DNA barcode for rambutan diversity in Thailand using chloroplast genome regions

Rambutan is one of the best-known fruits in Asia. Thailand is one of the largest producers of rambutan apart of Indonesia and Malaysia. The commercial rambutan, Nephelium lappaceum L., is considered closer to other Nepheliums, which are very difficult to distinguish from each other. Therefore, this study is to clarify the DNA barcode for diversity of rambutan using chloroplast genome regions (psbA, trnL and rpoC). Seventeen samples of rambutan were collected from the field at Chanthaburi Horticultural Research Center for analysis. Among these, 14 samples are classified as N. lappaceum. Six of the commercial cultivars and eight hybrid cultivars including ‘Rongrien’, ‘Seechompoo’, ‘Seethong’, ‘Bangyeekhan’, ‘Namtankraud’, ‘Jaemong’ and ‘Pliew 1-8’ were analyzed. The other three samples were Pulasan (N. ramboutan-ake (Labill.) Leenh.), Nephelium sp. No. 1 and Nephelium sp. No. 2. Extracted DNA samples were evaluated with 3 universal primers of psbA, trnL and rpoC. The result showed that using psbA primer separated the group of ‘Seethong’ and ‘Pliew 2’ (‘Seethong’ × ‘Jaemong’) and group of Nephelium sp. No. 2 from the others. Whereas trnL, rpoC and combination of three primers could not explicitly explain the diversity within rambutan. Our study will further examine more specific primers to confirm the relationships of the Thai rambutans. The genetic diversity of cultivated rambutan from this study will be used as a genetic database for development of a future breeding program.