To take a barcoding approach I need to amplify rbcL/matK/ITS of Sterculia villosa and some other members of Sterculiaceae (Chronquist, 1981). How should I select a suitable primer for a particular plant for proper amplifiation? Please suggest? Also if I want to test genetic diversity using ISSR, SSR or RAPD, what are the things I should do to select a marker? Thanks in advance.
Put the sequence in Primer3 software. Select the targeted region with the help of < and>. Put GC between 50 to 56 and product size within 230 to 270 bp. I hope that would help you.
Whatever the primers you mentioned (rbcL/matK/ITS) are universal and you can use any plant species to check the diversity.
First you need to isolate DNA, check, quantify, take one are two samples and try amplification. Once you see good amplification amplify all your samples. Then analyse, make 0,1 data sheet, you have variety of softwares NTSys PC etc. to creat phylogenetic trees.
The following "Ethnobotanical Study of Plants used for construction, handicrafts and fiber in Southern Shan State, Myanmar" is in press and one seq. is available in NCBI
Good Luck!!
The plant-specific universal primers for barcoading are suitable for over 85% of plants in most groups. In some cases, design of new taxon-specific primers or already existed primers for each group or modifications of existing primers, is used in DNA barcoading
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