Giving fruit a nutritional boost

Blue tomatoes, pink bananas and red-fleshed apples. Meet the next generation of healthy fruits.

An apple a day keeps the doctor away, or so the saying goes. Fruits represent an important part of our diet, providing valuable nutrients in a sweet package. For example, many plants such as berries, grapes, red cabbage or eggplants (aubergines) carry anthocyanins: red, purple or blue pigments found in the vacuoles of cells from leaves, stems, roots, flowers and fruit tissues that act as effective antioxidants.

However, to meet the demands of our ever-growing population, fruits have been bred over hundreds of generations to improve some of our favourite traits, such as sweetness, good looks or long shelf life. Along the way, valuable traits such as those governing the production of healthy phytochemicals or providing pest resistance have been lost.

Take the humble apple, Malus × domestica. Genetic data from multiple apple cultivars indicate that the oldest known apple lineage is Malus sieversii, a wild apple species still found in the Tian Shan mountains of Central Asia1,2. According to a long-held story, the first apple lineage formed thanks to an unlikely event involving a primitive plum from the Rosaceae family and meadowsweet, a flower belonging to the Spiraeae family: “the offspring were ‘crude apples…as tiny and bitter as rose hips’,” writes Marcia Reiss, quoting Frank Browning, in her 2014 book, Apple (ref. 3). The recent publication of the apple genome has confirmed the origin of the apple in these Central Asian mountains, but it has challenged the hypothesis of its formation, suggesting a different scenario where the first apple lineage formed after the duplication of the nucleus of a plant closely related to the genus Gillenia, a member of the Rosaceae family4. The study also places this duplication event some 48–50 million years (Myr) ago, a timing that matches archaeobotanical dates of a previous study5. A more recent study, published last month, places the origin of the genus Malus around 30 Myr ago6.

Origins aside, the Tian Shan mountains, now part of Kazakhstan, still boast some of the world's oldest apple trees. Reiss writes about the experience of a United States Department of Agriculture (USDA) horticulturist, P. Forsline, who found “entire forests of apples, three-hundred-year-old trees fifty feet tall and as big around as oaks, some of them bearing apples as large and red as modern cultivated varieties”. These ancient apples are bearers of rich genetic diversity and a wealth of physical traits7,​8,​9.

Since the formation of the first apple lineage, apples have diversified throughout the world, and for thousands of years humans have mingled apple lineages, cultivating, breeding and transforming them. Today, modern apples are found in every corner of the globe and are one of our favourite fruits. Over the years, thousands of apple varieties have been created and cultivated, but 90% of the apples you find in supermarkets today belong to about a dozen different varieties. “China, for instance, produces 54% of the global apple harvest and roughly 85–90% of this production is in the variety Fuji,” says Chris Richards, from the National Laboratory for Genetic Resources Preservation at the USDA. These popular varieties are a mere shadow of the nearly 900 varieties once cultivated in the United States10, or the more than 2,000 varieties currently grown in the United Kingdom's National Fruit Collection at Brogdale Farm, Kent11.

The most common modern cultivars have been designed to produce fruits with improved appearance, taste and storage life, and as an unintended consequence, apples have lost some of the nutritional glory of their ancestors, harbouring significantly reduced levels of healthy phytonutrients8,9,12.

Now, scientists around the world are using different approaches to bring more goodness into fruit: pink apples and purple tomatoes loaded with anthocyanins, and bananas rich in pro-vitamin A and iron, to mention just a few examples.

Red-fleshed apples and more

In a laboratory in Auckland, New Zealand, Andrew Allan is enjoying an unusual treat, a red-fleshed apple rich in cyanidin galactoside, the most abundant anthocyanin found in apples (Fig. 1). You won't find such apples in any supermarket near you, or any place other than the greenhouses of Plant & Food Research, where Allan works, along with Richard Espley, leader of the pipfruit (apple and pears) molecular biology group.

Figure 1: Scarlet to the core.
Figure 1

This apple is engineered to produce more than a hundred times the normal levels of cyanidin galactoside, giving the flesh its red colour. Image: © PLANT & FOOD RESEARCH

Your average apple contains about 90 μg of cyanidin galactoside. Allan's apples, on the other hand, play in a whole other league. “Our engineered apple: 11,000 micrograms per apple. That's a 120 fold increase!” he claims.

The idea of looking at anthocyanins in apples came from the input of apple breeders from Hawkes Bay, New Zealand, with whom Allan has been working for 15 years. At that time, Allan's group were studying transcriptional regulation of the cold response in the plant model system Arabidopsis thaliana. In this system, part of the plant response to cold is upregulation of anthocyanins, which helps the plant tolerate stressful conditions. However, the group was also interested in understanding the effect of cold on the apple fruits, which can be stored at 4 °C for extended periods. New Zealand's apple industry relies on such storage to get good quality fruit to distant markets.

“Then, one day the apples growers reminded us that apples achieve the best red colour with low night temperatures and sunny days,” says Allan, “and that gave us a clue”.

Allan's group needed to find a transcriptional regulator, a protein that controls how much of a gene product is made. In the case of apples, this turned out to be MYB10, a regulator that switches on the expression of the anthocyanin synthesis pathway, which controls apple skin colour. “The final skin colour affects market price, as well as providing apples’ health benefits to the consumer,” explains Allan. “Anthocyanin and carotenoids are high in the skin, both good for human health”.

Allan's apples have so far passed the test in terms of health and taste. One recent study showed that mice fed with these red apples experienced measurable benefits in their gut microbiome, as well as in inflammation markers, when compared with mice eating normal apples13,14. Now, Allan is looking at MYB10 in other closely related species, such as pears, peaches, raspberries, strawberries, cherries and plums, as well as in other not so closely related species, such as kiwifruit, avocadoes, bayberries, mangosteens and even potatoes. “Over the next decade new, highly coloured cultivars will be appearing in our supermarkets, giving novelty and a health boost to our produce, and hopefully also making growers and consumers happy,” says Allan.

However, you might need to wait a bit longer before seeing the new apples on your supermarket shelves. Breeding may take a long time, and the faster alternative, genetically modified (GM)fruits, are still a hard sale, according to Francesca M. Quattrocchio from the Swammerdam Institute of Life Sciences at the University of Amsterdam. “Despite the great advantages of manipulating genes to produce superior apple varieties, such as anthocyanin-rich apples, current times and people's minds might not be ripe to bring these plant products to the table,” she says.

Another potential problem involves the fate of anthocyanin in the red-fleshed fruits. Allan's apples have passed this test too; once they are out of the tree, their flesh remains red througout their shelf life. However, this is not the case for all fruits.

Anthocyanin and la pera cocomerina

Until recently, the improvement of anthocyanin content in crops has been sought after through the alteration of genes controlling anthocyanin synthesis, but no one has looked at the stability of the end product. “For fruits, flowers and leaves of several species it is known that anthocyanin may disappear again during development in a regulated manner that depends, for example, on environmental conditions,” says Quattrocchio.

Anthocyanin is a pigment that plants store in the vacuoles of cells from various tissues, including the flesh and skin of fruits. Quattrocchio, along with Ronald Koes, professor of developmental genetics at the University of Amsterdam, has been studying Petunia flower mutants where the colour of the flower quickly fades away after bud opening. Quattrocchio believes that her work is revealing that while there are external and internal factors playing a role in the stability of anthocyanins, the genetics of the variety or line is the most important factor.

“There are specific genes affecting the stability of the anthocyanins and they can be identified by the study of Petunia mutants in which fading is present as compared to those in which it is totally or partially absent,” Quattrocchio explains.

This phenomenon is well known and you have no doubt experienced it with fruits you have brought home yourself. “We all probably happened to buy nice red pears or apples, kept them in the kitchen and then ate a couple of days later a totally yellowish fruit in which the anthocyanins were not to be seen anymore,” she adds.

So the idea behind Quattrocchio's work is that once the genes involved in anthocyanin stabilization are known and molecular markers have been designed, breeders will be able to quickly identify plant varieties that have rich and stable anthocyanin content and will be able to develop better varieties.

“To proceed in this sense, it will be necessary to analyse the available varieties of fruits (but also vegetables), including old varieties that we do not use anymore, for their genetic composition as regard to the genes involved in fading,” says Quattrocchio.

For example, take the pink-fleshed ‘mela rossa dentro incarnato’ apple, a cultivar that produces fruits loaded with well-stabilized anthocyanin. This ancient variety was rediscovered recently in the Italian region Marche, after being mostly forgotten for the past 100 years. It could serve as a source of valuable genes for modern apple cultivars, according to Quattrocchio.

Quattrocchio rediscovered the mela rossa dentro incarnato apple during a bike trip through Italy, when she ran into a festival in the town of Ville di Montecoronaro celebrating an unusually pigmented pear. “I could remember that during a trip to Italy, I saw in some villages that people were celebrating the harvest of the ‘pera cocomerina’ [sagra della pera cocomerina], a pear with a strongly pigmented flesh,” she says (

The red-fleshed pear led Quattrocchio to the farm of Livio and Isabella Dalla Ragione, where mela rossa dentro incarnato is grown, along with nearly 40 other ancient apple varieties ( The eight hectare farm is located near Città di Castello, Northern Italy, and the orchard is currently home to nearly 500 trees representing rare varieties of fruits such as apples, cherries and pears.

Resurrecting such forgotten varieties, and injecting their traits into modern cultivars using a combination of traditional breeding and modern technology, may be a more efficient way to create new healthy fruits that can reach your table, believes Quattrocchio.

A seriously tasty tomato

In Gainesville, Florida, Harry Klee is using such combined approaches to create a new generation of tomatoes, bred to have superior flavours (Fig. 2). Harry has been working at the interface of biochemistry and genetics for the past 12 years, mapping down the genes involved in flavour, with the goal of introducing them into new tomato varieties. His approach is quite unusual, as it does not just employ gene mapping and breeding experiments. It also exploits active input from tomato consumers, who provide feedback about their preferences in terms of flavour, and the help of a small army of scientists specializing in different aspects of the problem, from biochemists and analytical chemists to food scientists and phycologists.

Figure 2: Taste tester.
Figure 2

Harry Klee with one of the products of his efforts to breed more flavoursome tomatoes. Image: UNIVERSITY OF FLORIDA, IFAS

“I focus on the chemistry of what's in a tomato. Trying to understand what is flavour. What chemicals make us recognize that we're eating a tomato and which of those actually determine whether we like it,” explains Harry. “My colleagues are experts at measuring how much people like each one. We cover the breadth of expertise from consumer testing to chemistry and genetics and we work really well together.”

Armed with this information, Harry is trying to build the world's tastiest tomato. When it comes to flavour, Harry says that today's modern tomato is a poor distant relative of the heirloom varieties, but he knows how to fix this. “We understand what's gone wrong and we believe we know how to fix it,” he claims, “but it's a long process due to the number of genes affecting flavour.”

A large panel of consumers gave their feedback on the flavour of a wide range of tomatoes, and Harry tried to identify which chemicals people like best. “We then mapped genes that affect the contents of those chemicals, identified superior alleles for those genes — many absent from modern varieties — and are now in the process of moving those superior alleles into modern varieties,” he adds.

And one of the best aspects of this work, says Harry, is that you can get a piece of the action. For a US$10 contribution, you can receive two packets of seeds from the first two varieties developed by Harry's team, Garden Gem and Garden Treasure. “We have now sent seeds to over 4,500 individuals in all 50 states [of the United States] and 33 countries,” he says.

It is not just taste that tomato researchers are after. In Norfolk, UK, Cathie Martin and Jonathan Jones from Norfolk Plant Sciences are developing a breed of purple-fleshed tomatoes rich in antioxidants and anthocyanins. Using genetic engineering technology, they have created a transgenic tomato that carries polyphenol-expressing genes derived from Arabidopsis and Antirrhinum, two model plant species. These tomatoes produce high levels of polyphenols, comparable to those produced in fruits like blueberries, blackcurrants, acai and pomegranate.

Bananas for the future

Apples and tomatoes are not the only fruits being supercharged; the technology used to breed a new generation of bananas in Queensland, Australia, will soon enable this fruit to reach the table of millions of Ugandan families. In Australia and Uganda, scientists are developing a new generation of bananas rich in iron and pro-vitamin A (α and β-carotene), a precursor of vitamin A in the human body. These ‘super bananas’ are poised to provide an important boost to the diet of millions of women and children who are at risk of developing blindness and even death due to a diet poor in vitamin A.

The project started in 2005 when James Dale, from the Centre for Tropical Crops and Biocommodities at Queensland University of Technology, and Wilberforce Tushemereirwe, from the National Agricultural Research Organisation of Uganda, joined forces.

“We were incredibly excited when we were informed that we were successful in winning a Grand Challenges in Global Health grant from the Bill & Melinda Gates Foundation,” Dale remembers. However, this was mixed with some trepidation as the task was huge with lots of potentially fatal hurdles. Later, the UK Department for International Development became a co-supporter.

According to World Health Organization (WHO) estimates, there are about 250 million pre-school children around the world suffering from vitamin A deficiency15. The problem is exacerbated in some parts of the world, such as in Uganda and other countries in sub-Saharan Africa, where 15–30% of all women and children are at risk of going blind and developing other diseases linked to low intake of vitamin A in their diet. While there have been substantial efforts to deal with this problem using dietary supplements and food fortification, the problem still remains.

“But what if it were possible to increase the level of pro-vitamin A and iron in matooke, a cooking banana and staple food for Ugandans”, asks Dale. “It could be an incredibly effective and sustainable way of reducing the impacts of these dreadful deficiencies.”

According to government estimates, bananas are the most important food item in Uganda, where more than 12 million tonnes are produced every year and people consume more than half a kilo of bananas every day. Bananas represent an affordable and readily available food for the majority of the population in the region, and with this in mind, Dale, Tushemereirwe and their teams proposed a simple solution to the vitamin A problem.

“We realized that if we could develop a nutritionally supercharged banana with essential micronutrients such as iron and pro-vitamin A and release it to Ugandan farmers, we could make a big difference,” explains Dale. His team set to work on improving the Cavendish banana, the most common banana cultivar in the world. In parallel, Tushemereirwe and his team were developing an efficient way to introduce new genes into the Ugandan staple banana, the East African Highland banana.

After eight years of research using genetic engineering technology, Dale and his team developed a Cavendish banana plant with extra copies of a gene for phytoene synthase, which leads to the production of α- and β-carotene. This version of the phytoene synthase gene is naturally found in Fe'i bananas (Fig. 3), orange-fleshed bananas rich in pro-vitamin A and commonly found in Micronesia.

Figure 3: Gold standard.
Figure 3

Fe'i bananas are naturally high in α- and β-carotene, giving them orange-coloured flesh. James Dale and Wilberforce Tushemereirwe have used phytoene synthase from Fe'i bananas to engineer a Cavendish banana that is rich in pro-vitamin A. Image: IMAGEBROKER / ALAMY STOCK PHOTO

“An average fruit from this newly developed super banana harbours around ten times more pro-vitamin A than your average supermarket banana,” explains Dale.

The technology for the development of β-carotene-rich bananas has now been transferred to the Uganda team. Their bananas are currently in a field trial to select the elite lines that will progress through to being released to farmers. In the meantime, Dale's team is fine-tuning the last steps of the gene transfer technology needed to develop iron-rich bananas. They expect that after one more field trial in Australia, his team will be able to transfer the technology to the Ugandan team.

“If the iron biofortification is successful, the plan is to develop one banana with both iron and pro-vitamin A. The iron target is a three- to four-fold increase. The plan is for Tushemereirwe and his team to have these super bananas ready for release to farmers in 2021,” explains Dale.

Once the bananas are ready to go, Tushemereirwe has proposed what Dale calls the reverse Ponzi scheme to introduce the new bananas into the diet of millions of people. Here ‘early adopter’ farmers will be given free planting material on the condition that they later provide double that amount to other farmers, who in turn have to distribute double the amount they received, and so on.

The cooking bananas should make a significant difference in Uganda and, if approved, in surrounding countries, where cooking bananas are also a staple food. “Of course, it is possible to transfer the technology to other types of bananas, such as plantains which are popular in West Africa,” continues Dale. “The next big advance will be to combine biofortification with disease resistance. We already have this in our sights,” he adds.

In the meantime, the super banana technology has also been shared with India, the world's largest banana producer. This country is also struggling with vitamin A and iron deficiency, due to the mostly vegetarian diet of its population. After an official visit from India's Secretary of the Department of Biotechnology to Dale's lab, the super-banana technology, including not only biofortification but also disease resistance, is now undergoing development in India too, where field trials are soon to be deployed.

Taken together, these efforts to supercharge fruits with increased nutritional properties show promising results. Along with biofortified rice, maize, wheat and cassava, this new generation of crops could significantly improve our health. However, before we can have any of these nutritionally enhanced foods on our table, we need to move past fears of genetically improved foods. It would be a pity if all of the effort and fantastic results did not bear fruit due to unfounded emotional objections16.

“Public unease regarding GM crops, including those that are nutritionally enhanced, may serve as a significant obstacle to the alleviation of malnutrition in developing countries in the future,” says Kathleen Hefferon, a professor at the University of Toronto, Canada, and author of two books on agricultural biotechnology.

Hefferon notes that in many instances, nutritionally improved crops could instead be generated through gene editing, a technology that is not considered by current regulatory bodies to result in the production of a GM organism. “The ease of gene editing will enable plant scientists to produce even more crop varieties with a whole spectrum of improved nutritional content, flavour and agronomic traits. This will pave the way toward more consumer choice, improved economic success for farmers and better health for all,” she adds.


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  1. Karl Gruber is a freelance writer based in Perth, Western Australia.

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Correspondence to Karl Gruber.