New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

Abstract

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.

Genomics of the origin and evolution of Citrus

“…Our study finds that domesticated citrus fruit crops, such as mandarins and sweet orange, experienced a complex history of admixture, conceptually similar to those well-recognized in annual crops, such as rice 42 and maize 43 , and in other fruit trees, such as apple 44 and grape 45 , for which the current genomic diversity is linked to widespread ancient introgression. Other cultivated citrus groups, the interspecific F1 hybrids in particular, originated from hybridizations of two pure parental species.…”

Status, distribution and use of threatened tree species in the walnut-fruit forests of Kyrgyzstan

“…M. Roem and M. pumila Mill. ; while according to the classification of wild apples species presented in Juniper and Mabberley (2006), these two species are the same, recent evidence suggests that this may not be the case (Cornille et al 2012). Clearly, the current results do not provide a robust assessment of the geographical range of each species within Kyrgyzstan, which is required to strengthen the Red List assessment (IUCN 2001), but the data do at least provide an initial indication of their relative abundance within the sites surveyed.…”

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

“…This affected all types of TEs, suggesting that the precursor of the modern apple underwent environmental changes with resulting stresses that led to the activation of these TEs 50 . The observed TE burst corresponds to the Miocene epoch (23 Mya to 5 Mya) and may coincide with two events: the divergence between pear and apple 48 and an uplift event occurring at the Tian Shan mountains 51 , which cover the region where the ancestor of the apple originates from 52 . We hypothesize that these TE bursts, which presumably must have been very different in the predecessor of pear and apple, have contributed to the diversification, and possibly even speciation, of these plants.…”