Evaluation of genetic diversity and population structure in elite south Indian tea [Camellia sinensis (L.) Kuntze] using RAPD and ISSR markers

Tea [Camellia sinensis (L.) Kuntze] has primarily been improved by selections and controlled hybridizations. In India, the genetic improvement programs are largely led by United Planters Association of South India (UPASI). Tea has robust vegetative propagation and several high yielding commercial elite tea clones released by UPASI have been cultivated across the world. In a previous study, we analysed 42 elite UPASI tea clones using cytological and molecular analysis (Sharma and Raina, Int J Tea Sci 5:21–28, 2006). Present work analysed the same clones using Random amplified polymorphic DNA (RAPD) and Inter simple sequence repeat (ISSR) markers to document the genetic diversity and delineate the genetically distinct superior tea clones. A total of 447 and 116 bands were generated with 52 RAPD and 27 ISSR primers, out of which 395 and 70 bands, respectively were observed to be polymorphic. RAPD markers outcompeted ISSRs when compared against various genetic diversity attributes. An overall low Nei’s gene diversity (0.23 and 0.19) and higher value of gene flow (6.5 and 5.0) with both markers indicated narrow genetic base for the clones. Dendrograms delineated 42 clones into three major clusters whereas population STRUCTURE analysis clustered them into 6 subpopulations without discrete morphotype based grouping. Presence of many admixtures in STRUCTURE indicates towards diverse genetic ancestry of the analysed tea clones. A high level of genetic variation (90.48%) was revealed with analysis of molecular variance (AMOVA) within populations as compared to a low (9.52%) level among populations. A few superior clones were found to be genetically distinct than others and can be fruitfully used in future tea breeding programme.