This paper reflects the research and thoughts of a student at the time the paper was written for a course at Bryn Mawr College. Like other materials on Serendip, it is not intended to be "authoritative" but rather to help others further develop their own explorations. Web links were active as of the time the paper was posted but are not updated.
2005 Final Paper
Apples. We eat an awful lot of them – about 19 pounds per person per year . They're America's second-favorite fruit, and a big business to boot. The annual American Apple crop is worth about $1.8 billion . On top of that, though, they may be the first known successful instance of mass cloning. All in all, they're a very interesting sort of fruit.
Like anything else that reproduces sexually, apple trees are heterozygous – the offspring of an apple tree is likely to be very different from the parent tree.  For human purposes, this is a bad thing. We want an apple to taste like an apple, or at least a Fuji apple to taste like a Fuji apple, a goal which would be difficult to meet if we had to wait 20 years from each tree's sprouting to know what kind of apple it would produce. Nevertheless, that's basically the process we once went through. In 1905, a USDA publication listed 14,000 varieties of apple grown in the United States. As on pomologist describes it, "They came in all shapes and guises, some with rough, sandpapery skin, others as misshapen as potatoes, and ranging from the size of a cherry to bigger than a grapefruit. Colors ran the entire spectrum with a wonderful impressionistic array of patterning—flushes, stripes, splashes, and dots." 
In order to ensure more consistency of quality, however, apple growers turned more and more toward the process of grafting, a form of asexual reproduction which genetically amounts to cloning. A seed is allowed to sprout and develop a root system. Shortly after a stem begins to appear from the new seedling, it is cut just above the surface. A twig is then cut from the tree one wishes to reproduce, and attached to the cut surface of the new seedling. After a short time, the stem and the twig grow together. After that, they will continue to grow as if they had been joined from birth. 
The resulting tree is an interesting specimen. Its DNA is actually different above and below the grafting point. The seedling DNA in the roots is not overwritten, rather, the roots never "know" that any cutting has taken place. The roots continue to do what they do, which is to grow and send water and minerals upward, not really "caring" those materials are going. The aboveground portion of the tree, on the other hand, is totally unaware that its root structure is not its own. As long as it keeps getting water and minerals from somewhere, it just keeps doing what it does, which is to grow, branch, and eventually flower and produce fruit for reproduction. Note that in this process, the root DNA is thrown away with every generation - only the stem DNA, which is identical to its parent, reproduces.
Grafting is a process known from ancient times, but little used until recently. First of all, it's time consuming. If you're just trying to get the food you need to survive, poor-tasting, inconsistent apples from dozens of spontaneously-sprouting apple seedlings is preferable to predictably tasty apples from one grafted tree. Additionally, however, early American apple growers had an idea that grafting was unnatural, and would reduce the vigor of the apple crop over the long term . With the advance of the economy and better guaranteed food availability, however, the first objection dwindled in importance, and pre-Mendel, pre-Darwin, the second objection couldn't compete with the appeal of bigger, tastier, hardier apples.
Virtually the entirety of America's commercial apple crop today is graft-grown. Additionally, compared to the 14,000 varieties eaten in 1900, the number today is closer to 90, with just a few varieties (especially Red and Golden Delicious, Fuji, Gala, and Granny Smith) making up the bulk of the apples grown. [1, 2] On a genetic level, the similarity is even more pronounced, as many of those 90 varieties are just hybrids of the others. The Fuji, for example, is a Red Delicious crossed with Thomas Jefferson's favorite apple, the Ralls Genet. People like the idea that anywhere you go, you can get an apple, and it will be the same as an apple anywhere else. It's the McDonald's factor. The difference, however, is that no biological systems rest on the diversity of fast-food restaurants. Genetic diversity in plants, however, serves (or, rather, served, when we had it) an important purpose.
Today's apple crops, genetically similar and genetically stagnant as they are, are extremely prone to pests and disease.  They present a standing target to other organisms which are constantly evolving to better target them. In recent years, diseases like apple scab, cedar apple rust and fireblight have appeared or become more prevalent , and growers have been forced to use more and more pesticides to keep the bugs off – about a dozen sprayings per season at this point.  A really good pandemic, as seen with Dutch Elm Disease, could even wipe out a crop. Growers and scientists alike, for that reason, have begun to search for ways to broaden the gene pool.
Just allowing more seedling reproduction would probably not do the trick, although botique orchards have begun increased cultivation of heirloom and new varieties.  At this point, it's estimated that 90% of the world's apples are descendants of two trees.  While I'm unable to address the scientific merits of that claim, it appears that at least in spirit it's correct – there just isn't enough diversity in the American commercial stock to reinvigorate the crop in the near future. For that reason, scientists have begun to go to the source – Central Asia, specifically Kazakhstan, where it is believed apples originated. The wild apple groves around Almaty (capital of Kazakhstan, "father of apples" in Kazakh), have proven to be highly disease resistant, and 15-20 thousand of their seedlings have been planted for study in American research orchards. 
One of the main dangers to the Kazakh solution, is, of course, human short sightedness. The Soviets cleared much of the Almaty apple forests, although that might be excused, since they had no idea they were anything other than just more apples. However, since the 1991 Soviet breakup, at which point the genetic importance of the forests was clear, there has been another spate of forest clearing, this time for luxury houses built with oil wealth. Since 1940, about 92% of the Almaty apple forests have been destroyed. 
The story of the apple teaches us a few lessons about mucking with nature – what we can and can't do. Creating hybrids is simply guiding the natural process, selecting among the possible random pollen mates a plant might have. It trades good qualities that might have developed by random selection for good qualities that will develop by intentional selection, and trades the random bad qualities of random selection for the unforeseen bad qualities of intelligent selection. Either way, motion continues. Stopping evolutionary motion entirely, on the other hand, is profoundly unnatural. Sexual reproduction has become the norm among life on Earth for a reason – because varying lifeforms constantly "trying out" new features have a survival advantage over those lifeforms which don't. It should come as no surprise then that, having created a clone army, we now see that those clones are suffering from rare diseases en masse. It's a consequence we could have foreseen by examining the geneology of any inbred family of European royalty.
1. Henseley, Tim; A Curious Tale: The Apple in North America, http://www.bbg.org/gar2/topics/kitchen/handbooks/apples/northamerica.html
2. Philips, Becky; Innovation, specialization
grow with world apple market, http://www.wsutoday.wsu.edu/completestory.asp?StoryID=1256
3. White, Gerald B.; Cornell 2005 Fruit Outlook, http://18.104.22.168/search?q=cache:7ffXZHV-raQJ:aem.cornell.edu/outreach/outlook/2005/Chap8Fruit2005.pdf+american+apple+crop+value&hl=en
4. Asexual Reproduction, http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AsexualReproduction.html
6. Levine, Steve, Kazakhstan's Eden of Apples May Also Be Their Salvation, http://www.mongabay.com/external/wild_apples.htm#1
7. Trivedi, Bijal P.; Quest for Better Apples Bears Fruit for U.S. Botanists, http://www.mongabay.com/external/wild_apples.htm#2
8. Frazer, Jennifer; Scientists Work to Preserve Apple Diversity, http://www.mongabay.com/external/wild_apples.htm#3