Variations in intergenic spacer rpl20-rps12 of mango (Mangifera indica) chloroplast DNA: implications for cultivar identification and phylogenetic analysis

We characterized rpl20-rps12 and atp-rbcL intergenic spacers of chloroplast DNA from 19 mango cultivars to analyze suitability of these regions for assessing intraspecific variation. Analysis of the atp-rbcL region showed no variation, while rpl20-rps12 spacer sequences revealed both intravarietal and inter-subspecific polymorphisms. The intravarietal SNP was at position 360 of rpl20-rps12 spacer [SNP type C(G)]. The first inter-subspecific genotype detected was a C-A variation at position 755 in 16 out of 19 mango cultivars tested. The second inter-subspecific genotype was an insertion of C at position 714 of the rpl20-rps12 spacer, which was detected only in the ??Langra?? cultivar. Phylogenetic tree construction based on the rpl20-rps12 region grouped ??Shane-e-khuda,?? ??Sonara,?? ??Padri,?? ??Neelum,?? ??Gulab Khas,?? ??Dusehri,?? ??Chonsa,?? and ??Cari Saloli?? cultivars together in one group; ??Anwar Ratol,?? ??Zafran,?? ??Tota Pari,?? ??Safada,?? ??Kalapahar,?? and ??Almas?? cultivars in a second group; and ??Bangan Palli,?? ??Lohatia,?? ??Kesar,?? and ??Bombay Alphonso?? cultivars in a third group. This study supports the applicability of the rpl20-rps12 intergenic region of cpDNA for mango cultivar identification and phylogenetics.