Comparison of PCR based marker systems for genetic analysis in different cultivars of mango

Native diversity is well represented in northern and eastern parts of India for mango. We evaluated three important polymerase chain reaction (PCR) based marker techniques viz., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplified mini satellite DNA (DAMD) and examined their suitability for depicting genetic relationships and discrimination among closely related group of 46 mango varieties grown in the different agro-ecological zones in Uttar Pradesh, Bihar and West Bengal. Nine RAPD, eleven ISSR and four DAMD primers generated 110, 160 and 43 discrete fragments, respectively, accounting for polymorphism of 87.3, 79.83 and 83.72%, respectively. Cumulative analysis of these markers resulted in comprehensive UPGMA based dendrogram where in native mangoes representing important breeding lines and varieties from Uttar Pradesh fall more or less in separate cluster, while Bihar and West Bengal cultivars represent genetically different lineage forming distinct separate cluster. The prime focus on the study was towards identification of genetic variability that warrants establishing origin and molecular evolution of mango cultivars of eastern and northern India because they are the rich gene pool for conservation. Highest diversity index (DI) and polymorphic information content (PIC) values were found in DAMD indicating it to be more informative than others. Similarly, high effective multiplex ratio (EMR) and marker index (MI) were recorded by ISSR reflecting ability to simultaneously detect a large number of bands. The study accomplished establishing genetic relationship and also DNA fingerprint development. The data is also useful for mapping studies for gene identification.