Fuzzy, Sweet, Sexy: How Man Shapes Peach

Chinese scientists recently revealed the history of domestic peach.

The fuzzy fruit has been one of mankind’s favourite sweet treats for thousands of years. Today, the world produces 23 million tons of peaches and nectarines a year, with China accounting for over half of global production.

Peach and its close relatives – stony fruits such as almonds, apricots, cherries and plums – are key agricultural crops, providing vitamins and antioxidants in many diets. Eating two peaches a week even reduces the relative risk of breast cancer.

In 2013, the US produced one million tons of peaches, according to the Department of Agriculture. Georgia, the Peach State, is the third-largest producer, with 35,250 tons. Then it’s South Carolina with 69,650 tons. But by far the country’s largest producer is California, where peach growers create 3,240 jobs and contribute $374 million to the state’s annual economy from 648,000 tons of fruit.

Peach’s value to both health and wealth explains why scientists are studying the genetics behind their appeal to consumers.

Peaches (CC BY 2.0: skyseeker / https://flic.kr/p/2MynV)

According to archaeological evidence, domesticated peach trees originated in China up to 7,000 years ago. Ornamental peach trees first appeared about 2,000 years ago. Written records indicate that peach spread to the West via the Silk Road and it got its scientific name, Prunus persica, after reaching Persia.

There are now over 1,000 cultivated varieties worldwide. DNA from 837 of those cultivars is stored in China’s National Germplasm Repository.

The history of peach was reconstructed by Professor Jun Wang of BGI Shenzhen near Hong Kong. His team of 28 researchers used Illumina machines to read DNA sequences of 84 cultivars – 74 cultivated and 10 wild varieties, a diverse 10% sample of the database. They then compared their genomes to spot the differences, which allowed them to build an evolutionary tree. This reveals that domestic species split from wild peach (red) in a single event, then split again into ornamental (yellow) and edible varieties (green, blue and purple).

The domestication history of peach. The genetic structure of 84 varieties is shown through color: edible peach (green, blue and purple); ornamental peach (yellow); wild (red). (Figure: Cao et al / Genome Biology)

Comparing the 84 cultivars identified 4.6 million single-letter DNA variants, about 10% of which are located within genes. Is the evolution of any of these genes being driven by man? To detect this, Wang’s team measured how fast each gene’s protein had changed relative to a background rate of random mutation. If a protein is changing faster than the background rate of mutation, its gene is probably being shaped by natural or artificial selection.

Why Do Peaches Taste So Sweet?

Jun Wang’s team detected 147 genes in edible peach that were evolving fast. The function of many of these genes shows that peaches are being selected for their flavour, which suggests human preference: one gene encodes a protein similar to an enzyme that helps produce sorbitol, commonly used in food as a sugar substitute.

Among the genes under selection, a disproportionate number are involved in photosynthesis and carbohydrate metabolism – processes that plants use to make and convert carbohydrates. “These processes basically can produce more sucrose and glucose, which is the basis of sweetness in edible fruit,” Wang explains.

Peach is a member of the rose family, Rosaceae, the world’s most valuable fruit-producing plants. The family includes species grown for ornamental quality (roses), lumber (black cherry trees) and food (apples, strawberries). Whereas many fruit trees are the result of crosses between species, peach is relatively pure-bred, making it a good model organism, a touchstone for studying the rose family, which is why it’s so important to read its DNA.

In 2013, the International Peach Genome Initiative published a draft of the fruit’s complete DNA sequence and some preliminary analysis of its genetics. The peach genome is relatively short, an estimated 265,000 letters long, with a predicted 28,000 genes. Scientists don’t know what all those genes are, or what they do, but the international team did map the location of 672 genes related to fruit quality onto the genome.

Compared to most other species, peach has a large number of genes for metabolising and transporting sorbitol, which is why their fruits taste so sweet. By contrast, peach has only 56 genes involved in fruit development and formation of the stone, a surprisingly small number given their prominence in peaches.

The peach genome with DNA diversity across its chromosomes. (Figure: The International Peach Genome Initiative / Nature Genetics)

The International Peach Genome Initiative also examined 11 /Prunus persica/ varieties and three related species to study genetic diversity across the genome. One of the most diverse regions is the end of chromosome 4, an area that includes genes which determine how long it takes for fruits to mature. This isn’t surprising if you know peaches can only be stored for a few weeks, so varieties with different maturity times are needed so fruit can be sold throughout peach season (April to October in the northern hemisphere). Man has therefore shaped chromosome 4 diversity by collecting varieties according to when they mature.

Why Are Peaches Covered In Fuzz?

Reading DNA letters is easy compared to identifying the gene behind a particular characteristic and finding its location on the genome, as shown by how scientists discovered the gene that makes peaches fuzzy.

Nectarines are a variety of peach. They’re fuzz-free because their skin isn’t covered by hair-like structures called trichomes. The existence of nectarines is not only good for people who like peach’s flavour but not its fuzzy feel, but is also important in heath: trichomes probably make two proteins that trigger oral allergy syndrome. Finding the ‘fuzzy gene’ is therefore important for consumers.

Close-up of fuzz on a peach (CC BY-NC-ND 2.0: Chris Rimmer / chrstopher / https://flic.kr/p/5f7yvL)

Mapping traits is achieved thanks to a statistical approach called genetic linkage, where two genes that are physically close together in DNA are more likely to be inherited together.

If you know the location of a unique genetic marker, you can figure out whether the gene controlling a characteristic – such as fuzziness – is nearby based on how often the offspring inherit both the marker and characteristic. Using a succession of markers lets you work out the location relative to each marker, and ultimately pinpoint where a gene is on a genome map. This is how Italian scientists found the ‘fuzzy gene’ in 2013.

After crossing a peach with a nectarine, the geneticists studied the markers and fruit produced by their 305 seedlings, eventually narrowing-down the fuzzy gene to near the end of chromosome 5. When peach DNA was compared to other plants, it was found to be similar to proteins involved in the development of trichomes. In nectarines, the fuzzy gene (which has the unsexy name PpeMYB25) carries a mutation that prevents peach from producing trichomes. This mutation is found in western nectarines and not traditional Chinese varieties, indicating that nectarines originated after domesticated peach had left China.

Professor Tom Gradziel of the University of California at Davis currently manages 80 acres of crops and works with the Californian cling peach industry to produce varieties with commercial benefits. He says comparing peach genomes “helps you understand how it’s evolved, and how it could be manipulated in future human-designed evolution, which is plant breeding.”

Desirable genes can’t be simply slotted into peach DNA as can be done in many organisms. Although the cells of peach and other stone fruit can be genetically modified, they aren’t easily engineered because they’ve lost the ability to regenerate from shoots. The RosBreed project is working out how to exploit genetic information to breed stone fruits.

One of the traits that Gradziel is currently trying to isolate is resistance to /Monilinia fructicola/, a fungus that causes brown rot of stone fruit. It’s tough to tell whether a plant is resistant to the disease based on appearance, as environmental factors such as temperature and humidity influence susceptibility.

Genetics can help identify resistance by association. Gradziel annotates the peach genome with markers relative to the trait to create a map of genetic linkage, in the same way Italian researchers discovered the fuzzy gene. Markers close to genes that control resistance can then by used in a DNA test, allowing Gradziel to select and breed peach varieties by detecting the marker.

This is called ‘marker-assisted selection’. It’s an indirect way to breed domesticated species with a particular trait by recognising an associated marker. The trait itself might be hard to identify just by looking at an animal or plant, such as immunity against as disease, so an associated marker is used instead. The gene behind the trait of interest is physically close to the marker on DNA (genetic linkage), which is why the two are found together. The marker can be an easy-to-spot physical trait or a genetic marker with a specific sequence that can be detected through a DNA test. Rather than waiting for plants to develop, you can detect a genetic marker for a trait of interest in seedlings, cutting down breeding time.

The problem is, peach has low genetic diversity. Unlike most species in the /Prunus/ genus, the plant will accept its own pollen, it is ‘self-compatible’. Peach is inbred, causing it to have a shallow gene pool compared to wild species. Of the 4.6 million genetic variants identified in Jun Wang’s survey, wild peach carries 74% (3.4 million) whereas edible peach has 45.9% (2.1 million).

A deep gene pool provides the raw material that allows species to adapt to an ever-changing environment, such as new pests or global warming. To deepen the gene pool, Gradziel has been crossing domesticated peach with its wild relatives and almonds (which are closely related) to bring in genes for traits like disease resistance and fruit quality. (Breeders have even created hybrids where the whole fruit is edible: peach flesh on the outside, almond-like stone inside.) At UC Davis, he grows about 30 varieties of peach destined for processing.

Wild peach species have more variability and can be cross with domesticated varieties to deepen the gene pool, but this also shuffles DNA around, making the genome map less accurate. This could be a problem for marker-assisted selection for example, as it breaks a marker’s genetic (physical) link with a trait you’re interested in. “For each population, you almost need its own sequence, its own map for that direct marker-assisted selection, for that direct thing of this gene is associated with this trait,” says Gradziel.

Marker-assisted breeding after cross-breeding is less reliable, but not impossible. One of the traits Gradziel has introduced from wild peach is the ability to remain on a branch for longer. The ‘Kader’ variety carries genetic variants that allow slower decay, a ‘long keeper’ line that not only maintains a tree-ripe quality for longer. Unlike apple, which store energy as starch, peach uses sugars, so extra time on the tree allows sugars to accumulate and makes the fruit even sweeter. This makes harvesting more economical too, because you don’t need to rush out and pick the fruit as soon as it’s ripe, you can harvest a whole tree in one go.

Processed peach slices (CC BY-SA 2.0: BrokenSphere / Wikimedia)

Desirable traits can also be better for your health. Gradziel says that consumers like yellow-gold fruit, and he has bred peach to produce vitamin A precursors such as beta-carotene, which is not only a desirable colour, it’s more nutritious.

Introducing desirable traits into domesticated species isn’t as straightforward as crossing two varieties and getting a better one, because you can also lose some of the traits that man has previously selected.

Breeding is like combining to playing cards. A domesticated species is like half a deck of cards created by selecting mostly high-value cards like Aces, Kings and Queens, whereas wild species are a random collection with one Joker card – the desirable trait. After you combine, shuffle and split these half-decks through sex, it’s unlikely that you won’t end-up with the high cards as well as the Joker.

But you can take the deck containing the Joker and mate it with a domesticated species again, what’s called backcrossing. Eventually you’ll end-up with high cards and a Joker. You can’t always look at an organism and see its traits, like having those cards face-down, but genetic markers and DNA tests can speed-up the backcrossing process by allowing you to mark the back of the Joker.

Peaches in underwear (Source: http://news.sdchina.com/show/3038402.html)

Why Do Peaches Look Like Butts?

While scientists were comparing peach genomes, bloggers were getting excited at the sight of fruit in underwear. Slip a peach into a pair of panties and it will sell for $9, at least in China. Although they cost $2 a pound in the West, in July an enterprising fruit shop owner in Nanjing managed to capitalise on Chinese Valentine’s Day by offering gift boxes of nine fruits for about 500 yuan, or $80.

Man shapes many traits, including shape itself. This raises one more question: What determines the morphology of /Prunus persica/? Or to put it less scientifically: Why do peaches resemble the human buttocks?

“I think it’s fascinating,” says Tom Gradziel, who explains that the shape of stone fruits is a consequence of how a fruit develops after fertilisation: plant tissue folds-in on itself to house the seed. Fruit development is like your hand closing into a fist, which leaves a seam between fingers and palm. In stone fruit, that seam is called a suture. As the fruit flesh grows and takes on water, everything is able to expand outwards except that suture, which exaggerates a peach’s buttocks.

And when it comes to crops, size is a commonly-selected trait – the bigger, the better. Wild peaches are smaller than domesticated ones. One consequence of artificial selection by man is ‘domestication syndrome’, a group of traits that separates domesticated species from their wild ancestors. “So it would make sense with just selection for bigger fruit, and uniform fruit, that you’re selecting that particular appearance.”