Dear Straight Dope:
Do different plants belonging to the same species have their own unique DNA sequences (just like us humans)? Another twist to the same question: Let's say I have an apple. Would I be able to tell, by DNA analysis, exactly which apple tree it came from?
Doug and Colibri reply:
Everything, even clonal and asexual organisms, has some difference that sets it apart from every other member of its species. The act of replicating DNA is not quite perfect, and there are always small glitches in the copying process. The trick is detecting these differences, and making use of them in a diagnostic way. Especially important is the level of variation between and within individual organisms. To use your apple example, if you actually could go in and sequence every single nucleotide in the genome of every cell in that apple, you’d find that no two cells were exactly the same. At that point, the question is this: is the level of difference between two cells in that fruit significantly less than the difference between any given cell in that fruit and, say, any given cell in another tree with the same parents? The answer is "probably." But sequencing an entire DNA strand could be awfully dang expensive.
Luckily there’s a shortcut that makes this kind of testing pretty routine, and not all that expensive. It’s really not necessary to analyze every single nucleotide in the genome to find significant differences between individuals. The trick is to select parts of the genome that do not code for genes. Because these sections (often known as “junk” DNA) are not expressed, mutations there are not weeded out by selection and are free to accumulate (unlike in coding sections of the genome where deleterious mutations are rapidly removed each generation). Such parts of the genome are highly variable (polymorphic) between individuals.
One common method of comparing this DNA is known as restriction fragment length polymorphism (RFLP, or “riflip”) analysis. (How’s that for a mouthful?) I won’t go into all the details, but certain enzymes (known as restriction enzymes) can be used to cut DNA wherever particular combinations of nucleotides occur, producing a set of fragments. Because the location of these nucleotide combinations varies between individuals depending on the specific mutations they carry, each individual will produce a quite specific array of fragment lengths. These fragments can then be sorted and compared through gel electrophoresis.
This technique is often known as “DNA fingerprinting.” While not as individualized as real fingerprints, it allows the calculation of the odds of two samples having come from the same individual as opposed to different individuals drawn from the same population. It also can be used to calculate the degree of relatedness between two or more different individuals. This is the method used in criminal forensics.
A complication with using DNA to identify plants is that many cultivated varieties, particularly fruit, are clones produced by grafting. Since the DNA of clones (including junk DNA) is nearly identical, DNA fingerprinting is less likely to catch the very few differences that would enable you to identify which tree an apple came from. Instead you’d have to sequence every nucleotide in the genome, an impractical task if your goal is merely identification. DNA fingerprinting can be used to identify plants that reproduce sexually in the wild, though.
For more info on "riplip," see users.rcn.com/jkim ball.ma.ultranet/BiologyPages/R/RFLPs.html.
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