Have sports and strains of apple varieties been DNA tested and found to be the genetically the same or different?
There are dozens of named strains of Red Delicious and Gala. Even 200 years ago Newtown Pippin was separated into Green and Yellow. Who knows how many Golden Russet and Winesap varieties there are and used to be? The original Gravenstein is different in appearance from Banks and Red Gravenstein. Appearance isn’t the only difference in some sports and strains; they may ripen at different times. If they genetically identical, can they look and behave differently?
The reason I ask is that when “Briggs Auburn” was genotypically identified as “Northwest Greening,” that may not mean they are one and the same — or does it?
Briggs Auburn is just one example several varieties that have recently been tested and discovered to be not what they seem.
(If this question has already been asked and answered, I haven’t found it.)
I know UC Davis says on their DNA testing site that “The service does not distinguish between bud-sports (somatic mutations, clones) within a given variety.”
I wonder if that’s because the technology can’t get that specific or they just can’t do it for cost reasons?
In most cases for sports, DNA won’t distinguish. Changes are usually a single gene or else a cell layer variant. DNA can show major changes, but won’t work for very small changes. If we ever get to the point where the entire genome can be read, we should be able to distinguish small changes.
That is correct. Only a few alleles are tested. Most are not really mapped. A trait or phenotype may involve multiple alleles. None of this is simple. We still have a lot to figure out yet.
Not quite accurate. 3 genes plus 2 chromosome segments differentiate domesticated maize from teosinte. Many more mutations have occurred in domestic maize due to high selection pressure for commercial traits. So while there are 3 genes and 2 chromosome segments different, actual genome changes amount to nearly 3 percent of the maize genome compared with teosinte.
I’ve looked around myself and never found anything very satisfying investigating the genetics/epigenetics of bud sports. I didn’t try searching exhaustively, there may be some studies out there that I didn’t find.
But based on what we know about plant genetics, we can speculate a bit on what could be going on.
Somatic mutations, which are mutations that happen during cell division as a plant grows new tissues. It could be due to cosmic rays, oxidative stress, viruses, or mobile genetic elements (transposons), or anything that damages the DNA. These would directly alter the DNA sequence of the genome, and as has correctly been stated in this thread, detecting these by sequencing just comes down to a precision/sensitivity problem. Actually I’d say it comes down to a money problem. The tech exists, it just takes some effort and money to get a full end to end (“telomere to telomere”) genome sequenced and assembled correctly.
Epigenetic changes, which are changes to the DNA state like chemical modifications or structural changes in how the DNA is packaged. These are independent of the actual sequence of the genome. In plants, a lot of the cytosines (the “C” base of the four A, T, G, C bases that make up DNA) are chemically modified with a methyl group. The details get quite complex, but overall this methylation often ends up silencing genes, meaning they are still part of the genome, but inactive. Also all DNA in plants (and animals) is wrapped around structural proteins (histones). Chemical modifications to these histones including methylation and acetylation can change how tightly things are compacted and this can also silence or turn on genes without affecting the actual DNA sequence. We have some fairly mature technologies to map out both DNA methylation and histone states of the genome. But they are again fairly labor intensive, not cheap, and the interpretation of the data is still a challenge because we just don’t have a good handle on how it all fits together.
One major challenge is that mutations and epigenetic changes are pretty frequent, but many of them have very little effect. Any grafted species that has been propagated for decades or centuries has accumulated many different genetic and epigenetic changes. While most of these don’t have any major obvious effects, in other cases one small change to a single gene can have a cascade of effects because that gene interacts with many other genes.
Because these technologies are still relatively new, require a lot of expertise to apply correctly, and remain somewhat expensive, they mainly get applied to high value crops like corn and soybean. And even there we don’t fully understand what we’re looking at. I think it’ll be a while before we get satisfying answers here.