elements in waters used for agricultural irrigation is a latent problem in Lake Chapala, Mexico. Four sites in the polluted area of Chapala lake were studied in this research. Samples of irrigation water and soil were collected from each site in both the dry (DS) and rainy (RS) seasons. Arsenic (As), cadmium (Cd), chromium (Cr), and lead (Pb) were measured in all the samples. Comet assay was used to measure the migration of DNA from the nucleus in order to detect genotoxicity in fruits. ISSR molecular markers were used to assess the detection power of this marker in correspondence with amounts of metals in the samples. The results show a variation of metal concentrations in the DS and RS soil and water samples. The metalloid As in DS water samples exceeded the permissible limits in three of the sampling areas. Cd and Pb exceeded the prescribed limits from collected water in three of the sampling areas in RS. Cd exceeded the maximum permissible limits in soil collected during both DS and RS in the four sampling sites. Data on the concentration of metals shows significant differences between the sampling areas and the control site. Genetic damage (DNA migration from the nuclei) was found in the chayote fruit and the major migration of DNA was associated principally with the presence of As in DS water samples as well as Pb in soil in RS.
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