Hilde Nybom, et al., DNA fingerprinting in botany: past, present, future, Investigative Genetics 5:1, 2014
In the 1980s, the REFP methodology was also first applied to the chloroplast DNA (cpDNA) molecule.
Since the cp DNA molecule is highly conserved, there is very little intra-specific variation, and cpDNA-based RELP studies have therefore mostly been conducted on an inter-specific level.
While the plant mitochondrial DNA (mtDNA) sequence is usually highly conserved, the size and structure of mtDNA molecules may vary widely even within individual plants. Moreover, recent studies indicated that substitution rates of mtDNA genes can vary enormously even among closely related plant species.
A special situation is encountered when products from protected trees are involved since woody tissues usually yields heavily degraded DNA. Nevertheless, a set of SNP markers derived from cpDNA intergenic spacers have proven useful for identification of tropical tree species using wood-derived DNA samples.