Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract

BackgroundThe amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.ResultsA Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.ConclusionsThe variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0818-0) contains supplementary material, which is available to authorized users.

The origins and evolutionary history of feral apples in southern Canada

“…For example, expected heterozygosity ( H E ) in ferals was 0.801, similar to our reference set of commercial cultivars ( H E = 0.807), which are largely self‐incompatible and outcrossing. The high heterozygosity in feral populations is also comparable to values observed in other studies on genetic diversity in apple collections such as Urrestarazu et al (), Urrestarazu et al () ( H E = 0.82), Liang et al () ( H E = 0.81), and Lassois et al () ( H E = 0.82). In contrast, the feral trees have much higher heterozygosity values than woody species such as Rubus occidentalis and Pinus resinosa , both self‐pollinating species, which display much lower levels of heterozygosity ( H E = 0.53 and H E = 0.508, respectively; Boys, Cherry, & Dayanandan, ; Dossett, Bassil, Lewers, & Finn, ).…”

“…Other studies have found genetic substructure within apple cultivars (Liang et al, ; Urrestarazu et al, ). Liang et al () observed two major groupings of 192 Italian apple cultivars, each with two subgroups.…”

“…Liang et al () observed two major groupings of 192 Italian apple cultivars, each with two subgroups. Urrestarazu et al () detected three major groupings and eight subgroups in a much larger European data set of 1859 apple cultivars. In contrast to our study, pairwise genetic differentiation among these groups was higher (range: F ST = 0.015 to 0.042), possibly owing to the larger geographic scale of the study.…”

Genetic Diversity and Structure of the Portuguese Pear (Pyrus communis L.) Germplasm

“…The genetic diversity of fruit trees is nowadays assessed using DNA-based molecular markers [7][8][9][10][11][12] and the Portuguese Pyrus diversity has already been studied using RAPDs [13], AFLPs [14] and microsatellites-SSRs [15]. SSRs have become markers of choice because they are highly informative, reliable, and easy to use for cultivar identification thereby improving the management of collections by enabling the identification of duplicates, synonymies, and homonymies [15][16][17].…”

Prediction of fruit texture with training population optimization for efficient genomic selection in apple

“…Several studies have for instance showed the 473 impact of genetic structure on genomic prediction, demonstrating that taking genetic structure 474 into account can improve GS efficiency (Guo et al, 2014;Isidro et al, 2015;Rio et al, 475 2019). Although in apple the genetic structure is known to be weak, with substantial levels of 476 admixture in apple cultivars (Urrestarazu et al, 2016;Vanderzande et al, 2017;Cornille et 477 al., 2019), it could still have a relevant effect on predictions, depending on the population 478 composition and the trait under investigation. Significant genetic structure has been identified, 479 for instance, between dessert and cider apples, which could potentially be correlated with fruit 480 quality traits (Lassois et al, 2016).…”