Gen om e d iver si ty

IPK-LIMS. For the data publication, the e!DAL aPi (http://edal.
ipk-gatersleben.de) is adapted. e!daL provides an advanced 
file system and related infrastructure for the storage and publi-
cation of primary phenotypic data. We completely fulfil the re-
commendations of datacite (http://www.datacite.org) and the 
German Research Foundation (dFG). the e!daL-aPi is modular 
and can easy integrated into any JaVa software. alternatively, 
it offers the possibility of a client-server architecture to act as a 
central repository. Furthermore, we taking part on the develop-
ment of a file format for exchange of phenotypic information 
between databases, web services and data analysis tools. this 
format based on the iSa-tab structure (d. arend, M. Lange in 
cooperation with all iPk dPPn partners). 
in the TRITEx project we provided the data storage and assem-
bly of 454 and illumina sequenced barcoded bac (bacterial ar-
tificial chromosome) pools. We also produced whole-genome 
shotgun long jumping distance libraries of various sizes (3 kb, 
5 kb, 8 kb, 20 kb and 40 kb) for the barley cultivar Morex which 
were used by collaborators to enhance the whole-genome 
shotgun assembly of barley. Pipelines for assembling and scaf-
folding large pools of bacs (up to 672 samples per hiSeq 2000 
lane) were implemented. in total more than 15,000 bac assem-
blies were calculated with the illumina pipeline while more 
than 5,000 bac assemblies were calculated with the 454 pipe-
Research Group: Bioinformatics and Information Technology
head:  dr. uwe Scholz
Scientists
IPK financed
arend, daniel (SaW-Pakt, 01.04.-31.08.2012)
Lange, Matthias, dr.
Schmutzer, thomas (SaW-Pakt, 01.04.-31.05.2012)
Steuernagel, burkhard (SaW-Pakt, till 31.03.2012)
Grant Positions
arend, daniel (bMbF, 01.09.-30.09.2012; bMbF/dPPn, since 
01.10.2012)
beier, Sebastian (bMbF, since 01.04.2012)
Grafahrend-belau, eva (0,25 eu, since 01.09.2013)
Mascher, Martin (bMbF)
Schmutzer, thomas (bMbF, till 31.03.2012; since 01.12.2012)
Weise, Stephan, dr. (bMbF)
Visiting Scientists/Scholars
czernicka, Malgorzata, dr. (self-financed, since 31.12.2013)
Schmutzer, thomas (Scholarship of French embassy, 01.06.-
30.11.2012)
Steuernagel, burkhard (self-financed, since 01.04.2012)
Goals
development of information systems, data integration pipe-
lines, life science search engines, and usage/adaptation of 
bioinformatics tools for nGS analysis. Moreover, the research 
group is responsible for the it infrastructure of the whole in-
stitute as well as for the establishment and the operation of the 
laboratory information management system (LiMS) at the iPk.
Research Report
the group contributed to different international and national re-
search projects. examples are the eu FP 7 program, the German 
Plant Phenotyping network (dPPn) or the Plant2030 initiative.
the bMbF funded bioenergy2021 project OPTIMAS (started 
in 2009) explores diverse biological processes with the aim of 
increasing yield and biomass production in maize. in 2012 the 
development of the oPtiMaS data warehouse (OPTIMAS-DW) 
was finished. oPtiMaS-dW is a comprehensive data warehouse 
for maize containing multiple omics data. the system allows 
the storage and retrieval of experimental data as well as corre-
lation analysis results. With oPtiMaS-dW, we have established 
a public resource for maize related research supporting sys-
tems biological research in particular (c. colmsee, M. Mascher 
in collaboration with the research group Plant bioinformatics).

67
the  RyE-SELECT project is aimed to support genome-based 
breeding for rye with a genome size of 7.9 Gb. therefore 1.25 
terabyte of raw sequences of 11 genotypes and one deep se-
quencing of a reference line (Lo7) were produced. this data 
has been integrated into a draft reference (4.5 Gb) comprised 
by 629,592 scaffolds. Reads of the 11 genotypes were mapped 
against the established reference covering on average 90 % of 
the Lo7 reference (min. 84 % in Secale vavilovii and max. 92.3 % 
in Lo90). Variations analysis within these mappings revealed 6.5 
million unique SnP positions that will support future rye bre-
eding approaches (t. Schmutzer).
the  PreBreedyield project aims at developing a diverse set 
of plant materials as well as “omics” technologies and precise 
phenotyping strategies in order to enhance rapeseed pre-bree-
ding. our research group is responsible for the analysis of re-
sequencing data of 52 Brassica genotypes, the mapping to the 
B. napus reference genome and the development of a specific 
data warehouse solution, thus enabling to manage and analy-
se the project data. in collaboration with the Justus Liebig uni-
versity Gießen a pipeline has been developed to process the 
sequencing data (> 3.5 terabyte) and to finally retrieve relevant 
SnP information among the Brassica genus (3.2 million SnP po-
sition). these 52 mappings (266 Gb baM files and 73 % mapped 
reads) are the pre-requisite for a detailed variation calling to 
study the evolutionary history and develop marker to support 
performance in breeding. For the data management, all neces-
sary developments (database structures, data exchange temp-
lates, data integration pipeline) were performed; the available 
data was imported and was made available via a web applica-
tion based on user requirements. thereby, attention was paid 
line. With this effort the minimal tiling paths of chromosomes 
1h and 3h of barley have been fully sequenced and assembled 
while chromosome 4h will arrive at this status by the end of 
January 2014. using newly developed protocols for mate-pair 
sequencing on the illumina platform we sequenced pooled 
bacs to further use this resource for scaffolding and increasing 
connectivity in the bac assemblies. to support the sequen cing 
project, we started the development of the web based bac 
network database. the system provides a data access as well 
as visual representations of overlaps between bacs. We have 
developed the POPSEQ approach for sequence-based ultra-
dense genotyping of genetic mapping populations and used 
the method to substantially improve the genetic anchoring of 
both the whole-genome shotgun assembly and the physical 
map of barley (S. beier, M. Mascher, c. colmsee in collaboration 
with the research group Genome diversity).
Within the NuGGET project, we have established computatio-
nal pipelines for the high-throughput analysis of re-sequencing 
experiments in maize and barley. the streamlined integration 
of tools for short read mapping and variant calling together 
with custom visualization and data mining functions in the R 
statistical environment provides a flexible toolkit that is adap-
table to diverse datasets. We applied our methods to examine 
mapping-by-sequencing and genotyping experiments em-
ploying whole-genome shotgun, genotyping-by-sequencing 
and exome sequencing strategies and were able to fine-map 
or identify target genes underlying mutant phenotypes affec-
ting flowering time in maize and inflorescence architecture in 
barley  (M. Mascher and c. colmsee in collaboration with the 
research groups heterosis and Genome diversity).
Fig. 22
General workflow for publica-
tion of phenotypic data within 
the dPPn project (d. arend,  
u. Scholz, M. Lange).

Abteilung Cytogenetik und Genomanalyse/
Department of Cytogenetics and Genome Analysis
68
M
ayer
, k.F.X., R. W
augh
, P. L
angridge
, t.J. c
lose
, R.P. W
ise
, a. G
raner
, 
t. M
atsumoto
, k. S
ato
, a. S
chulman
, R. a
riyadasa
, d. S
chulte
, n. 
P
oursarebani
, R. z
hou
, b. S
teuernagel
, M. M
ascher
, u. S
cholz
, b. 
S
hi
, k. M
adishetty
, J.t. S
vensson
, P. b
hat
, M. M
oscou
, J. R
esnik
, G.J. 
M
uehlbauer
, P. h
edley
, h. L
iu
, J. M
orris
, z. F
renkel
, a. k
orol
, h. 
b
ergès
, S. t
audien
, M. F
elder
, M. G
roth
, M. P
latzer
, a. h
immelbach
, 
S. L
onardi
, d. d
uma
, M. a
lpert
, F. c
ordero
, M. b
eccuti
, G. c
iardo
, 
Y. M
a
, S. W
anamaker
, F. c
attonaro
, V. V
endramin
, S. S
calabrin
, S. 
R
adovic
, R. W
ing
, M. M
organte
, t. n
ussbaumer
, h. G
undlach
, M. 
M
artis
, J. P
oland
, M. P
feifer
, c. M
oisy
, J. t
anskanen
, a. z
uccolo
, 
M. S
pannagl
, J. R
ussell
, a. d
ruka
, d. M
arshall
, M. b
ayer
, d. S
war
-
breck
, d. S
ampath
, S. a
yling
, M. F
ebrer
, M. c
accamo
, t. t
anaka
, S. 
W
annamaker
, t. S
chmutzer
, J.W.S. b
rown
, G.b. F
incher
 & n. S
tein
: 
a physical, genetic and functional sequence assembly of 
the barley genome. nature 491 (2012) 711-716.
M
ehlhorn
, h., M. L
ange
, u. S
cholz
 & F. S
chreiber
: idPredictor: pre-
dict database links in biomedical database. J. integr. bioin-
form. 9 (2012) e190.
S
chlüter
, u., M. M
ascher
, c. c
olmsee
, u. S
cholz
, a. b
räutigam
, h. F
ah
-
nenstich
 & u. S
onnewald
: Maize source leaf adaptation to ni-
trogen deficiency affects not only nitrogen and carbon me-
tabolism but also control of phosphate homeostasis. Plant 
Physiol. 160 (2012) 1384-1406.
S
chreiber
, F., c. c
olmsee
, t. c
zauderna
, e. G
rafahrend
-b
elau
, a. h
art
-
mann
, a. J
unker
, b.h. J
unker
, M. k
lapperstück
, u. S
cholz
 & S. W
eise
: 
Metacrop 2.0: managing and exploring information about 
crop plant metabolism. nucleic acids Res. 40 (2012) d1173-
d1177.
S
ilvar
, c., d. P
erovic
, u. S
cholz
, a.M. c
asas
, e. i
gartua
 & F. o
rdon
: 
Fine mapping and comparative genomics integration of 
two quantitative trait loci controlling resistance to powde-
ry mildew in a Spanish barley landrace. theor. appl. Genet. 
124 (2012) 49-62.
t
hiel
, J., J. h
ollmann
, t. R
utten
, h. W
eber
, u. S
cholz
 & W. W
eschke
: 
454 transcriptome sequencing suggests a role for two-
component signalling in cellularization and differentia-
tion of barley endosperm transfer cells. PLoS one 7 (2012) 
e41867.
z
akhrabekova
, S., S.P. G
ough
, i. b
raumann
, a.h. M
üller
, J. L
undqvist
, 
k. a
hmann
, c. d
ockter
, i. M
atyszczak
, M. k
urowska
, a. d
ruka
, 
R. W
augh
, a. G
raner
, n. S
tein
, b. S
teuernagel
, u. L
undqvist
 & M. 
h
ansson
: induced mutations in circadian clock regulator 
Mat-a facilitated short-season adaptation and range ex-
tension in cultivated barley. Proc. natl. acad. Sci. u.S.a. 109 
(2012) 4326-4331.
2013
b
iselli
, c., S. u
rso
, G. t
acconi
, b. S
teuernagel
, d. S
chulte
, a. G
ianinetti
, 
P. b
agnaresi
, n. S
tein
, L. c
attivelli
 & G. V
alè
: haplotype variabi-
lity and identification of new functional alleles at the Rdg2a 
leaf stripe resistance gene locus. theor. appl. Genet. 126 
(2013) 1575-1586.
c
olmsee
, c., t. c
zauderna
, e. G
rafahrend
-b
elau
, a. h
artmann
, M. L
an
-
ge
, M. M
ascher
, S. W
eise
, u. S
cholz
 & F. S
chreiber
: oPtiMaS-dW, 
Metacrop and Vanted: a case study for data integration, 
curation and visualisation in life sciences. Proc. odLS, Lect. 
notes inform. (Lni) P-220 (2013) 455.
to obtain synergy effects with the BARSELECT project, which 
aims at increasing the yield in barley and to improve the ad-
aptation in climate change. For the baRSeLect project, the re-
search group is also responsible for the data management part, 
thus using the same developments (t. Schmutzer, S. Weise in 
cooperation with the research groups Genome diversity and 
Molecular Plant nutrition).
Publications
Peer Reviewed Papers
2012
c
ockram
, J., t. t
hiel
, b. S
teuernagel
, n. S
tein
, S. t
audien
, P.c. b
ailey
 & 
d.M. o’S
ullivan
: Genome dynamics explain the evolution of 
flowering time cct domain gene families in the Poaceae. 
PLoS one 7 (2012) e45307.
c
olmsee
, c., e.R.J. k
eller
, c. z
anke
, a. S
enula
, t. F
unke
, M. o
ppermann
, 
S. W
eise
 & u. S
cholz
: the Garlic and Shallot core collection 
image database of iPk presenting two vegetatively main-
tained crops in the Federal ex situ genebank for agricultural 
and horticultural crops at Gatersleben, Germany. Genet. Re-
sour. crop evol. 59 (2012) 1407-1415.
c
olmsee
, c., M. M
ascher
, t. c
zauderna
, a. h
artmann
, u. S
chlüter
, n. 
z
ellerhoff
, J. S
chmitz
, a. b
räutigam
, t.R. P
ick
, P. a
lter
, M. G
ahrtz
, 
S. W
itt
, a.R. F
ernie
, F. b
örnke
, h. F
ahnenstich
, M. b
ucher
, t. 
d
resselhaus
, a.P. W
eber
, F. S
chreiber
, u. S
cholz
 & u. S
onnewald
: 
oPtiMaS-dW: a comprehensive transcriptomics, metabo-
lomics, ionomics, proteomics and phenomics data resource 
for maize. bMc Plant biol. 12 (2012) 245.
k
ohl
, S., J. h
ollmann
, F.R. b
lattner
, V. R
adchuk
, F. a
ndersch
, b. S
teuer
-
nagel
, t. S
chmutzer
, u. S
cholz
, k. k
rupinska
, h. W
eber
 & W. W
esch
-
ke
: a putative role for amino acid permeases in sink-source 
communication of barley tissues uncovered by Rna-seq. 
bMc Plant biol. 12 (2012) 154.
M
ameaux
, S., J. c
ockram
, t. t
hiel
, b. S
teuernagel
, n. S
tein
, S. t
audien
, P. 
J
ack
, P. W
erner
, J.c. G
ray
, a.J. G
reenland
 & W. P
owell
: Molecular, 
phylogenetic and comparative genomic analysis of the cy-
tokinin oxidase/dehydrogenase gene family in the Poaceae. 
Plant biotechnol. J. 10 (2012) 67-82.
M
artis
, M.M., S. k
lemme
, a.M. b
anaei
 M
oghaddam
, F.R. b
lattner
, J. M
a
-
cas
, t. S
chmutzer
, u. S
cholz
, h. G
undlach
, t. W
icker
, h. Š
imková
, 
P. n
ovák
, P. n
eumann
, M. k
ubaláková
, e. b
auer
, G. h
aseneyer
, J. 
F
uchs
, J. d
oležel
 , n. S
tein
, k.F.X. M
ayer
 & a. h
ouben
: Selfish su-
pernumerary chromosome reveals its origin as a mosaic of 
host genome and organellar sequences. Proc. natl. acad. 
Sci. u.S.a. 109 (2012) 13343-13346.
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.

69
S
chlüter
, u., c. c
olmsee
, u. S
cholz
, a. b
räutigam
, a.P.M. W
eber
, n. z
el
-
lerhoff
, M. b
ucher
, h. F
ahnenstich
 & u. S
onnewald
: adaptation 
of maize source leaf metabolism to stress related disturban-
ces in carbon, nitrogen and phosphorus balance. bMc Ge-
nomics 14 (2013) e442.
Books and Book Chapters
2012
a
rend
,  d., M. L
ange
, c. c
olmsee
, S. F
lemming
, J. c
hen
 & u. S
cholz
: 
the e!daL JaVa-aPi: Store, share and cite primary data in 
life sciences. in: G
ao
, J., R. a
lhaij
, W. d
ubitzky
, L. u
ngar
, c. W
u
, 
a. c
hristianson
, M. L
iebman
 & X. h
u
 (eds.): ieee international 
conference on bioinformatics and biomedicine (bibM), 
04.-07.10.2012, Philadelphia, u.S.a., ieee catalog number: 
cFP12bib-uSb. (2012) 511-515.
a
rend
,  d.: the e!daL JaVa-aPi – store, share and cite primary 
data in life sciences. in: h
ofestädt
,  r.  &  n.  k
olchanov
 (eds.): 
German/Russian network of computational Systems biolo-
gy: Report 2012, berichte aus der Medizinischen informatik 
und bioinformatik. Shaker-Verlag, aachen (2012) 46-47.
L
ange
, M.: Management of scientific data at the iPk Gatersleben. 
in: h
ofestädt
, r. & n. k
olchanov
 (eds.): German/Russian net-
work of computational Systems biology: Report 2012, be-
richte aus der Medizinischen informatik und bioinformatik. 
Shaker-Verlag, aachen (2012) 32-33.
L
ange
, M., J. c
hen
 & u. S
cholz
: the LaiLaPS Search engine. in: u. 
G
oltz
, M.  M
agnor
, h.-J.  a
ppelrath
, h.  k.  M
atthies
, W.-t.  b
alke
 
& L. W
olf
 (eds.): inFoRMatik 2012, 42. Jahrestagung der 
Gesellschaft für informatik e.V. (Gi), 16.–21.09.2012, braun-
schweig, Lect. notes inform. (Lni) P-208. Ges. für informatik, 
bonn (2012) 1552-1558.
2013
a
rend
,  d., M. L
ange
, J. c
hen
, c. c
olmsee
, S. F
lemming
 & u. S
cholz
: 
the e!daL JaVa-aPi: Store, share and cite primary data in 
life sciences. in: S
chreiber
, F., R. h
ofestädt
, M. L
ange
, u. S
cholz
, 
t. c
zauderna
, R. S
chnee
 & S. W
eise
 (eds.): Proceedings of the 
9
th
 international Symposium on integrative bioinformatics 
2013, 18.-20.03.2013. Leibniz institute of Plant Genetics and 
crop Plant Research (iPk), Gatersleben (2013) 143-154.
M
ehlhorn
,  h., M. L
ange
, u. S
cholz
 & F. S
chreiber
: extraction and 
prediction of biomedical database identifier using neural 
networks towards data network construction. in: o
rdóñez
 
de
 
P
ablos
, P., M.d. L
ytras
, R. t
ennyson
 & J.e. L
abra
 G
ayo
 (eds.): cases 
on open-Linked data and Semantic Web applications. iGi 
Global, (2013) 58-83.
S
chreiber
, F., R. h
ofestädt
, M. L
ange
, u. S
cholz
, t. c
zauderna
, R. S
chnee
 
& S. W
eise
 (eds.): Proceedings of the 9
th
 international Sym-
posium on integrative bioinformatics 2013, 18.-20.03.2013. 
Leibniz institute of Plant Genetics and crop Plant Research 
(iPk), Gatersleben (2013) 224 pp.
h
ofestädt
, R., b. k
ormeier
, M. L
ange
, F. S
chreiber
, b. S
ommer
 & S. W
eise
: 
editorial. J. integr. bioinform. 10 (2013) e226.
L
üpken
, t., n. S
tein
, d. P
erovic
, a. h
abekuss
, i. k
ramer
, u. h
ähnel
, b. 
S
teuernagel
, u. S
cholz
, R. z
hou
, R. a
riyadasa
, S. t
audien
, M. P
lat
-
zer
, M. M
artis
, k. M
ayer
, W. F
riedt
 & F. o
rdon
: Genomics-based 
high-resolution mapping of the baMMV/baYMV resistance 
gene rym11 in barley (Hordeum vulgare L.). theor. appl. Ge-
net. 126 (2013) 1201-1212.
M
artis
, M.M., R. z
hou
, G. h
aseneyer
, t. S
chmutzer
, J. V
rána
, M. k
ubalá
-
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Abteilung Cytogenetik und Genomanalyse/
Department of Cytogenetics and Genome Analysis
70
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