If you want to distinguish inter- and intraspecific taxa, you must use highly variable markers. Such markers in most cases are uncoding regions, such as intergenic spacers, introns etc. There are a lot of such markers are already developed for similar approaches. If you want to use some of them you may look on the series of general works on it.

If you plan to use ITS, you must compare secondary structure of this region. See works of Annette Coleman

http://nar.oxfordjournals.org/content/35/10/3322.short

http://link.springer.com/article/10.1007/PL00006217#page-1

http://www.sciencedirect.com/science/article/pii/S1055790308005009

http://www.sciencedirect.com/science/article/pii/S0168952503001185

http://www.sciencedirect.com/science/article/pii/S0378111908005374

If you plan to use highly variable cp-markers you must look on series of works of Joey Shaw

https://www.researchgate.net/publication/51200968_The_tortoise_and_the_hare_II_relative_utility_of_21_noncoding_chloroplast_DNA_sequences_for_phylogenetic_analysis

https://www.researchgate.net/publication/51186853_Comparison_of_whole_chloroplast_genome_sequences_to_choose_noncoding_regions_for_phylogenetic_studies_in_angiosperms_The_tortoise_and_the_hare_III

https://www.researchgate.net/publication/267815561_Chloroplast_DNA_sequence_utility_for_the_lowest_phylogenetic_and_phylogeographic_inferences_in_angiosperms_The_tortoise_and_the_hare_IV

I hope it will be helpful for you. But also you can serch for another ones.

The next step of your work - go to NCBI, serch for sequences of such noncoding regions for all present here Tordylieae or closely related ones. So you will be able to compare and choose most appropriate markers.

Best wishes 

Article The tortoise and the hare II: relative utility of 21 noncodi...

Article Comparison of whole chloroplast genome sequence to choose no...

Article Chloroplast DNA sequence utility for the lowest phylogenetic...

Hi Fahim,

I also agree with the suggestions of Andrii above. There are several genomic regions avaiable...and you will be have to try which works better in your species of interest...and for the type of analysis you are interested in..

best regards

It depends on your specific focus zone.You can consult these sites:

http://nar.oxfordjournals.org/content/35/10/3322.short

http://link.springer.com/article/10.1007/PL00006217#page-1

http://www.sciencedirect.com/science/article/pii/S1055790308005009

Dear Altınordu;

I dont know your question's ansver. You can ask this question Hatice Güneş from Muğla Unv. 

have a nice day...

Hi!

As far as I am concerned markers commonly used to infer phylogenies on specific/intraspecific level in Apiaceae are ITS (nuclear) and plastid rps16, rpoC1 intron, rpoB-trnC, as well as (less popular) psbA-trnH, trnQ-rps16 and exon of rpoC1. If genetic distance beteween taxa is very small try WAXY (but it's very challenging to obatin its sequences).

Best regards