Theor Appl Genet (2017) 130:1801–1817
QTL mapping and comparative genome analysis of agronomic
traits including grain yield in winter rye
· Stefan Haffke
· Franz Joachim Fromme
· Steffen R. Roux
· Dörthe Musmann
· Andrzej Kilian
· Thomas Miedaner
Received: 1 February 2017 / Accepted: 15 May 2017 / Published online: 31 May 2017
© Springer-Verlag Berlin Heidelberg 2017
of 258 experimental hybrids in multi-environmental ﬁeld
trials. A genetic linkage map covering 964.9 cM based on
SSR, conserved-orthologous set (COS), and mixed-phase
dominant DArT markers allowed to describe 22 QTL with
signiﬁcant effects for grain yield, heading date, tiller num-
ber, and thousand grain weight across seven environments.
Using rye COS markers, orthologous segments for these
traits have been identiﬁed in the rice genome, which carry
cloned and functionally characterized rice genes. The ini-
tial genome scan described here together with the existing
knowledge on candidate genes provides the basis for sub-
sequent analyses of the genetic and molecular mechanisms
underlying agronomic important traits in rye.
Rye (Secale cereale L.) belongs to the Triticeae tribe of the
grasses and contributes to increase crop species diversity par-
ticularly in European agroecosystems. Winter rye offers mod-
est requirements to the germination temperature, low demands
on soil and climatic conditions and excellent winter hardiness.
This small grain cereal is a multipurpose crop whose grain is
traditionally used for bread making and as feed for livestock.
In addition, rye continues to emerge as a renewable energy
source for the production of bioethanol and biomethane.
Rye is outstanding among the small grain cereals with
respect to its outbreeding nature. Cytoplasmic male sterility
(CMS) as genetic fertilization control mechanism as well as
efﬁcient restorer genes successfully enable hybrid breeding
(Geiger and Miedaner 2009). The exploitation of heterosis
by a systematic evaluation of the genetic divergent gene
pools ‘Petkus’ and ‘Carsten’ (Hepting 1978) resulted in a
signiﬁcant gain in grain yield (Laidig et al. 2017), which is
economically the most important trait in rye breeding.
Key message Genetic diversity in elite rye germplasm as
well as F
testcross design enables fast QTL mapping
to approach genes controlling grain yield, grain weight,
tiller number and heading date in rye hybrids.
Abstract Winter rye (Secale cereale L.) is a multipurpose
cereal crop closely related to wheat, which offers the oppor-
tunity for a sustainable production of food and feed and
which continues to emerge as a renewable energy source
for the production of bioethanol and biomethane. Rye con-
tributes to increase agricultural crop species diversity par-
ticularly in Central and Eastern Europe. In contrast to other
small grain cereals, knowledge on the genetic architecture
of complex inherited, agronomic important traits is yet
limited for the outbreeding rye. We have performed a QTL
analysis based on a F
design and testcross performance
Communicated by Aimin Zhang.
Electronic supplementary material The online version of this
article (doi:10.1007/s00122-017-2926-0) contains supplementary
material, which is available to authorized users.
* Bernd Hackauf
Julius Kühn-Institut, Federal Research Centre for Cultivated
Plants, Institute for Breeding Research on Agricultural Crops,
Groß Lüsewitz, 18190 Sanitz, Germany
HYBRO Saatzucht GmbH and Co. KG, 17291 Schenkenberg,
State Plant Breeding Institute, University of Hohenheim,
70593 Stuttgart, Germany
Bundessortenamt, Osterfelddamm 80, 30627 Hannover,
Diversity Arrays Technology, Bruce, ACT 2617, Australia