Theor Appl Genet (2017) 130:1857–1866
Insights into the genetic relationships among plants of Beta
section Beta using SNP markers
· Karine Henry
· Pierre Devaux
· Daphné Verdelet
· Stéphanie Manel
Received: 31 January 2017 / Accepted: 30 May 2017 / Published online: 6 June 2017
© Springer-Verlag GmbH Germany 2017
test for statistical associations between genetic markers and
Plants closely related to crops (crop wild relatives) have the
potential to contribute beneﬁcial traits for crop improve-
ment (Maxted et al. 2006) and are receiving increased
attention in plant breeding (Warschefsky et al. 2014).
Assessing genetic diversity and structure of crops and their
wild relatives is useful for determining levels of genetic
variability and estimating potential losses of genetic diver-
sity associated with selection and domestication. A descrip-
tion of the genetic structure of wild and cultivated plants
is also needed to identify markers under selection through
genome–environment association methods (Schoville
et al. 2012), which require a characterization of the neu-
tral genetic structure of the data, and to correctly estimate
the linkage disequilibrium between markers (Mangin et al.
2012), which can then be used to infer the selection history
of genetic pools and to design genome-wide association
studies for quantitative trait loci (e.g. Mangin et al. 2015).
Germplasm collections represent the core resource to con-
duct genetic diversity analysis on crops and their wild
The sugar beet (Beta vulgaris subsp. vulgaris) is one of
the most important crops in terms of metric tonnage (about
140 Mt in year 2000) and accounts for approximately one-
fourth of the world’s sugar production (Draycott 2006). The
domestication of sugar beet started late, in the eighteenth
century, and is, therefore, relatively recent when compared
to that of other major crop plants (Biancardi et al. 2012).
Wild and cultivated relatives of the sugar beet are included
in Beta section Beta (Kadereit et al. 2006; Frese 2010).
Key message Using a much higher number of SNP
markers and larger sample sizes than all the previ-
ous studies, we characterized the genetic relationships
among wild and cultivated plants of section Beta.
Abstract We analyzed the genetic variation of Beta sec-
tion Beta, which includes wild taxa (Beta macrocarpa, B.
patula, B. vulgaris subsp. adanensis and B. vulgaris subsp.
maritima) and cultivars (fodder beet, sugar beet, garden
beet, leaf beet, and swiss chards), using 9724 single nucle-
otide polymorphism markers. The analyses conducted at
the individual level without a priori groups conﬁrmed the
strong differentiation of B. macrocarpa and B. vulgaris
subsp. adanensis from the other taxa. B. vulgaris subsp.
maritima showed a complex genetic structure partly fol-
lowing a geographical pattern, which confounded the dif-
ferences between this taxon and the cultivated varieties.
Cultivated varieties were structured into three main groups:
garden beets, fodder and sugar beets, and leaf beets and
swiss chards. The genetic structure described here will be
helpful to correctly estimate linkage disequilibrium and to
Communicated by André J. Bervillé.
Electronic supplementary material The online version of this
article (doi:10.1007/s00122-017-2929-x) contains supplementary
material, which is available to authorized users.
* Marco Andrello
EPHE, PSL Research University, CEFE UMR 5175,
CNRS, Université de Montpellier, Université Paul-Valéry
Montpellier, Biogéographie et Ecologie des Vertébrés, 1919
route de Mende, 34293 Montpellier Cedex 5, France
Florimond Desprez, 59242 Cappelle En Pévèle, France