Optimization of DNA extraction protocol in various varieties of papaya for genotyping and molecular diagnosis

Carica papaya L. is a polygamous diploid fruit crop originated from tropical and subtropical regions. Papaya fruit is a good source of vitamin A, B, C (Purnima and Sandhya, 1988), important proteolytic enzyme such as papain and chymopapain with several commercial applications. In tropical plants, higher concentration of RNA, polyphenols, polysaccharides etc, complex the separation and purification of DNA (Qi-Xing Huang et al., 2013). The objectives of the present study were to optimize DNA isolation protocol for 13 different papaya varieties and selectively amplifying the genomic DNA for Polymerase chain reactions. In papaya DNA extraction, there is a problem of browning of pellet, RNA and lipid contamination which decreases yield and quantity. The changes in sample weight, conc. of â-mercaptoethanol, RNAse addition in extraction buffer and no use of liquid nitrogen eliminated contamination and also save time taken for extraction. The DNA A260/280 ratio for varieties were in range between l.6-2.1. Genomic DNA concentration in Pusa nanha was maximum out of 13 varieties. An efficient and fast DNA extraction protocol has been developed without using liquid nitrogen for inter simple sequence repeat (ISSR) and sequence characterized amplified region (SCAR) analysis. The resulted purified genomic DNA showed intact bands in all papaya varieties and was successfully amplified by PCR for several molecular analysis such as, sex determination, diversity analysis, genetic fidielity testing etc.