Establishment of core Short Tandem Repeat (STR) markers for rice (Oryza sativa L.) varietal identification
2019
Dalusong, V.G. | Santos, L.H. | Perez, L.M.
The genetic identity of rice cultivars is important to acquire plant variety protection and breeders' right. DNA-based cultivar identification can help to establish the varietal genetic identity of rice based on unique DNA profile. Short Tandem Repeat (STR) marker selection and validation were conducted following the recommendations of the Scientific Working Group in DNA Analysis Method (SWGDAM) in establishing the STR markers for rice varietal identification. Forty-one STR markers were selected based on its polymorphism, sensitivity, stability, and species specificity. Polymorphism Information Content (PIC) values of the markers range 0.1889 to 0.7568 and detected an average number of 3.4 alleles per marker indicating high level of polymorphism. Genetic diversity index was 0.9609 indicating high level of genetic variation detected among rice cultivars used. Sensitivity test showed that the DNA concentration optimum for PCR analysis was 10.0 ng. Stability test showed that STR markers were able to amplify degraded DNA samples. Species specificity test revealed that STR markers generated PCR amplifications in both target (Oryza sativa L.) and non-target DNA sources including wild rice species, weeds, corn, rats, and human. This paper discusses details of STR marker selection for rice identification following SWGDAM parameters for DNA analysis.
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