Your idea of a consortium of growers to pool together to plan and contribute specific plants (and help fund) to test the feasibility of species identification is a good one, but I suspect we are still a few years away from easy enough access to the technology.
Is this jenmanii alba?
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I have a very good friend at Illumina and we have discussed this a bit. The key is finding a lab that does this all the time for other plants already and has brought the cost structure down and simplified the logistics of sample processing and data generation. If I could send a leaf or root + $50 and get back data on 7 genes that are already identified as having the necessary resolving power, the rest is pretty easy. The necessary primer sequences for those genes are already out there and I've spoken a little with Cassio van de Berg via email about this. He is certainly aware of and working on other genes and necessary primers to evaluate an even larger array of markers. Once a motivated person has the data for a bunch of plants, building a model is actually not that bad. Turning that into a service in itself is probably a long way off as there just aren't enough orchid breeders to make it financially viable, but being able to do this once there is a published baseline for the species and comparing individual plant data against it is again pretty easy even for a motivated hobbyist. This is why I would love to talk with Monocotman further. It hadn't really occurred to me that other plant breeders are already doing this for other more commercially important plants.
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Geoff
it sounds like you are already half way there!
Certainly you know more about the mechanics of the procedure than I do.
I just send off leaf or grain samples to the lab and receive marker data back already analysed.
Most plant breeders approach the marker issue from a different angle to Cassio.
We use a set of markers than takes a snapshot of the entire genome, not just a few genes. The markers are called SNP (single nucleotide polymorphisms) or snips for short. These are individual base pairs in functional genes only where the A,T,C or G base pair can vary at specific sites for different breeding lines.
As you must know, functional genes are highly conserved and these SNP’s are few and far between.
It has taken much effort to find these sites.
An individual call means little but when you have 2000 of them for each line, you can use it to characterise the variety and compare it to others. Parentages can be calculated and lots of further analysis performed, most of which is commercially sensitive.
I work for a large multinational plant breeder and we just have a single lab doing the analysis of all the crops for the whole of the company across the world. The lab is state of the art and fully automated.
regards
David
it sounds like you are already half way there!
Certainly you know more about the mechanics of the procedure than I do.
I just send off leaf or grain samples to the lab and receive marker data back already analysed.
Most plant breeders approach the marker issue from a different angle to Cassio.
We use a set of markers than takes a snapshot of the entire genome, not just a few genes. The markers are called SNP (single nucleotide polymorphisms) or snips for short. These are individual base pairs in functional genes only where the A,T,C or G base pair can vary at specific sites for different breeding lines.
As you must know, functional genes are highly conserved and these SNP’s are few and far between.
It has taken much effort to find these sites.
An individual call means little but when you have 2000 of them for each line, you can use it to characterise the variety and compare it to others. Parentages can be calculated and lots of further analysis performed, most of which is commercially sensitive.
I work for a large multinational plant breeder and we just have a single lab doing the analysis of all the crops for the whole of the company across the world. The lab is state of the art and fully automated.
regards
David
Part of my prep in doing research for my orchid presentations have come across this conundrum of genetic analysis for species identification and familial relationships. The need for the identification of true species is important to maintain the genetic stability of the wild population for the future and to determine taxonomic associations.
The problem we face is that the newer and bigger 'species' from line breeding and selection may be contaminated unknowingly or deliberately through the use of dubious parent species (like walkeriana 'Kenny' etc) and continued for generations, until one day it appears on the judging table as a superior species that has 0.5% hybrid genes. Through the use of genetic testing of certain SNPs, it may not be detected. So these can masquerade into the breeding population as pure. As David says, the entire genome may need to be analyzed through a comparison with a baseline of that species (extract from a confirmed jungle plant). It must take into account of the ploidy variability.
In the old days, certain species were thought to be one and the same and so were crossed with each other (such as violacea and bellinas, loddigesii and harrisonniana, etc). There are also different forms of the same species that may have been better off to separate like the different populations of trianae (typo vs sangretoro types), and were cross bred. Some were sold mistakenly as one species (eg guttata sold as tigrina) and bred onto a true tigrina, and perpetuated by breeders unbeknownst. These are the true infiltrators that can confuse the entire picture. I have seen plants of these in South America, posing as a species and being defended to the death of its authenticity by the owners.
As Geoff proposed, a systematic protocol of genotyping based on David's methods of full genome and SNPs analysis is the ideal way to truly identify a pure species from a mole. It is a costly endeavor but it is the only way. Cassio and Chase have led the initial stages to show the science has practical applications. It is now up to the universe pull this together as it did for barley lol.
I, for one, am ready to support this! Maybe we should start a crowdfund for this project.
The problem we face is that the newer and bigger 'species' from line breeding and selection may be contaminated unknowingly or deliberately through the use of dubious parent species (like walkeriana 'Kenny' etc) and continued for generations, until one day it appears on the judging table as a superior species that has 0.5% hybrid genes. Through the use of genetic testing of certain SNPs, it may not be detected. So these can masquerade into the breeding population as pure. As David says, the entire genome may need to be analyzed through a comparison with a baseline of that species (extract from a confirmed jungle plant). It must take into account of the ploidy variability.
In the old days, certain species were thought to be one and the same and so were crossed with each other (such as violacea and bellinas, loddigesii and harrisonniana, etc). There are also different forms of the same species that may have been better off to separate like the different populations of trianae (typo vs sangretoro types), and were cross bred. Some were sold mistakenly as one species (eg guttata sold as tigrina) and bred onto a true tigrina, and perpetuated by breeders unbeknownst. These are the true infiltrators that can confuse the entire picture. I have seen plants of these in South America, posing as a species and being defended to the death of its authenticity by the owners.
As Geoff proposed, a systematic protocol of genotyping based on David's methods of full genome and SNPs analysis is the ideal way to truly identify a pure species from a mole. It is a costly endeavor but it is the only way. Cassio and Chase have led the initial stages to show the science has practical applications. It is now up to the universe pull this together as it did for barley lol.
I, for one, am ready to support this! Maybe we should start a crowdfund for this project.
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Genetic stability of wild populations.. Sounds like a project an organization like the AOS could help seed a small amount of money to fund a grad student at a land grant institution tied to one of the national labs like USDA ARS. Or an orchid conservation effort through the Smithsonian? Where is Tom Merinda when you need him. Maybe someone here could write an article for the AOS bulletin.. start the ball.
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Besides traditional farmers that are doing this for cash crops, the biggest driver appears to be marijuana growers. I think this might be the key as there are a number of testing services that are starting to combine genotypic and phenotypic screening for a price sensitive group that isn't planting millions of acres of a crop but something more similar to orchid breeding where one is trying to tweak strains.
I agree that if one wants to set an individual plant as the taxon genetic reference similar to the type species and compare against that, it requires a larger set of SNPs and the data set necessary to get to reasonable resolving power is pretty big. One needs to know the inter and intra species variability in order to resolve. I think this is where Cassio is headed at the moment to try and look at a lot more genes so one can characterize the intra species variability to refine specific taxa concepts and for in situ preservation and/or repopulation purposes.
If we want to do things like show 'kenny' is a hybrid today, that requires very little data. The one can of worms that this will assuredly open is that our definitions of individual species are often a lot more rigid than reality. Walkeriana and nobilior have gene flow and while separated as taxa, there are plenty of plants in the wild that aren't quite so black and white. Assuredly there have been thousands of wild versions of 'Kenny' (perhaps not semi albas) that have existed and introgressed back into loddigesii or walkeriana. Tirgnia and guttata are more of a man made problem, but wild plants from over the entirety of the distribution range are not quite as clear either and likely several of the separated distributions of each species are somewhat distinct from one another. Bicolor for example is assuredly a complex and depending upon its specific habitat, has gene flow from several unrelated species.
Perhaps this is something we could look at as three different problems. One is the evaluating the purity of a plant with regard to a specific reference standard, the second is what is the variability in the wild of a specific taxa and how to understand that with regard to biogeography and the third is what the heck are actually in our collections and how well does that map to what is in the wild with regard to specific taxa concepts.
I really like the idea of trying to evaluate what we have in our collections and either crowdsourcing the funding and/or getting the AOS to help with finding someone that is intersted in doing the work. The key difficulty is in getting the plant source material from our collections and from people like Jerry Fischer, Fred Clarke, Ben Oliveros, and many others that are doing the majority of cattleya breeding and own many of the famous clones that have been used to make current generations of plants. That can be solved by motivated individuals contributing source material. The reality is that the number of plants that have been used to breed pretty much all of the plants we are growing as Cattleya species are derived from perhaps a few thousand clones. This is a product of a few imported plants that win awards and then become the founders of the next generation. Because generation times are long, we have perhaps a handful of generations at most from a wild ancestor in all but the most aggressively line bred plants. The same can be said for the slipper orchids.
DrLeslieEe and anyone else interested, I'd be happy to speak further about how to scope out a project proposal and then approach the AOS or others to see what could be done to make this actually happen.
I agree that if one wants to set an individual plant as the taxon genetic reference similar to the type species and compare against that, it requires a larger set of SNPs and the data set necessary to get to reasonable resolving power is pretty big. One needs to know the inter and intra species variability in order to resolve. I think this is where Cassio is headed at the moment to try and look at a lot more genes so one can characterize the intra species variability to refine specific taxa concepts and for in situ preservation and/or repopulation purposes.
If we want to do things like show 'kenny' is a hybrid today, that requires very little data. The one can of worms that this will assuredly open is that our definitions of individual species are often a lot more rigid than reality. Walkeriana and nobilior have gene flow and while separated as taxa, there are plenty of plants in the wild that aren't quite so black and white. Assuredly there have been thousands of wild versions of 'Kenny' (perhaps not semi albas) that have existed and introgressed back into loddigesii or walkeriana. Tirgnia and guttata are more of a man made problem, but wild plants from over the entirety of the distribution range are not quite as clear either and likely several of the separated distributions of each species are somewhat distinct from one another. Bicolor for example is assuredly a complex and depending upon its specific habitat, has gene flow from several unrelated species.
Perhaps this is something we could look at as three different problems. One is the evaluating the purity of a plant with regard to a specific reference standard, the second is what is the variability in the wild of a specific taxa and how to understand that with regard to biogeography and the third is what the heck are actually in our collections and how well does that map to what is in the wild with regard to specific taxa concepts.
I really like the idea of trying to evaluate what we have in our collections and either crowdsourcing the funding and/or getting the AOS to help with finding someone that is intersted in doing the work. The key difficulty is in getting the plant source material from our collections and from people like Jerry Fischer, Fred Clarke, Ben Oliveros, and many others that are doing the majority of cattleya breeding and own many of the famous clones that have been used to make current generations of plants. That can be solved by motivated individuals contributing source material. The reality is that the number of plants that have been used to breed pretty much all of the plants we are growing as Cattleya species are derived from perhaps a few thousand clones. This is a product of a few imported plants that win awards and then become the founders of the next generation. Because generation times are long, we have perhaps a handful of generations at most from a wild ancestor in all but the most aggressively line bred plants. The same can be said for the slipper orchids.
DrLeslieEe and anyone else interested, I'd be happy to speak further about how to scope out a project proposal and then approach the AOS or others to see what could be done to make this actually happen.
Im definitely into this endeavour. I’m sure we can corral some interested individuals into this topics including David and Terry.
I can also ask Tom Miranda and possibly Drs Griesbach, Pradhan, Stig Daelstrom and Wesley Higgins to add their experiences into this effort.
And of course, your contact Cassio would be a prime source of info and help too.
If our proposal is doable, I can approach Rob Fuch, president of AOS to see if they are amendable to support this kind of project. Rob has been very supportive of my judging apprenticeship through many shows and guided me kindly.
I can also ask Tom Miranda and possibly Drs Griesbach, Pradhan, Stig Daelstrom and Wesley Higgins to add their experiences into this effort.
And of course, your contact Cassio would be a prime source of info and help too.
If our proposal is doable, I can approach Rob Fuch, president of AOS to see if they are amendable to support this kind of project. Rob has been very supportive of my judging apprenticeship through many shows and guided me kindly.
wanted to add the cattleya symposium might be a good group to drum up support and having the perspective of a taxonomists like Francisco Miranda who might be able to help procures samples from existing plants in the dwindling jungle habitats or existing overseas collections.
Yes let’s add you Pete and Francisco.
I do have contacts in South America who can help sourced the jungle plants as well.
I would contribute some money to such an adventure. I would think we would pick a demonstration specie to work on and make mistakes - what would you pick?
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This is very cool how intersted people are. I will set up another thread shortly. I second Terry's idea of picking one or a couple of species to think through how to do something like this on a small scale and show it can be done and then how it could be expanded.
pick the controversial - walkeriana. Just need material from the 'jungle', not in nursery plants to start with.
As in any science experiment, the most logical is to test the hypothesis in question. With that I agree with Terry (and Geoff).
I also concur with OzPaph to start with the controversial species that we know has interlopers within its ranks. Walkerianas and mossiaes are the most easily available test subjects, since jungle plants are easy to sourced from reputable growers.
And Pete, great idea to approach filed guides like Francisco Miranda and conservation committees to help with the project.
Could it be funded through AOS, to which we could contribute funds? I agree we need verified native plants to be a bench mark. We also need to identify a lab and at least plant (if not orchid) genetics experts to analyze data. Maybe a simple demonstration project would take one native plant and figure out what could be sequenced with existing technology. If this is too difficult or too expensive, then this isn't the time to move forward.
Phred
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So here’s some food for thought:
1) There are, from what I find, 49 accepted species of Cattleya
2) There are, from what I find, 2,821 known primary hybrids.
Questions:
1) It seems obvious that nature is probably as good at this as we are... as long as the two species are in proximity to each other.
2) It seems obvious that wild crosses could have happened, even if rarely, way back in time. The resulting offspring from (species A x species B = hybrid C) could be crossed back to one of the parent species (C x a plant from species A). This could happen for several generations and with each generation of offspring. Since the “hybrid” plant in each generation can only contribute 50% of its genetics to its offspring then each consecutive generation species A is crossed back in, the genetics from the original species B parent is reduced. At what point would an offspring be considered a species?
3) What determines... or should determine what places a plant into a particular species? Should it be numerous genes that are the same or should one gene put it out?
4) What happens when the wild plants you test show an odd gene or two for the species but everything else looks the same as the group?
Correct me if I’m wrong but I’m guessing that all Cattleya have at least some genes that are the same. What we need to look at are the ones that are different and decide if those genes actually separate them.
1) There are, from what I find, 49 accepted species of Cattleya
2) There are, from what I find, 2,821 known primary hybrids.
Questions:
1) It seems obvious that nature is probably as good at this as we are... as long as the two species are in proximity to each other.
2) It seems obvious that wild crosses could have happened, even if rarely, way back in time. The resulting offspring from (species A x species B = hybrid C) could be crossed back to one of the parent species (C x a plant from species A). This could happen for several generations and with each generation of offspring. Since the “hybrid” plant in each generation can only contribute 50% of its genetics to its offspring then each consecutive generation species A is crossed back in, the genetics from the original species B parent is reduced. At what point would an offspring be considered a species?
3) What determines... or should determine what places a plant into a particular species? Should it be numerous genes that are the same or should one gene put it out?
4) What happens when the wild plants you test show an odd gene or two for the species but everything else looks the same as the group?
Correct me if I’m wrong but I’m guessing that all Cattleya have at least some genes that are the same. What we need to look at are the ones that are different and decide if those genes actually separate them.
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Looks like a C. gaskelliana var alba. Nice whatever it is.
WOW, lots of historic names here. All I can say is Weird looking Paphs! 
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