How Did the Modern Apple Come About?

Figure 1. The map of apple domestication along the Silk Road. Note that the primary progenitor species M. sieversii and the “fate determining” species M. sylvestris and M. baccata are distributed in the Tian Shan Mountains area in central Asia, Europe, and China, respectively. Asi-M. asiatica; Bac-M. baccata; Dom-M. domestica; Hup-M. hupehensis; Rob-M. robusta; Sie_K-M. sieversii in Kazakhstan; Sie_X-M. sieversii in Xinjiang, China; Syl-M. sylvestris. Adapted from Duan et al (2017).

Most cultivated crops, if not all, are domesticated from their wild relatives. There is no exception in the case of apple. When enjoying the delicious apple fruit, have you ever wondered how apples acquired their exceptional quality attributes, such as large fruit, crispy texture, tasty flavor, and long storage life?

Here I would like to briefly introduce some major research findings from a comprehensive genomic study geared to understand the history of apple domestication along the ancient Silk Road.
Nuclear genome is a total collection of the genetic material DNA in a cell. It is genetically responsible for variations and similarities among species as well as within a species. Sequencing the genome of a cultivated crop and their wild relatives is regarded as the most effective approach to elucidate the domestication process. This was, however impossible just a few years ago. Thanks to the latest advancements in genome sequencing technologies, direct sequencing of multiple genomes for important crops is now feasible.

The study sequenced the genome for 117 diverse accessions from 24 Malus (apple) species, including “35 Malus domestica (24 scion and 11 rootstock cultivars), 29 M. sieversii, 10 M. sylvestris, 9 M. robusta, 6 M. baccata, 4 M. asiatica, 4 M. hupehensis, and 20 in the remaining 17 wild species with one or two accessions per species.”

Comparison of their genome sequences revealed that nearly one-half (46%) of the genome of modern domesticated apples (M. domestica) was contributed by M. sieversii while 21% by M. sylvestris. The remaining 33% were uncertain. Based on these observations, the study concludes that the cultivated apples were domesticated from M. sieversii, which are distributed in the area of the Tian-Shan Mountains between Xianjiang, China and Kazakhstan in Central Asia (Figure 1). This conclusion, in general, is consistent with the findings in previous studies based on other evidence.

Westbound on the Silk Road
The fruit of M. sieversii are of medium-large size, soft flesh and undesirable taste. The ancient cultivated apples were likely slightly better than M. sieversii in fruit quality. The major contribution of M. sylvestris (native to Europe) to the genome of modern cultivated apples indicates a westbound traveling of the ancient domesticated apples or M. sieversii along the Silk Road (Figure 1).

The fruit of M. sylvestris are small, but firm and sour. The substantial contribution (21%) of the genetic materials from M. sylvestris improved fruit quality as the contribution of M. sylvestris to the genome of apple rootstocks, which are also M. domestica but poor in fruit quality, is only 11%. Other evidence in support of this notion includes the identification of genomic regions harboring genes known for their involvement in fruit firmness, and sugar and malic acid contents that were coincidentally selected intensively by humans. As a result, domesticated apples progressively became firmer, larger, juicier, and more balanced in sugar and acid content.

European settlers later spread the more improved domesticated apples to the New World. The modern domesticated apples (M. domestica) have been adapted worldwide for at least a century and are currently responsible for the global production of more than 80 million metric tons (176.4 billion pounds) per year.

Figure 2. Fruit of Chinese soft apple (M. asiatica) at harvest (URL:

Eastbound on the Silk Road
Historical records show that Chinese soft apples (M. asiatica, M. prunifolia), such as ‘Pinpo’ and ’Xiangguo’ have been cultivated for fruit consumption for longer than 2,000 years. These fruits are sweet, but small (1 to 1.5 inches in diameter) and soft, and cannot be stored well (Figure 2).

Surprisingly, the study finds that Chinese soft apples are also closely related to M. sieversii. Approximately 80% of the genome of Chinese soft apples are from M. sieversii. The other 20% are from a local species, M. baccata. These genomic data strongly suggest that M. sieversii traveled eastbound along the Silk Road to become Chinese soft apples.

The modern apples (M. domestica) have been grown in China since 1870s. Due to their tremendous advantages in fruit size, taste, firmness, and storability, the modern domesticated apples currently dominate the orchards in China.

Two-stage Enlargement model
Another fresh insight into apple domestication is the two-stage model for fruit enlargement proposed in the study. The model postulates that the increase of fruit size comprises two steps. The first step occurred prior to domestication, causing medium-large fruit in M. sieversii. The second occurred during domestication, which further increased fruit size.

The second step highlights the uniqueness of apple domestication compared with other crops. That is apple domestication began with large fruit, way different from other crops such as tomato, which was domesticated from tiny fruit. The supportive genomic evidence is the co-localization of multiple genomic regions where they were strongly selected by humans also contain genes controlling fruit size.

In summary, ample genome sequence evidence supports that M. sieversii in the Tian Shan Mountains in Central Asia is the primary progenitor species for both the modern cultivated apples and Chinese soft apples. Their different fates were determined by the direction the progenitor species traveled along the Silk Road.

Traveling westbound and met with M. sylvestris led to the modern cultivated apples, now dominating apple orchards throughout the world. Traveling eastbound and married M. baccata produced Chinese soft apples, which today has become a minor crop. It seems that the apple domestication history revealed by the study tells startling stories between the marriages of two M. sieversii sisters.

Information for this article is taken from research by Duan N, Bai Y et al. 2017. Nature Communications 8:249.