The difference in length of an intron among the individuals at the genome-wide scale is exploited as DNA markers which is known as Intron Length Polymorphic (ILP) markers. ILP markers have several advantages such as co-dominant in nature, neutral, convenient, and reliable and high rates of cross-transferability across the related species. Further, ILP markers have high transferability rates among the plant species. With the aid of comparative genomics, the prediction of exon and intron junctions are possible in homologous gene sequences of plants. This is exploited to develop potential intron polymorphism (PIP) markers by designing primers from the flanking exon sequences of an intron that vary in length.

Here we discover and characterize 4011 ILP markers from the assembled TV1 tea genome. Initially, to predict putative ILP loci, the forward and reverse primers were designed from the 100 bp flanking sequences of an intronic sequence of ≤400 bp. The non-redundant primers were mapped against TV1 genome to extract out the primers producing single amplimers and these a primers were finally defined as potential non-redundant ILP marker. A total 4811 ILP markers were predicted and were found distributed throughout all 15 chromosomes of TV1.