Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin

Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin Bourguiba et al. Bourguiba et al. BMC Plant Biology 2012, 12:49 http://www.biomedcentral.com/1471-2229/12/49 Bourguiba et al. BMC Plant Biology 2012, 12:49 http://www.biomedcentral.com/1471-2229/12/49 RESEARCH ARTICLE Open Access Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin Hedia Bourguiba1,2,3, Jean-Marc Audergon2, Lamia Krichen3, Neila Trifi-Farah3, Ali Mamouni4, Samia Trabelsi5, Claudio D’Onofrio6, Bayram M Asma7, Sylvain Santoni1 and Bouchaib Khadari1,8* Abstract Background: Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. Results: According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification. Conclusions: A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits. Background Domestication of plants is a complex evolutionary process in which human selection favours phenotypic transitions making them more useful for humans and better adapted to landscape management. It is a crucial step in the evolution of crop species since humans have an important impact on their origins and changes. Moreover, selection pressure and local diversification * Correspondence: 1 INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France 8 CBNMED, UMR 1334 AGAP, F-34398, Montpellier, France Full list of author information is available at the end of the article lead to an ongoing process [1]. Two major impacts on plant diversity result from domestication. Firstly, changes in traits selected for human use, called the “domestication syndrome” [2], lead to selection signatures at specific loci [3,4]. In fact, according to the intensity of the selection process, the degree of change in populations can vary along a continuum from their wild ancestors to the domesticated populations, which cannot reproduce or survive without human intervention. Several highly domesticated plants such as maize, rice and wheat express domestication traits and have lost their ability to survive on their own in the wild [5]. Other crops like trees and forage are generally considered to be © 2012 Bourguiba et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bourguiba et al. BMC Plant Biology 2012, 12:49 http://www.biomedcentral.com/1471-2229/12/49 partially domesticated while conserving some ability to survive in natural environments [6]. In seed-propagated crops, domesticated types are characterized by a lack of seed dispersal at maturity and a lack of seed dormancy [7], while in clonally propagated crops, the reduction of sexual fertility and adaptations facilitating vegetative propagation have generally been reported [8]. The second major consequence of domestication is the reduction of genetic diversity in crops relative to their wild progenitors due to human selection and genetic drift through bottleneck effects [9]. Contrary to selection which only affects genetic diversity at target genes [3,4], bottleneck processes reduce neutral genetic diversity across the entire genome [10-12]. The strength of genetic drift during the domestication bottleneck is determined by its duration and the effective population size [13]. Thus, according to their life-history traits and evolutionary history, diversity loss differs considerably among crop plants. The reduction of gene diversity in crops compared to wild relatives has been observed in soybean (34%), maize (38%) and wheat (70–90%) [10-12]. However, introgressive hybridization between domesticated forms and their wild relatives has often expanded genetic diversity, counteracting the effects of the initial domestication bottleneck [14]. For perennial fruit species, domestication means changing the reproductive biology from sexual reproduction (in the wild) to vegetative propagation (under cultivation) [15]. Few studies have reported the impact of the domestication history and how bottleneck effects may reduce the genetic diversity of crops relative to the wild relatives. Miller and Schall [16] provided phylogeographic evidence of multiple domestication of a cultivated fruit tree, Spondias purpurea, within the Mesoamerican centre of domestication. About 29% of the total diversity was not recovered in wild populations, suggesting that either new alleles have arisen during cultivation or, alternatively, contemporary extinction of tropical dry forests has occurred in Mesoamerican areas leading to genetic erosion of the wild gene pool. In Mediterranean zones, only a weak bottleneck effect on diversity in olive and grapevine was observed when comparing the wild and cultivated forms [17,18]. For Prunus species, Mariette et al. [19] reported that in the case of sweet cherry a marked genetic bottleneck due to plant (...truncated)