Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level
Fecha
2016Autor
Versión
Acceso abierto / Sarbide irekia
Tipo
Artículo / Artikulua
Versión
Versión publicada / Argitaratu den bertsioa
Impacto
|
10.1186/s12870-016-0818-0
Resumen
Background: The 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 geog ...
[++]
Background: The 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.
Results: A 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.
Conclusions: The 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. [--]
Materias
Malus x domestica Borkh,
Genetic resources,
Population structure,
Variability,
SSR markers,
Differentiation,
Parentage analysis
Editor
BioMed Central
Publicado en
BMC Plant Biology (2016) 16:130
Departamento
Universidad Pública de Navarra. Departamento de Producción Agraria /
Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
Versión del editor
Entidades Financiadoras
This work has been partly funded under the EU seventh Framework
Programme by the FruitBreedomics project N°265582: “Integrated approach
for increasing breeding efficiency in fruit tree crops”. Genotyping of the Spanish
collection was partially funded by INIA, Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (project grant no RF2004-008-C03-00).
Genotyping of the Swiss collection was funded by the Swiss Federal Office
for Agriculture. Genotyping of the French collection was funded by the FRB,
‘Fondation pour la Recherche sur la Biodiversité’. Initial genotyping of the UKNFC
material was funded by the UK Depart for the Environment Food and Rural
Affairs (Defra), grant GC0140. Providing of VNIISPK material (DNA isolation and
delivery) have been done with support of Russian Scientific Fund, Project 14-
1600127. JU has been partially supported by an Early Stage Research Fellowship
of the Institute of Advanced Studies (University of Bologna).
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