When visiting Melanesia, one cannot help but be amazed by the striking blond hair of some of its inhabitants, since these Pacific islands are populated by some of the darkest skinned people in the world.  So where does the blond hair come from?  Is it caused by exposure to the sun or a diet rich in fish?  Or was it brought to Melanesia by early European explorers?

Together with colleagues from Stanford University, the University of Bristol, UC San Francisco and the Max Planck Institute for Evolutionary Anthropology, we recently answered this question and our report was published in Science magazine.  We traveled to the Solomon Islands and collected saliva and measured hair pigmentation in about 1000 people.  The saliva provided us with DNA and we simply looked for differences between 43 blond- and 42 dark-haired individuals at about 600,000 variable sites across the human genome.  Only one stretch of the genome appeared different between the two groups and within that stretch we found only one gene called TYRP1.

When we searched online for information about TYRP1, we were certain we were on the right track.  This gene is known to be involved in pigmentation: mutations in TYRP1 can cause albinism in humans and coat colour changes in mice, dogs and horses.  So, we sequenced the TYRP1 gene in 12 blond- and 12 dark-haired Solomon Islanders and found a single DNA variant that clearly differentiated the two groups.  This single variant results in an amino acid change in a crucial portion of the TYRP1 protein.  Out of the 3.4 billion DNA letters of the human genome, we were confident we found the single letter involved in Melanesian blond hair.

We confirmed our hunch by looking at this single variant in about 1000 Solomon Islanders from whom we had measured hair pigmentation using a spectrophotometer.  Indeed, blond hair appears to be largely recessive (you need two copies of the variant to be blond) and this single variant, taking age and sex into account, explains a remarkable 46% of the variation in hair color.

So where did this variant come from?  To answer this, we looked for this variant in about 1000 individuals from all over the world but it was absent everywhere but in Melanesia.  So, it’s now clear that early European explorers did not leave their blond hair genes behind in Melanesia.  The variant in TYRP1 is unique to Melanesians.  Blond hair therefore arose at least twice during human evolution, once in the ancestors of Europeans and once, on the opposite end of the earth, in the ancestors of Melanesians.  This represents a fascinating example of convergent evolution: when the same outcome (i.e. blond hair) is achieved by different means (i.e. independent genetic variants).

Nice story so far, but so what?  What are the implications of our findings?

Currently, medical genomics research focusses almost exclusively on populations of European origin.  We spend billions of dollars searching for genes underlying disease in a tiny fraction of humanity’s diversity, a fraction that is also the wealthiest.  We have found a genetic variant causing blond hair that exists in Melanesia and nowhere else and we argue that other such variants likely exist all over world in underrepresented populations, and affect not only hair pigmentation but also disease-related traits.  In a future of personalized medicine, where doctors looks up patients’ genome sequences to assess disease risk and pharmaceutical companies create drugs tailored for specific genetic variants, individuals of European origin will benefit most while others will be left behind.  This scenario seriously threatens to increase the already alarming health care disparities between rich and poor nations.  This intense focus on such a small fraction of human genetic diversity not only threatens to widen the health care gap between developed and developing nations, but also between minority and majority groups in the USA and Canada, for example.

Our result is therefore a call for action.  We must take steps now to ensure that the benefits of current genomics research extend beyond privileged populations and provide an increase in well-being for people everywhere.  Humanity’s natural genetic diversity is vast and fascinating – we should be measuring and assessing it all!  The same applies for genomics research in agriculture.  A continued focus on a small number of elite individuals in plant and animal breeding is myopic and dangerous.  An immense amount of existing genetic diversity that is essential to our future well-being is being ignored.  Whether it’s us or our food that we research, our aim is to cultivate an appreciation for natural genetic diversity.  Our future depends on it.

Breeders scrutinize potential parents carefully when deciding which cultivars to cross together in the making of a new cultivar. The mistaken identity of Honeycrisp seems to suggest that such scrutiny is superfluous, that the choice of parent is irrelevant and that the success of a cultivar has nothing to do with the genes of its parents. After all, Honeycrisp is one the world`s most popular cultivars but its parents were not even chosen on purpose!

This suggestion is ridiculous. We know that offspring resemble their parents. If your mother and father are both tall, chances are that you will be tall as well. The same applies for many traits in apples. So we know that the choice of what two apples to cross together has an influence on the traits of the resulting offspring. Thus, we argue that it is not the case that scrutiny is superfluous, rather that the scrutiny in traditional apple breeding is limited by the measures employed. The fact that Honeycrisp, one of today’s most successful commercial cultivars, was generated essentially from random parents suggests that the metrics used by breeders in selecting parents are sometimes ineffective. Of course, extensive evaluations were required to choose Honeycrisp as the most promising from among its hundreds of siblings. But any apple breeder will admit that their evaluations involve lots of noisy and subjective measures. Could it be that one of Honeycrisp’s siblings would have had equal success in the marketplace?

We are dedicated to improving the suboptimal toolkit that apple breeders currently have to work with. Apple breeders are dedicated to improving our food: they spend decades evaluating tens of thousands of apple trees that will never attain commercial success in order to pick out the one tree that is worthy of further propagation. By measuring the natural genetic diversity among apple cultivars and determining how this diversity affects commercially important traits, our lab aims to optimize the choice of which apples to cross together. The DNA from the resulting offspring will also be sequenced at the seedling stage, while the trees are small and still in the greenhouse. At this stage, we aim to predict from their genetic information how they will perform as adult trees. Seedlings with undesirable genetic profiles will be discarded, and only the seedlings with the most promising genomes will be planted out in orchards and be evaluated extensively by breeders. This process is called marker-assisted selection and it does not involve producing a genetically modified organism (GMO). We simply use DNA information to enhance traditional breeders’ toolkits, providing them with natural diversity that has been pre-screened. This pre-screening promises to significantly reduce the enormous effort and cost that goes into evaluating tens of thousands of commerically useless trees. “Genetics” is often considered a dirty word in agriculture because of the public`s perception of GMOs. But DNA information promises to help breeders more efficiently and cost-effectively develop tasty cultivars that require less chemical input. There will be no more mistaken identities in the age of genomics.

The distinct red colour that covers one quarter of this apple is caused by a mutation in the apple’s DNA sequence – a mutation that came about naturally. Nature is not perfect: it understandably makes mistakes sometimes when copying the 500 million letters of DNA sequence during each round of the billions of cell divisions that take place during the growth of an apple. These copying mistakes are called mutations. They happen in us too – some of them may change your hair colour while others may cause cancer. The mutation that led to the unique colour pattern in this apple happened during an early stage of fruit development – likely when the apple was made up of only 4 cells.

In one of those cells, a mutation occurred in the gene responsible for colour. This mutated cell then underwent cell division to create daughter cells which then also divided, and this process continued and eventually led to one quarter of the apple containing cells that contain the mutation. We call this apple a mosaic – it contains two populations of cells with different genotypes. Nature does some strange and wonderful things, which become even more fascinating as we learn more about them. We might just sequence the DNA from the two different populations of cells in this apple and try find the mutation that causes the colour difference. Stay tuned to see what we find!