DNA Testing Question

[maitaman]

The DNA testing is to determine species relationships and would be as much as useless in determining hybrid lines. even with only two species crosses, there is not going to be more than a half-marker determination. We have a long way to go before we can even determine which plant of a given species is involved, much less which in a series.

[Vulpes Velox]

Originally Posted by cirillonb

DNA testing for humans and animals is extremely expensive (in terms of thousands of dollars.) Remember just within the last 10 years has the human genome (a list of all the chromosome sites on the DNA strand) been defined at the cost of several Billion (that's with a B) dollars.
Furthermore, what Ray said is exactly true. Parentage is not easily determined this way.
Nick Cirillo

true, however.. this is because they are looking at the entire genome. that is not needed to just identify the species, you can just look at a specific sequence. it greatly reduces cost and can be done very fast. as people mention there is databases being build, but they are actually already very big, i wouldnt be suprised if they already contain loads of orchids.

(not saying everyone can just order something like that (labs that analyze these things normally work with big orders))

not sure if a hybrid might be difficult to identify, but if its in the database and you know what to look for i cant see why? (someone can probably correct me though ) but why would a hybrid be different to look at than an original species?

[Andrew]

Vulpes Velox,
A couple of things that need to be clarified. Sequence analysis is used to assess the evolutionary relationship between taxa (species, genera, etc.). It involves comparing how much a homologous DNA sequence has changed between two taxa so you can assess how different the two taxa are. This can certainly be extended to the point where you can group different plants into the same species based on the similarity in DNA sequences. The problem with applying this to hybrids is that hybrids are an amalgam of chromosomes from different species, so comparing one sequence on one chromosome set will only tell you about the presence of two species in the hybrids (or one species if mitochondrial or plastid DNA is examined). To determine the species make up of a hybrids you'd need to sample identifiable sequences from all chromosomes and work out the percentage of species in the hybrid. However, this would really only tell you that a hybrid is 50% species A: 25% species B: 25% species C. You still would not know if the hybrid was Ax(BxC) or (AxB)x(AxC) which would be considered two different hybrids. Even if this percentage information was useful, you would still need to define the appropriate chromosomal gene sequences to examine. Most of the orchid sequence analysis being carried out by taxonomists uses very highly conserved DNA such as NOR's. As these regions are so highly conserved, you can often piggy back off the work that others have done in designing primers against these regions. Trying to look at other regions on all of the chromosomes that are specific to the species requires a better knowledge of the sequences of the taxa being examined. Realistically, orchids are of limited scientific importance and of very little genetic importance so there is little incentive in sequencing the genomes of large numbers of orchid species. The bulk of the plant genomes in the various databases belong to agriculturally important plants or established genetic models.

[Vulpes Velox]

your probably right, since i havent really looked that much into plant DNA ... the databases consist ofcourse of "important" plants such as agriculture as you mention. but you can also find many others. i jsut did a quick search on Phalaenopsis gigantea in NCBI for example (posting the sequence would take alot of room )

as i said your probably right about hybrids and such, but im not really sure i understand why it in theory should be a problem?

"hybrid is 50% species A: 25% species B: 25% species C"
if your two hybrids have the exact same DNA, wouldnt that make them the exact same kind of plant? and if they dont have the same DNA, why isnt it possible to tell them apart?

[Mahon]

Originally Posted by Vulpes Velox

true, however.. this is because they are looking at the entire genome. that is not needed to just identify the species, you can just look at a specific sequence. it greatly reduces cost and can be done very fast.

Vulpes,

I don't think that using specific sequences of an accession is accurate for identification purposes (please correct me if I'm wrong). However, identifying relationships between species (and even genera) has proven more accurate. This approach is being used to rid of Dracula xenos from the genus Dracula.

It should be remembered that we are looking at a small piece of something huge, and not to uphold it as a definite answer, but a 'tool'. Let the Prosthechea scheme be a better example of how definite molecular evidence really is. Still, nothing can override morphology; it can just make it more useful.

Lastly, assuming a person had a Brassalaeliocattleya hybrid that they wanted to know what species and hybrids it is comprised of, and if there were many Cattleya multigeneric hybrid accessions (and there were some HUGE steps made! lol), it would be the equivalent of finding the needle in the haystack, on fire, blindfolded, and hands tied.
Chances are, that person would be better off guessing not only the parentage in their hybrid, but the exact date, time, and location Jim Carey will say something funny... there wouldn't be a person out there willing to waste valuable time and money in entering in random hybrids to be accessed later. That time and money can be put in 'checking' intergeneric and intrageneric relationships, which is the sole use of 'DNA testing' concerning orchids.

Lisa,
Do you have a pic of the plant you are curious about its parentage? Sometimes, primary and natural hybrids are more apparent in what their parentage can be...

-Pat

[Vulpes Velox]

now genetics is certainly not my strong area, so if someone who is very much into that says something else, then im willing to believe it... however im pretty sure identifying a species isnt that difficult.. i worked with sequences on mykorrhiza a year back, to compare different forest areas in sweden. the main point wasnt as much to identify them as to just tell them apart.. but, the mykorrhiza species that is known (alot arent) could be identified... again plants and genetics arent my strong side, so i could be totally wrong.. and as some have said hybrids make it more difficult maybe? i dont know, i would jsut be suprised if you couldnt easily identify a plant species, especially since they are most likely much more well documented than mykorrhiza ...
but seems like im a bit outnumbered so again it might just be me that is wrong

[Mahon]

Originally Posted by Vulpes Velox

now genetics is certainly not my strong area, so if someone who is very much into that says something else, then im willing to believe it... however im pretty sure identifying a species isnt that difficult.. i worked with sequences on mykorrhiza a year back, to compare different forest areas in sweden. the main point wasnt as much to identify them as to just tell them apart.. but, the mykorrhiza species that is known (alot arent) could be identified... again plants and genetics arent my strong side, so i could be totally wrong.. and as some have said hybrids make it more difficult maybe? i dont know, i would jsut be suprised if you couldnt easily identify a plant species, especially since they are most likely much more well documented than mykorrhiza ...
but seems like im a bit outnumbered so again it might just be me that is wrong

Well, you are for the most part correct then
The main use for the 'DNA analysis' in orchids is to determine relationships. But, in your case, the sequences were used to demonstrate differences between taxa, not to identify a specific taxon with accessions in a database.

-Pat

[Vulpes Velox]

well that was just because it wasnt really relevant to us to know what species it was (dont worry wont bore you with to much details about the research ). we did identify some of the species this way however.

[Andrew]

Originally Posted by Vulpes Velox

"hybrid is 50% species A: 25% species B: 25% species C"
if your two hybrids have the exact same DNA, wouldnt that make them the exact same kind of plant? and if they dont have the same DNA, why isnt it possible to tell them apart?

They can have the same DNA but the registered names are different.
eg Dendrobium (speciosum x tetragonum) x (kingianum x tetragonum)= Jannine Banks
Dendrobium (speciosum x kingianum ) x tetragonum= Ku-Ring-Gai

Most people with a NOID are more interested in a name rather than a species background. If you simply want to know what species are in the background, most experienced breeders can take a good guess.