Cross-species transferability of IRAP retrotransposon markers and polymorphism in black pepper (Piper nigrum L.)

Black pepper is one of the most important spices, known for its use worldwide. Retrotransposons, class I mobile elements abundantly appear in the plant genome and can play role in gene activation or silencing by their copy and paste mechanism in the respective genome of an organism. In this study, the Piper nigrum L. genome was scanned for identification of retrotransposon activity in terms of insertional polymorphism using IRAP retrotransposon-based molecular marker system. Seven LTR IRAP primers (Sukkula, Nikita, 3′LTR, 5′LTR1, 5′LTR2, LTR6149, and LTR6150) in single and combination were used to analyse insertional polymorphism among nineteen varieties of black pepper. In single primer analysis Sukkula, Nikita, 3′LTR, and LTR6150 primers showed amplification in all the nineteen varieties. Out of these Sukkula, Nikita and 3′LTR were found to be polymorphic in nature with 33.33%, 53% and 56.25% polymorphism, with PIC values of 0.131, 0.183 and 0.197 respectively. Out of the 21 combinations of primer pairs tried, 16 showed amplification in all the nineteen varieties and 14 combinations among them were polymorphic in nature with the percentage of polymorphism and PIC value in the range between 50–100% and 0.04–0.350 respectively. This is the first report of horizontal transferability and identification of retrotransposons Sukkula, BARE1, and Nikita in black pepper (Piper nigrum L.) indicating an evolutionary relationship between black pepper (Piper nigrum L.) and other genome such as barley (Hordeum vulgare). These polymorphic markers (single and combination of primer pairs) were also useful for the evaluation of genetic diversity among the nineteen varieties of black pepper used in the study.