Assessment of genetic diversity, population structure, and phylogenetic relationships among the Northeast Indian and South Indian commercially released tea cultivars using TE-AFLP markers

Commercially cultivated tea clones from Northeast and Southern India were analyzed using TE-AFLP markers. Analysis of molecular variance (AMOVA) and structure analysis showed high genetic variance (74%) within five distinct populations. This study also confirmed that Assam and UPASI (Nilgiri) tea clones have originated from two different tea populations introduced from imported China tea seeds by British. We evaluated the genetic variation and population structure in 30 tea clones of Tea Research Association (TRA), Tocklai Experimental station (Tockali ES), Jorhat, from North Eastern India and 30 clones of United Planters Association of South India (UPASI), Valparai, from South-India, released for commercial plantations and four C. japonica accessions (Total 64) used as outliers using Three Endonuclease-AFLP markers. Six primer combinations were selected from the best 10 primer combinations that were used on a set of 24 tea accessions as a standardization procedure. Dendrograms were constructed by using Jaccard’s similarity coefficient and Unweighted Pair Group Method of Arithmetic Averages (UPGMA) clustering method based on high coefficient correlation ratios obtained. High level of genetic diversity and clustering of accessions according to morphological proximity was established with minor aberrations. Analysis of molecular variance (AMOVA) showed highest genetic variance (79%) within five populations whereas the lowest variance (21%) was found among populations. These values change to the highest 87% and the lowest 13% when Camellia japonica accessions were removed from the analysis. Population structure analyses were performed to establish the genetic diversity and exact type each clones vis-a-vis to their molecular and morphological characteristics at present. Attempts were made to find out the population structure of Northeast and Southern India tea germplasm with their relatedness to existing morphological type. These analyses confirmed that all tea clones were genetically diverse and grouped based on their morphological characteristics and geographic regions.