Molecular characterisation of coconut (Cocos nucifera L.) varieties using ISSR and SSR markers

Abstract

ABSTRACTThe present study was carried out to standardise a DNA isolation protocol for coconut and to characterize five coconut varieties using 18 inter-simple sequence repeat (ISSR) and 14 simple sequence repeat (SSR) markers. DNA was extracted from tender young leaf samples collected from the fronds of five different trees of each coconut variety. A protocol using 0.095 g ml−1 glucose, 0.025 g ml−1 polyvinylpyrrolidone, 0.0045 g ml−1 sodium bisulphite, 0.0055 g ml−1 sodium dodecyl sulphate, and 50 µl ml−1 sarcosine produced good quality DNA. The average polymorphism percentages revealed using ISSR or SSR markers between the five varieties were 31.9% or 92.9%, respectively. Using ISSR markers, the overall similarity between all five varieties ranged from 0.657 to 0.775, whereas it was 0.037–0.304 using SSR markers. The levels of polymorphism detected using ISSR markers among the five samples each of ‘Banawali’, ‘Gangabondum Green Dwarf’, ‘Pratap’, ‘Konkan Bhatye Coconut Hybrid-I’, and ‘East Coast Tall’ were 23.2%, 24.2%, 25.6%, 27.1%, and 21.2%, respectively. The levels of polymorphism detected using SSR markers among the five samples of the same five varieties were 85.7%, 86.9%, 85.7%, 100%, and 92.9%, respectively. This study indicated that genetic variation existed both between and within samples of each of the five varieties of coconut. SSR markers were superior to ISSR markers. The extent of genetic variation obtained within a variety was not expected, so it is essential to maintain seed purity via artificial pollination.