Generation of silver stained TE-AFLP markers in tea (Camellia sinensis) and their assessment in filling gaps with construction of a genetic linkage map

• Selection of primer combinations and evaluation of the information content of the selected primer combinations assessing four statistical parameters.
• Construction of preliminary linkage maps of tea (Camellia sinensis) based on TE-AFLP markers.
• Sequence analysis of TE-AFLP markers.

Silver stained TE-AFLP markers were generated in tea (Camellia sinensis). Thirty six primer combinations were screened leading to identification of five primer combinations which showed high polymorphism (average 43.75%) among 17 tea accessions studied. The efficacy of these five primer combinations was evaluated using four parameters, namely Polymorphic Information Content, Effective Multiplex Ratio, Marker Index and Resolving Power. The selected five primer combinations were employed for further study on construction of preliminary linkage maps based on a two-way pseudo-testcross strategy in a F1 population of bi-clonal seed stock TS463 (TV1 and TV19 clones) of tea. A total of 153 markers were detected of which 100 markers segregated in a 1:1 ratio. TV1 parent map consisted of 36 loci, spread over 10 linkage groups spanning a total length of 388.9 cM while in TV19 map, 30 loci were distributed in 11 linkage groups spanning over 410.7 cM. The observed genome coverage was determined, i.e., 50.76% and 45.91% for TV1 and TV19, respectively. Furthermore, sequences of the TE-AFLP fragments were subjected to BLAST analysis. Many of the sequences showed positive hit with the database of whole genome shot gun contigs of tea (Camellia sinensis var. sinensis). The identification of markers in these linkage maps may be an important resource for further research and would be helpful for marker-assisted selection breeding programmes in tea.