Ok I never thought that would be so much to find out about apples. I was intrigued by a podcast I listened on Gastropod  and the recent BBC: Inside the Factory episode and since then I got hooked, I had to find out more details about the biology of apples.

There are 7,500 different kinds of apples worldwide, although a few of them dominate the markets and are destined for consumption (dessert apples) or the making of beverages (cider)  or various food products (juice, dried, purees etc) (University of Illinois). Today, around 89 millions tons of apples are produced annually with China being the biggest producer with 40% of global production (Cornille et al., 2019).

Ok let’s take things from the beginning.

Apple origin

The apple belongs to the Rosaceae family, together with other fruit tree species (e.g., pear, apricot, peach, plum, cherry, and almond). The genus Malus consists of about 30 species including only one domesticated species, the Malus domestica (can also be referred to as Malus x domestica) (Cornille et al., 2014;2019).

Collection of wild apples is thought to have started at Neolithic and Bronze Age as evidence was found in archaeological sites across Europe (Cornille et al., 2014). Evidence indicate fruit similar to Malus sylvestris, the European wild apple or crabapple. Crabapple, comes from the Old English ‘crabbe’ meaning bitter or sharp tasting and refers to wild apple species that usually produce small acidic tasting fruits (Cornille et al., 2019). However, the ancestor of today’s domesticated apple, is believed to have originated from Malus sieversii, a species found in central Asia, in the Tian Shan Mountain area of Kazakhstan.

The development of grafting, which appeared 3,800 years ago, facilitated the propagation of  cultivated apples. Grafting refers to an ancient technique where you cut a bud of a desired species and attach it to a ‘rootstock’(= a stem with well-developed roots) and in that way you merge two plants and force them to grow together. One plant contributes to the upper part of the combined plant (which provides the aerial parts and fruit) and is called the ‘scion’ and the other plant contributes to the lower part (which provides the roots), the ‘rootstock’ (Cornille et al., 2019). This way you can propagate apple crops that are uniformly the same (clones), without using genetic editing techniques but rather selecting to cultivate the desired fruit with the desired characteristics (or gene combination).

Evidence for apple cultivation dates from the Greek period (i.e., from about the 3rd century BC). The Greek philosopher and botanist Theophrastus (ca. 320 BCE) studied the apples brought to Greece by Alexander the Great and described six apple cultivars and cultural practices such as grafting. The Romans probably learned the general tree care methods from the Greeks, and brought this knowledge to the rest of their empire (Cornille et al., 2014;2019). Thus, it is believed that the domesticated apple passed from Middle East to Greeks and Romans and overall via the ‘Silk Road’ reached the West (Figure 1) (Velasco et al., 2010). During this journey, the central Asian species, Malus sieversii was crossed with the European wild species Malus sylvestris. The result was large fruit (trait from M. sieversii), with firm texture and appetizing flavour (trait from M.sylvestris). This new species continued to be crossed with different species by grafting, in order to achieve better flavour and texture (Duan et al., 2017). However, M. sieversii can be still found in wild forests in the Tian Shan, at the border of Kazakhstan and China, in southern Kazakhstan, and sporadically in Kyrgyzstan, Turkmenistan, Uzbekistan, Tajikistan, and northeastern Afghanistan (Cornille et al., 2019)

In contrast to the production of dessert apples, cider has been produced for centuries in Western Europe especially by Celts using wild crabapples before the invasion of the Romans (Leforestier et al., 2015). However, today’s cider apples are not originated from the European M.sylvestris wild crabapple as first thought, but is possible that they are too originated from Central Asia (Cornille et al., 2014).

Figure 1: Apple evolutionary map (Duan et al., 2017)

Apple genome

If you want to plant an apple tree in your garden and you kind of like let’s say the ‘Golden Delicious’ variety, you might think that the only thing you have to do is take a seed from a ripe fruit and plant it. The truth is that the result will be an apple tree, however the fruit will be a complete different type of apple. Why is that? The truth is hiding in the genome.

In 2010, Velasco et al, sequenced for the first time the genome of Golden Delicious, since it has been cultivated for about a century and it is still popular today. Golden delicious, as many other cultivated species of apple, is highly heterozygous with high rate of SNPs (single nucleotide polymorphisms). SNPs are variations of the DNA sequences that are normally present in large proportions of the population. Other key discoveries of this study was that the apple genome comprises of 17 chromosomes that was the result of a genome-wide duplication of a 9 chromosome ancestor. It was also confirmed that the M. sieversiiM. domestica are more closely related genetically than the M.sylvestris M. domestica (Velasco et al., 2010).

A second sequencing study in 2017, emphasized the presence of transposable elements (TE) (=highly repetitive sequences) mostly retrotransposons (=genetic sequences that can copy and paste themselves in different locations in the genome) in the apple genome which overall represented 60% of the apple genome. It was estimated that there was a major burst of TEs around 21 MYA. This event was suggested to coincide with the divergence of apples from pears and the uplift of the Tian Shan mountains (Daccord et al., 2017)! The importance of the TEs playing a major role in gene expression of apple genome, was shown by the discovery of a TE near a gene (a transcriptional factor = factor regulating gene expression) responsible for the regulation of anthocyanin biosynthesis (=red skin colour). So in the presence of this TE, the red colour was expressed (Figure 2) (Zhang et al., 2019).

Figure 2: Images of 12 apple varieties with non-red or red skin colour (upper panel) and PCR-based screen showing the absence (right) or presence (left) of the retrotransposon insertion in the upstream of MdMYB1 (=gene controlling the red colour). A 750 bp fragment corresponding to the retrotransposon that is absent in non-red-skinned varieties (lanes 1 to 6) and is present only in red-skinned varieties (lanes 7 to 12) (Zhang et al, 2019).

Apart from the complexity found in the DNA of the apple genome, epigenetics (= changes in gene expression that do not involve changes in DNA sequence) can affect the gene expression. Methylation of the DNA was shown to affect different aspects of the fruit development (Daccord et al., 2017). In addition,  the expression of a microRNA (=a non-coding RNA associated with gene expression silencing) regulating the apple size was shown to be fixed in cultivated apples and its wild progenitors with large fruit. This reinforced the theory that the trait of size was determined in two phases: one before domestication and one after. That means that the main ancestor of the domesticated apple, M. sieversii was already selected for its large size by big mammals (or even humans) before domestication unlike e.g. tomatoes that the domestication started with ancestors with small fruit (Yao et al., 2015; Duan et al., 2017).

Lastly, the apples are also known to be ‘self-incompatible’ meaning that the one variety cannot be fertilized by the same variety, it always have to be cross-pollinated (Cornille et al., 2019), making the apple one of the most genetically varied fruit.


The apple genome is everything but a simple one. SNPs, TEs, epigenetics, self-incompatibility, are all elements making any correlation between genes (=genotype) and looks (=phenotype) hard. However, important steps have been taken to understand the functional importance of genes of interest such as genes regulating fruit quality (e.g., colour, shape),  taste (e.g., fruit acidity, sugar content), texture (fruit flesh firmness), or resistance to apple scab. This knowledge can be used to target specific genes and create the ‘perfect’ apple with new gene editing technologies such as CRISPR/Cas.

However, propagating clonal varieties reduces biodiversity and possibly favours the accumulation of rare mutations (and epimutations for that matter). It is in the nature of the apple (it is in its genes really) to be highly diverse and humans have interfered for thousands of years in its evolution. Humans have selected desirable traits and have made clones of a parent tree of choice. All the trees, in any one orchard today, are all clones.

If you ask my opinion, we should be able to do both. Learn more about the genes of the apple and produce an apple suitable to our needs, but at the same time let nature take its course as there is still so much to learn.


Cornille A., Giraud T.,  Smulders M.J. M.,  Roldán-Ruiz I.,  Gladieux P. (2014) The domestication and evolutionary ecology of apples. Trends Genet. 30(2):57-65.  DOI: 10.1016/j.tig.2013.10.002

Cornille A., Antolín F., García E., et al. (2019) A multi- faceted overview of apple tree domestication. Trends Plant Sci. 24 (8), pp.770- 782. 10.1016/j.tplants.2019.05.007. DOI: 10.1016/j.tplants.2019.05.007

Daccord N., Celton J.-M., Linsmith G.(2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat. Genet. 49(7):1099-1106. DOI: 10.1038/ng.3886

Duan N., Bai Y., Sun H. et al. (2017) Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nat Commun, 8 (1):249. DOI: 10.1038/s41467-017-00336-7

Leforestier D., Ravon E., Muranty H. (2015) Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 8(7):650-61. DOI: 10.1111/eva.12270

Peace C. P., Bianco L., Troggio M. (2019) Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6:59. DOI: 10.1038/s41438-019-0141-7

Velasco, R., Zharkikh, A., Affourtit, J. et al. (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42 (10):833–839. DOI: 10.1038/ng.654

Yao J.-L., Xu J., Cornille A. (2015) A microRNA allele that emerged prior to apple domestication may underlie fruit size evolution. The Plant Journal. 84, 417–427. DOI: 10.1111/tpj.13021

Zhang L., Hu J., Han X.(2019) A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat. Commun. 10(1):1494. DOI: 10.1038/s41467-019-09518-x



University of Illinois:

BBC: Inside the Factory, Series 6.1: Cider







Golden Delicious

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