Gen om e d iver si ty

PhD and Diploma Theses
2012
M
etzner
, e.M.: barley infected by powdery mildew – host tran-
scriptome and proteome changes and the integration 
of both data sets. (Phd thesis) Martin-Luther-universität 
halle-Wittenberg, naturwissenschaftliche Fakultät i biowis-
senschaften, halle/S. (2012) 219 pp.
2013
k
reszies
,  t.: experimental validation of Rna interference effi-
ciency and off-target prediction in barley. (bachelor thesis)
 
hochschule Mittweida, Fakultät für Mathematik/ naturwis-
senschaften/informatik, Mittweida (2013) 65 pp.
Patents
2012
s
chweizer
, P., d. d
ouchkov
 & S. l
ück
: Method for producing trans-
genic plants having increased resistance to pathogens. 
Wo 2012/172498, Veröffentlichung: 20.12.2012, iPk-nr. 
2011/03-04.
2013
s
chweizer
,  p.,  s.  l
ück
  &  d.  d
ouchkov
: Method of producing 
plants having increased resistence to pathogens (WRkY). 
Wo2013/050611, Veröffentlichung: 11.4.2013, iPk-nr. 
2011/28 (industrieanmeldung).
s
chweizer
, p., s. l
ück
 & d. d
uchkov
: Method of producing plants 
having increased resistance to pathogens (QtL-5h3). 
Wo2013/050318, Veröffentlichung: 11.4.2013, iPk-nr. 
2011/19 (industrieanmeldung).
s
chweizer
, p., s. l
ück
 & d. d
ouchkov
: Method of producing plants 
having increased resistance to pathogens (unkoWn_1). 
Wo2013/050593, Veröffentlichung: 11.4.2013, iPk-nr. 
2011/24 (industrieanmeldung).
s
chweizer
,  p.,  s.  l
ück
  &  d.  d
ouchkov
: Method of producing 
plants having increased resistance to pathogens (PRX_1). 
Wo2013/053711, Veröffentlichung: 18.4.2013, iPk-nr. 
2011/14 (industrieanmeldung).
Schweizer, P., S. Lück & d. douchkov: Method of producing 
plants having increased resistance to pathogens (RLk_2). 
Wo2013/053686, Veröffentlichung: 18.4.2013, iPk-nr. 
2011/21 (industrieanmeldung).
Integration of biotic and abiotic stress responses:
at least hvLsd1a, which mediated powdery-mildew susceptibil-
ity in barley, may also be relevant for cold- and drought tolerance 
in plants according to public and iPk internal mutant- and allele 
data (eXbaRdiV project). transgenic hvLsd1a Rnai lines pro- 
vided by the group of J. kumlehn were more resistant to pow-
dery mildew and will be tested for altered drought tolerance in 
2014.
Publications
Peer Reviewed Papers
2012
G
owda
 R
ayapuram
, c., M.k. J
ensen
, F. M
aiser
, J.V. S
hanir
, h. h
ornshoj
, 
J.h. R
ung
, P.L. G
regersen
, P. S
chweizer
, d.b. c
ollinge
 & M.F. L
yng
-
kjaer
: Regulation of basal resistance by a powdery mildew-
induced cysteine-rich receptor-like protein kinase in barley. 
Mol. Plant Pathol. 13 (2012) 135-147.
G
uerra
, d., a.M. M
astrangelo
, G. L
opez
-t
orrejon
, S. M
arzin
, P. S
chwei
-
zer
, a.M. S
tanca
, J.c. 
del
  P
ozo
, L. c
attivelli
 & e. M
azzucotelli
: 
identification of a protein network interacting with tdRF1, 
a wheat RinG ubiquitin ligase with a protective role against 
cellular dehydration. Plant Physiol. 158 (2012) 777-789.
S
pies
, a., V. k
orzun
, R. b
ayles
, J. R
ajaraman
, a. h
immelbach
, P.e. h
ed
-
ley
 & P. S
chweizer
: allele mining in barley genetic resources 
reveals genes of race-non-specific powdery mildew resis-
tance. Front. Plant Sci. 2 (2012) 22 pp.
2013
F
lorschütz
,  k., a. S
chröter
, S. S
chmieder
, W. c
hen
, P. S
chweizer
, F. 
S
onntag
, n. d
anz
, k. b
aronian
 & G. k
unze
: ‘Phytochip’ – on-
chip detection of phytopathogenic Rna viruses by a new 
surface plasmon resonance platform. J. Virol. Methods 189 
(2013) 80-86.
o
stertag
, M., J. S
tammler
, d. d
ouchkov
, R. e
ichmann
 & R. h
ückelhoven
: 
the conserved oligomeric Golgi complex is involved in 
penetration resistance of barley to the barley powdery mil-
dew fungus. Mol. Plant Pathol. 14 (2013) 230-240.
P
liego
, c., d. n
owara
, G. b
onciani
, d.M. G
heorghe
, R. X
u
, P. S
urana
, 
e. W
higham
, d. n
ettleton
, a.J. b
ogdanove
, R.P. W
ise
, P. S
chweizer
, 
L.V. b
indschedler
 & P.d. S
panu
: host-induced gene silencing in 
barley powdery mildew reveals a class of ribonuclease-like 
effectors. Mol. Plant Microbe interact. 26 (2013) 633-642.
P
oursarebani
, n., R. a
riyadasa
, R. z
hou
, d. S
chulte
, b. S
teuernagel
, M.M. 
M
artis
, a. G
raner
, P. S
chweizer
, u. S
cholz
, k.F.X. M
ayer
 & n. S
tein
: 
conserved synteny-based anchoring of the barley genome 
physical map. Funct. integr. Genomics 13 (2013) 339-350.
Other Papers
2013
R
edaktion
  P
flanzenforschung
.
de
: neue Perspektiven für den 
Pflanzenschutz mit hiGS. interview mit dr. habil. Pat-
rick Schweizer über das Projekt “dsRnaguard”. http://

Abteilung Cytogenetik und Genomanalyse/
Department of Cytogenetics and Genome Analysis
82
nium-chip was used to genotype all varieties, delivering a solid 
foundation for the establishment of marker-trait associations. 
For heading date, genome-wide associations were analysed by 
comparing the use of microsatellite data and SnP data, and a 
novel Hd6-related gene marker was detected by exploiting the 
synteny between wheat and rice (c. zanke, Ji. Ling, M. Röder) 
(see Fig. 26, p. 83). For validating previously detected marker-
trait associations for resistance to Fusarium head blight and 
yield, for six cross combinations bc
2
-lines were established by 
using marker-assisted selection (M. Röder).
the intention of the project SeLect is to establish and apply 
procedures for the targeted identification of molecular markers 
in wheat by using sequence capture technologies. For this 
purpose, four chromosomal regions of the hexaploid wheat 
genome were selected as capture baits and the capture pro-
cedure of the company aGiLent was carried out on a panel of 
24 wheat lines (c. zanke). in collaboration with traitGenetics 
Gmbh, the captured dna was sequenced on the MiSeq, map-
ped to reference sequences and analysed for SnPs. in addition, 
for four cross combinations bc
2
-lines were established to map 
and validate previously detected marker-trait associations for 
thousand-grain weight.
a gene family of pectin esterase inhibitor (PEI)  genes  was 
identified and further characterized in the genomic region 
around the gene Rrs2 rendering resistance against leaf scald in 
barley caused by the fungal pathogen Rhynchosporium com-
mune. in collaboration with the group Plant Reproductive bio-
logy (J. kumlehn, G. hensel), stable transgenic overexpression 
lines were generated for the genes PEI2, PEI3 and PEI4 in the 
background of the barley variety ‘Golden Promise’ and tested 
for their resistance to Rhynchosporium commune by applying 
qPcR to measure the abundance of fungal dna. Furthermore, 
virus-induced gene silencing (ViGS) was carried out to silence 
the complete known family of Pei genes and measure the ef-
fects on resistance to scald (S. Marzin).
the sequence of the genomic region of QTL QTgw.ipk-7D for 
grain size in wheat was further analyzed and synteny was 
established to the respective genomic regions in barley, rice, 
Sorghum bicolor and Brachypodium distachyon. Further wheat 
bacs were obtained from J. doležel and h. Simkova (institute 
of experimental botany, olomouc, czech Republic) and se-
quenced in collaboration with the group Genome diversity (a. 
himmelbach, n. Stein). candidate genes were tested for the 
presence of SnPs between the parental lines and diagnostic 
nearly-isogenic lines (c. Jaenecke).
a collection of ethiopian Triticum durum landraces was tested 
for genetic diversity with different sets of markers related to re-
sistance against the stem rust pathovar UG99. Furthermore, 
Research Group: Gene and Genome Mapping
head:  dr. Marion Röder
Scientists
IPK financed
haile, Jemanesh kifetew (0,50, 01.01.-31.03.2013)
Grant Positions
Jaenecke, cornelia, dr. (dFG, since 01.02.2012)
Ling, Jie, dr. (bMbF, since 01.01.2012)
Marzin, Stephan, dr. (dFG)
zanke, christine, dr. (bMbF, since 01.02.2012)
Visiting Scientists/Scholars
antonova, elena, dr. (dFG, 06.10.-30.12.2012)
bisaria, dinisha (daad, 15.02.-15.11.2012)
diaz de Leon alvarez, José Luis, dr. (self-financed, 01.01.-
30.09.2012; 19.08.-26.09.2013)
ilyas, Mehmoona (Research Fellowship of higher education 
commission, till 17.02.2012) 
kalladan, Rajesh (self-financed, 01.05.-31.08.2013)
kifetew haile, Jemanesh kifetew (daad, 01.01.-31.12.2012; 
self-financed, 01.04.bis 31.12.2013)
kumar, Suneel (bMbF, 25.05.-31.07.2012 ; 25.06.-22.11.2013)
kumar, uttam, dr. (bMbF, 25.05.2012-30.06.2013)
Leonova, irina, dr. (bLe-Scholarship, 19.11.-19.12.2012)
terrile, ignacio ismael (Monsa beachell-borlaug international 
Scholars, 04.02.-03.05.2013)
Vas, eszter (dbu, 06.09.2012-31.07.2013)
Goals
exploitation of the natural genetic diversity in wheat and barley 
for identification, genetic mapping and cloning of genes for ag-
ronomically important traits.
Research Report
the comprehensive approach for association mapping in 
Euro pean winter wheat was continued in the project Va-
Lid by adding 146 new varieties to the existing panel of 372 
wheat varieties. in collaboration with breeding companies 
(kWS-Lochow Gmbh, Syngenta Seeds) and the Julius kühn in-
stitute varieties were evaluated for important agronomic traits, 
drought tolerance (F. ordon, c. balko), and for various fungal 
diseases, such as Fusarium head blight (Fusarium graminearum 
and Fusarium culmorum), Septoria tritici blotch (Mycosphaerel-
la graminicola), tan spot (Pyrenophora tritici-repentis) and eye 
spot (Pseudocercosporella herpotrichoides) (b. Rodemann). in 
collaboration with traitGenetics Gmbh (M. Ganal) besides the 
existing genome-wide microsatellite data, a 90k iSeLect infi-

83
doubled-haploid population Solitär × Mazurka. Mol. breed. 
29 (2012) 813-830.
k
önig
, J., d. k
opahnke
, b.J. S
teffenson
, n. P
rzulj
, t. R
omeis
, M.S. R
ö
-
der
, F. o
rdon
 & d. P
erovic
: Genetic mapping of a leaf rust 
resistance gene in the former Yugoslavian barley landrace 
MbR1012. Mol. breed. 30 (2012) 1253-1264.
M
atthies
, i.e., S. S
harma
, S. W
eise
 & M.S. R
öder
: Sequence variation 
in the barley genes encoding sucrose synthase i and sucro-
se phosphate synthase ii, and its association with variation 
in grain traits and malting quality. euphytica 184 (2012) 73-
83.
M
atthies
, i.e., t. 
van
 h
intum
, S. W
eise
 & M.S. R
öder
: Population struc-
ture revealed by different marker types (SSR or dart) has an 
impact on the results of genome-wide association mapping 
in european barley cultivars. Mol. breed. 30 (2012) 951-966.
P
aliwal
,  R., M.S. R
öder
, u. k
umar
, J.P. S
rivastava
 & a.k. J
oshi
: QtL 
mapping of terminal heat tolerance in hexaploid wheat (T. 
aestivum L.). theor. appl. Genet. 125 (2012) 561-575.
W
eidner
,  a., M.S. R
öder
 & a. b
örner
: Mapping wheat powdery 
mildew resistance derived from Aegilops markgrafii. Plant 
Genet. Resour. 10 (2012) 137-140.
X
ie
, W., R. b
en
-d
avid
, b. z
eng
, a. d
inoor
, c. X
ie
, Q. S
un
, M.S. R
öder
, 
a. F
ahoum
 & t. F
ahima
: Suppressed recombination rate in 
6VS/6aL translocation region carrying the Pm21 locus in-
trogressed from Haynaldia villosa into hexaploid wheat. 
Mol. breed. 29 (2012) 399-412.
X
ie
, W., R. b
en
-d
avid
, b. z
eng
, M.S. R
öder
, a. d
inoor
 & t. F
ahima
: iden-
tification and characterization of a novel powdery mildew 
resistance gene PmG3M derived from wild emmer wheat, 
haplotype analysis was conducted for the same set of lines with 
markers linked to known stem rust resistance genes (J. k. haile).
in collaboration with ciMMYt, Mexico, a project was started to 
develop early flowering wheat lines for hot and dry areas in in-
dia. the genotyping of candidate genes of the photoperiodic 
pathway was started (c. trautewig, M. Röder).
Publications
Peer Reviewed Papers
2012
b
örner
, a., e.k. k
hlestkina
, S. c
hebotar
, M. n
agel
, M.a. R
ehman
 a
rif
, 
k. n
eumann
, b. k
obiljski
, u. L
ohwasser
 & M.S. R
öder
: Molecular 
markers in management of ex situ PGR – a case study. J. 
biosci. 37 (2012) 871-877.
d
awit
, W., k. F
lath
, W.e. W
eber
, e. S
chumann
, M.S. R
öder
 & X. c
hen
: 
Postulation and mapping of seedling stripe rust resistance 
genes in ethiopian bread wheat cultivars. J. Plant Pathol. 94 
(2012) 403-409.
h
aile
,  J.k., M.M. n
achit
, k. h
ammer
, a. b
adebo
 & M.S. R
öder
: QtL 
mapping of resistance to race ug99 of Puccinia graminis f. 
sp. tritici in durum wheat (Triticum durum desf.). Mol. breed. 
30 (2012) 1479-1493.
k
elm
, c., S.M.t. G
haffary
, h. b
ruelheide
, M.S. R
öder
, S. M
iersch
, W.e. 
W
eber
, G.h.J. k
ema
 & b. S
aal
: the genetic architecture of seed-
ling resistance to Septoria tritici blotch in the winter wheat 
Fig. 26
Left: Field plots of wheat varie-
ties showing different heading 
times. (Photo: courtesy e. eb-
meyer); Right: Manhatten plots 
of  (A) SSR and (B) SnP marker 
alleles associated with head-
ing date.  this plot presents 
significant allele associations 
at threshold – log
10
 (P-value) 
≥  3.0 for eight environments 
plus bLues sorted according to 
their chromosomal location. the 
green line indicates the thresh-
old -log
10
 (P-value) ≥  4.82 (SSR) 
and ≥  5.89 (SnP), respectively, 
for bonferroni correction. Red 
diamonds represent the associ-
ated alleles for a single environ-
ment and blue squares for the 
marker-trait associations of the 
bLues (c. zanke).

Abteilung Cytogenetik und Genomanalyse/
Department of Cytogenetics and Genome Analysis
84
t
imonova
, e.M., i.n. L
eonova
, M.S. R
öder
 & e.a. S
alina
: Marker-assis-
ted development and characterization of a set of Triticum 
aestivum lines carrying different introgressions from the T. 
timopheevii genome. Mol. breed. 31 (2013) 123-136.
Other Papers
2012
b
örner
, a., F. F
leischer
, e.i. G
ordeeva
, J.k. h
aile
, t. k
arceva
, e.k. k
hlest
-
kina
, b. k
obiljski
, S. L
andjeva
, u. L
ohwasser
, M. n
agel
, M.a. R
ehman
 
a
rif
, n. t
ikhenko
, M.S. R
öder
 & c. V
olkmar
: items from Germa-
ny. ann. Wheat newsl. 58 (2012) 68-71.
b
örner
, a., e.k. k
hlestkina
, S. P
shenichnikova
, S.V. o
sipova
, b. k
obiljski
, 
a.F. b
alint
, S. L
andjeva
, a. G
iura
, M.R. S
imon
, M.a. R
ehman
 a
rif
, 
k. n
eumann
, u. L
ohwasser
 & M.S. R
öder
: cereal genetic stocks 
– examples of successful co-operation (2008-2011). Pro-
ceedings of the 15
th
 international eWac conference, 07.-
11.11.2011, novi Sad/Serbia, european cereals Genetics 
co-operative newsletter (2012) 13-18.
S
alem
,  k.F.M., M.S. R
öder
 & a. b
örner
: evaluation of genetic di-
versity among egyptian bread wheat (Triticum aestivum L.) 
varieties during the period 1947-2004 using microsatellite 
markers. Proceedings of the 15
th
 international eWac con-
ference, 07.-11.11.2011, novi Sad/Serbia, european cereals 
Genetics co-operative newsletter (2012) 185-191.
2013
b
örner
, a., a. b
akhsh
, e.i. G
ordeeva
, e.k. k
hlestkina
, S. k
ollers
, J. L
ing
, 
u. L
ohwasser
, M. n
agel
, S. n
avakode
, S.V. o
sipova
, a.V. P
ermyakov
, 
M.d. P
ermyakova
, t.a. P
shenichnikova
, M.a. R
ehman
 a
rif
, M.S. R
ö
-
der
, M.R. S
imon
, n. t
ikhenko
 & c. V
olkmar
: items from Germany. 
ann. Wheat newsl. 59 (2013) 9-14.
n
agel
, M., S. n
avakode
, M.M. n
achit
, M. b
aum
, M.S. R
öder
 & a. b
örner
: 
durum in a changing climate – drought stress during grow-
ing seasons in Syria. tagungsband der 63. Jahrestagung 
der Vereinigung der Pflanzenzüchter und Saatgutkaufleute 
Österreichs, 19.-21.11.2012, Vereinigung der Pflanzenzüch-
ter und Saatgutkaufleute Österreichs, Raumberg-Gumpen-
stein/austria (2013) 83-85.
PhD and Diploma Theses
2012
h
aile
, J.k.: Genetic mapping of resistance to race ug99 of Puc-
cinia graminis f. sp. tritici, diversity analysis and identifica-
tion of stem rust resistance genes in ethiopian tetraploid 
wheats. (Phd thesis) universität kassel, kassel (2012) 118 
pp.
Triticum dicoccoides. theor. appl. Genet. 124 (2012) 911-
922.
z
aynali
 n
ezhad
, k., W.e. W
eber
, M.S. R
öder
, S. S
harma
, u. L
ohwasser
, 
R.c. M
eyer
, b. S
aal
 & a. b
örner
: QtL analysis for thousand-
grain weight under terminal drought stress in bread wheat. 
euphytica 186 (2012) 127-138.
2013
h
aile
, J.k., k. h
ammer
, a. b
adebo
, M.M. n
achit
 & M.S. R
öder
: Genetic 
diversity assessment of ethiopian tetraploid wheat landra-
ces and improved durum wheat varieties using microsatel-
lites and markers linked with stem rust resistance. Genet. 
Resour. crop evol. 60 (2013) 513-527.
h
aile
, J.k., k. h
ammer
, a. b
adebo
, R.P. S
ingh
 & M.S. R
öder
: haplotype 
analysis of molecular markers linked to stem rust resistance 
genes in ethiopian improved durum wheat varieties and 
tetraploid wheat landraces. Genet. Resour. crop evol. 60 
(2013) 853-864.
h
aile
, J.k. & M.S. R
öder
: Status of genetic research for resistance 
to ug99 race of Puccinia graminis f. sp. tritici: a review of cur-
rent research and implications. afr. J. agricult. Res. 8 (2013) 
6670-6680.
k
alladan
, R., S. W
orch
, h. R
olletschek
, V.t. h
arshavardhan
, L. k
untze
, 
c. S
eiler
, n. S
reenivasulu
 & M.S. R
öder
: identification of quan-
titative trait loci contributing to yield and seed quality pa-
rameters under terminal drought in barley advanced back-
cross lines. Mol. breed. 32 (2013) 71-99.
k
ollers
, S., b. R
odemann
, J. L
ing
, V. k
orzun
, e. e
bmeyer
, o. a
rgillier
, M. 
h
inze
, J. P
lieske
, d. k
ulosa
, M.W. G
anal
 & M.S. R
öder
: Whole ge-
nome association mapping of Fusarium head blight resis-
tance in european winter wheat (Triticum aestivum L.). PLoS 
one 8 (2013) e57500.
k
ollers
, S., b. R
odemann
, J. L
ing
, V. k
orzun
, e. e
bmeyer
, o. a
rgillier
, 
M. h
inze
, J. P
lieske
, d. k
ulosa
, M.W. G
anal
 & M.S. R
öder
: Ge-
netic architecture of resistance to Septoria tritici blotch 
(Mycosphae rella  graminicola) in european winter wheat. 
Mol. breed. 32 (2013) 411-423.
k
ruppa
, k., a. S
epsi
, e. S
zakács
, M.S. R
öder
 & M. M
olnár
-L
áng
: cha-
racterization of a 5hS-7dS.7dL wheat-barley translocation 
line and physical mapping of the 7d chromosome using 
SSR markers. J. appl. Genet. 54 (2013) 251-258.
L
eonova
, i.n., e.d. b
adaeva
, o.a. o
rlovskaya
, M.S. R
öder
, L.V. k
hoty
-
leva
, e.a. S
alina
 & V.k. S
humny
: comparative characteristic of 
Triticum aestivum/Triticum durum and Triticum aestivum/Tri-
ticum dicoccum hybrid lines by genomic composition and 
resistance to fungal diseases under different environmental 
conditions. Russ. J. Genet. 49 (2013) 1112-1118.
M
atthies
, i.e., S. W
eise
, J. F
örster
, V. k
orzun
, n. S
tein
 & M.S. R
öder
: 
nitrogen-metabolism related genes in barley – haplotype 
diversity, linkage mapping and associations with malting 
and kernel quality parameters. bMc Genetics 14 (2013) e77.
P
eukert
, M., S. W
eise
, M.S. R
öder
 & i.e. M
atthies
: development of 
SnP markers for genes of the phenylpropanoid pathway 
and their association to kernel and malting traits in barley. 
bMc Genet. 14 (2013) e97.

85
between them.
 
Moreover, this SnP class is highly abundant. 
it was tested whether sequence resources available for the 
progenitors of B. napus (aacc), Brassica rapa (aa) and Brassica 
olera cea  (cc), can be exploited for the design of intergenomic 
SnP assays. as a proof of concept, intergenomic SnPs were 
identified for corresponding regions located on B. rapa and  
B. oleracea chromosomes a1 and c1, respectively. importantly, 
many polymorphisms that had been detected based on se-
quence alignments of the B. rapa and B. oleracea sequences 
were also present in B. napus. intergenomic SnPs mapping 
throughout the chosen homoeologous chromosome segments 
were included in illumina’s GoldenGate
®
 Genotyping assay and 
used to screen multidimensional pools of the B. napus bacterial 
artificial chromosome library. the screening of the bac pools 
with these intergenomic SnPs yielded contigs that spanned 
most of the homoeologous regions of interest in the B. napus 
genome. Selected results are shown in Fig. 27. thus, owing to 
their high abundance and ease of identification, intergenomic 
SnPs proved to be a powerful tool for the development of bac 
contig maps for defined regions of the B. napus genome (h.X. 
cao, R. Schmidt).