The Potential Role of Plastid DNA as a Biomarker and Biosensor Using Real-time Quantitative Polymerase Chain Reaction
Authors: Pandey Amita , Chaudhary Shifa , Bhat Binu 
Published: April 2021

Abstract
Plastids are plant specific semiautonomous organelles, which differentiate to perform many cardinal functions including photosynthesis, energy generation, development, stress perception and response, storage, flowering, and fruit ripening. Additionally, plastids are of immense nutritional value to humans, underscoring the need to develop reliable assays to determine the plastid content of plant based products. Studies have shown that the number of plastids present in various plant organs is regulated by both internal and external factors, however determination of plastid number is time consuming and requires sophisticated instruments. Interestingly, studies have shown that the plastome number, small circular DNA molecules present in the plastids is also regulated by both internal and external stimuli and therefore can be potentially used to estimate the plastid content in a plant organ. This study hypothesizes that plastome copy number, determined by real-time quantitative polymerase chain reaction (qPCR) in different plant samples can be used as a plant biomarker and biosensor. Samples of cotton seed (CS), leaf (CL) and lint (Clt) and seeds of rice (RS), soybean (SS), maize (MS) and sesame (SeS) were obtained over a period of two years, their plastome copy number was determined by the Ct values obtained using real-time qPCR assays using chloroplast tRNA specific primers. Regression analysis was performed to ensure reliability of the real-time qPCR data. Subsequent, data analysis revealed that the mean log plastome copy number showed a statistically significant difference for the plant species including seeds of cotton, soybean, maize, and sesame suggesting that the log plastome copy number is plant species specific and therefore can be used as a biomarker. Furthermore, evidence in support of the use plastids as biosensors was obtained by calculating the range of log plastome copy number, where range represents the difference between lowest and highest log copy number values. A low range value indicated that the log copy values do not deviate from the mean copy number value, suggesting that the samples have encountered consistent and similar internal and external factors during growth and post-harvest storage and processing, Whereas, high range values indicated large deviations from mean copy value suggesting that the samples have encountered changing internal and external conditions. These conclusions are supported by observation of low range for all the seed samples including CR (0.31), CS (0.58), RP (0.05), SeS (0.31), seeds have a protective coat to withstand variations in environmental conditions. Whereas, observation of high range values for CL (4.11), Clt (3.63), and RS (3.09) could be explained by different developmental stage of CL samples, different post-harvest conditions for Clt samples and broken RS samples. In conclusion, the study present preliminary data in support of use of plastome copy number as a plant biomarker and biosensor.