matK is a chloroplast gene, matR is in the mitochondrial genome. Most studies found mtDNA in plants not as informative as nuclear or cpDNA, so you might want to stick with matK.

Agree with Ingo. See the following paper, explains about matR being mitochondrial sequence.

http://www.biomedcentral.com/1471-2148/7/217

Thank u Michalak Sir for providing information. :-)

I also thank Angelika mam for providing the link.