The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties

Abstract

Domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge extent of genetic exchanges between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense investigations. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wildcrop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, M. baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata-M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wildto-crop introgressions of M. sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographic area. This study provides an overview of the complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programs.

Evidence of an additional centre of apple domestication in Iran, with contributions from the Caucasian crab apple Malus orientalis Uglitzk. to the cultivated apple gene pool

“…Sequencing genomes of Iranian and European varieties will probably give a more accurate view of the domestication history of apple in the Caucasus and Iran. First, it would help to get more genetic markers and resolve the relationships among apple populations (Chen et al, 2022). Second, the existence of distinct genomic regions under selection in the European and Iranian cultivated gene pools, for instance related to apple taste or size, would be a hallmark of multiple de novo domestication events, as shown in apricot and pear trees (Groppi et al, 2021; Wu et al, 2018).…”

“…The problem seems to be caused when the program is forced to cluster individuals into an inappropriately small number of clusters (Cullingham et al, 2020; Kalinowski, 2011; Puechmaille, 2016). A more powerful method for identifying the best K value is to look at the bar plots and choose the highest K value for which no clusters is only represented by admixed individuals, indicating that we have reached the highest K value for which new genuine clusters could be delimited (Chen et al, 2022; Cornille et al, 2012, 2015; Cornille, Giraud, et al, 2013; Cornille, Gladieux, & Giraud, 2013; Fontaine et al, 2013; Vercken et al, 2010). The K value we therefore considered corresponded to the finest one, which can be higher than the K value of the strongest population structure level identified by Δ K .…”

Human‐associated genetic landscape of walnuts in the Himalaya: implications for conservation and utilization

“…On the other hand, the natural walnut hybrids in the Himalaya harbour high levels of genetic and phenotypic diversity (Table 1) and could provide valuable genetic resources for walnut breeding. Generally, hybridization can produce new genotypes and introduce novel adaptive traits to resist exotic pests and diseases or promote adaptation to the changing climate (Fritz, 1999), and it has been a driving force in the evolution of cultivars, such as apples (Chen et al., 2022). In walnut breeding, artificial crossing is a conventional technique (Vahdati et al., 2019), but this approach is limited by the long generation time and larger growing space of walnut trees.…”

The potential range of west Asian apple species Malus orientalis Uglitzk. under climate change

“…Apple tree serves as a noteworthy example among woody perennials, exhibiting gene flow from various wild species across multiple geographical areas. Its origins may be independent of its current geographical distribution [ 71 , 72 ]. Furthermore, the enduring cultivation of fruit trees renders them vulnerable to dynamic environmental shifts resulting from climate change and pathogen outbreaks [ 35 ].…”