Gene flow, the movement of genes among lineages, plays an important role in the evolution of organisms by shuffling the genetic diversity within species (Rieseberg 1997; Petit and Excoffier 2009). Gene flow is quantitatively a major source of genetic variation within populations, thus acting as a primary force to balance the detrimental effects of genetic drift and maintain high effective population sizes (Lynch 2010). Because cultivated species have generally suffered strong bottlenecks through domestication (Doebley et al. 2006), gene flow involving wild species and their domesticated counterparts is valuable in the enrichment of their effective population sizes. Such genetic exchanges have long been reported and exploited by humans (Ellstrand et al. 1999). Wild species have been historically used as a source of genetic variation for crop improvement programs, resulting in important applications for plant breeding (Papa 2005). For example, based on genetic evidence on grapevine, Myles et al. (2011) demonstrated that Western European Vitis vinifera cultivars experienced introgression from local Western European Vitis sylvestris. In addition, crop-to-wild gene flow has received growing attention in the last decade (Felber et al. 2007; Arrigo et al. 2011). The phenomenon has important evolutionary consequences for local relatives because it may promote the origin of highly competitive genotypes, resulting in the exclusion of vulnerable wild species (Ellstrand et al. 1999) or into the development of aggressive weeds (Trucco et al. 2009).
The Rosaceae family provides an excellent model for exploring gene flow between domesticated and wild species. Indeed, hybridization has played a central role in the evolutionary history of the family (Coart et al. 2006), resulting in several large reticulated species complexes. Here, we focus on the almond tree, Prunus dulcis (Mill.) D.A. Webb (syn Amygdalus communis L. and Prunus communis Archang.), an economically important Rosaceae cultivated as a nut crop. The annual world production of almonds exceeds 1.83 million tons (FAO 2008), with half of the production located in California and the other half in Mediterranean Europe.
Almond trees belong to the subgenus Amygdalus (L.) Focke, an Irano-Turanian complex of Prunus including more than 30 species (Browicz and Zohary 1996) that radiated recently (Ladizinsky 1999; Potter et al. 2002; Yazbek, unpublished data). Although several Amygdalus species have been sporadically used for human consumption, only P. dulcis was domesticated to produce sweet almonds. The spatio-temporal origin of domestication is still controversial although several lines of evidence suggest that P. dulcis domestication originated in the Fertile Crescent during the first half of the Holocene (Browicz and Zohary 1996; Ladizinsky 1999; Willcox et al. 2009; Delplancke 2011). Archeobotanic remains of P. dulcis show that almond trees were already cultivated about 11 000 years ago (Willcox et al. 2008) and used throughout the Near East, complementing meat and other plant food (Martinoli and Jacomet 2004).
Prunus orientalis (Duhamel) is one of the wild counterparts of the cultivated almond tree. This taxon is one of the most common Amygdalus representatives occurring in the Near Eastern Mediterranean. It is widespread from northeast Iraq to south and central Anatolia, and commonly grows in contact with P. dulcis orchards. Because it shows substantial genetic differentiation with almond trees, P. orientalis is not considered as the sole potential wild ancestor of P. dulcis (Zeinalabedini et al. 2010). The ancestry of the latter species remains controversial, with a probable diffuse domestication process featuring several wild species that contributed to its current genetic pool (see Zeder 2006).
Several hybridization events involving the almond tree and wild relatives from the Amygdalus group have been reported. For instance, spontaneous wild-to-crop gene flow was detected in several Italian almond orchards, in which self-compatibility (i.e., species are otherwise self-incompatible) and specific morphological characters had presumably been introgressed from Prunus webbii (Spach) (Socias i Company 1998; Godini 2000). Moreover, crop-to-wild exchanges have long been suspected because of the wide range of intermediate phenotypes observed throughout western and central Asian species (Grasselly 1977; Grasselly and Crossa-Raynaud 1980; Denisov 1988; Browicz and Zohary 1996; Gradziel 2009). Such pervasive gene flow is consistent with the mating system (i.e., self-incompatibilty), insect-mediated pollination (Dicenta and Garcia 1993; Socias i Company 1998), and the perennial life cycle of almond, which promotes outcrossing and hybridization (Goodwillie et al. 2005; Petit and Hampe 2006). Finally, gene flow among Amygdalus taxa might be facilitated because a large proportion of the group shares a similar diploid chromosome number (2n = 16 chromosomes), including P. dulcis and P. orientalis (Grasselly 1977; Corredor et al. 2004), which may lead to viable hybrids (Browicz and Zohary 1996). In the current context of global genetic erosion, there is urgent need for a comprehensive understanding of the genetic relationships and the coexistence between cultivated, feral, and wild Prunus species in their centers of origin.
Because the reality of genetic exchanges between the cultivated form P. dulcis and one of its most widespread wild relatives P. orientalis has never been examined, we investigate gene flow and hybridization between these two key almond species in the Fertile Crescent, their supposed native area, using nuclear and chloroplastic markers. We outline the reciprocal genetic contributions of one species to the other, relying on microsatellite genotyping [hereafter simple sequence repeat (SSRs)], a category of molecular markers widely used for investigating evolutionary relationships between lineages having diverged recently. Moreover, by combining highly polymorphic, bi-parentally inherited nuclear SSRs with nonrecombinant, maternally inherited chloroplastic SSRs, we aim to
- 1Assess whether nuclear and chloroplastic microsatellites are efficient markers for delineating species in the Amygdalus complex.
- 2Characterize the genetic diversity of P. dulcis and P. orientalis.
- 3Investigate the relative genetic contribution of a common wild species to the gene pool of the cultivated almond crops.
- 4Assess the level of crop-to-wild gene flow.