Gen om e d iver si ty

Research Group: Image Analysis
head:  dr. christian klukas
Scientists
IPK financed
entzian, alexander (till 14.09.2013)
Pape, Jean-Michel (15.05.-14.09.2013)
Grant Positions
chen, dijun (0,50 bMbF, since 13.07.2012)
dornfeldt, Stefanie (0,50 bMbF/dPPn, 15.05.2013-14.11.2013)
Pape, Jean-Michel (bMbF/dPPn, since 15.11.2013)
Visiting Scientists/Scholars
Pape, Jean-Michel (self-financed, 29.04.-14.05.2013)
Goals
establishment of proven and stable image analysis methods 
for processing high-throughput phenotyping data, the devel-
opment of statistical approaches for post-processing of the 
image-derived data, and the integration of phenotypic data 
with other omics-domains.
Research Report
the development of the first version of our image analysis 
software IAP (integrated analysis Platform) has been finished 
and is publicly available at http://iap.ipk-gatersleben.de. iaP is 
an powerful framework for phenotypic image analysis and con-
tains a broad collection of user documents for several specific 
application tasks. the software is already used in several colla-
borations. together with the Max Planck institute Jena and with 
the group heterosis, an approach for the detection of leaf and 
flower movements in tobacco plants is in development. For the 
Julius kühn institute in Groß Lüsewitz and other potential users 
we created an add-on for iaP to load images from a custo-
mized imaging setup and to analyse photos of detached barley 
leaves to extract color- and geometric features. in collaboration 
with the group Pathogen Stress Genomics (dept. cytogenetics 
and Genome analysis) approaches to process barley leaf ima-
ges are in development. the goal is to identify and to quantify 
disease spots caused by powdery mildew (S. dornfeldt, J.-M. 
Pape, d. chen). 
to improve the monitoring of our high-throughput phenoty-
ping system, the development of a database for the tracking and 
visualization of carrier positions over time was started (M. ulrich).

Abteilung Molekulare Genetik/
Department of Molecular Genetics
116
Publications
Peer Reviewed Papers
2012
J
unker
, a., h. R
ohn
, t. c
zauderna
, c. k
lukas
, a. h
artmann
 & F. S
chrei
-
ber
: creating interactive, web-based and data-enriched 
maps using the Systems biology Graphical notation. nature 
Protocols 7 (2012) 579-593.
J
usufi
, i., c. k
lukas
, a. k
erren
 & F. S
chreiber
: Guiding the interactive 
exploration of metabolic pathway interconnections. infor-
mation Visualization 11 (2012) 136-150.
k
lukas
,  c., J.-M. P
ape
 & a. e
ntzian
: analysis of high-throughput 
plant image data with the information system iaP. J. integr. 
bioinform. 9 (2012) e191.
R
ohn
,  h., a. J
unker
, a. h
artmann
, e. G
rafahrend
-b
elau
, h. t
reutler
, 
M. k
lapper
 
stück
, t. c
zauderna
, c. k
lukas
 & F. S
chreiber
: Vanted 
v2: a framework for systems biology applications. bMc Syst. 
biol. 6 (2012) 139.
fer protocols are FtP, ScP, httP, WebdaV, and more. Results are 
published on the joint project website http://www.phenomics.
cn. this web-space is also used to store a diverse set of example 
datasets for demonstration and testing purposes (d. chen). iaP 
has been furthermore extended to support program exten-
sions by custom R-scripts, a programming language commonly 
used for statistical data analysis.
in a collaboration project with partners from the Plant acce-
lerator at the university of adelaide, australia (funded by the 
daad), comprehensive example phenotyping datasets were 
exchanged and analyzed using the iaP analysis software and 
the Lemnatec-based analysis pipelines from our partners (c. 
klukas, d. chen, a. entzian). to make this possible, we made 
extensive adaptations to iaP, in order to support different 
phenotyping setups, including different server- and imaging-
configurations. We matched the analysis results and created a 
mapping table to make the results comparable, so that in the 
future post-processing routines can be more easily adapted to 
the differing data formats (J.-M. Pape).
Fig. 35
detection and modelling of image-derived parameters (iaP) in crop plants. 
(a) detection of maize leaves with iaP. two distinct methods were implemented to detect maize leaves: a skeleton-based method and the SuSan corner detection algorithm. 
(b) Leaf shape modelling during plant growth. (c) Modelling of plant growth based on digital biomass. (d) Pairwise comparison of model-derived parameters, image-derived 
data and experimentally determined fresh weight or dry weight. (e) comparison of plant growth between control and stress conditions. R
iP
 represents the growth rate at the 
inflection point of control plants. R
rec
 denotes the recovered growth rate in recovery phase of stress plants. ϵ
stress
, referred to “stress elasticity”, is calculated as the ratio of R
rec
 
and R
iP
 (image created by J.-M. Pape and d. chen).

117
2013
L
u
, X., d. c
hen
, d. S
hu
, z. z
hang
, W. W
ang
, c. k
lukas
, L.L. c
hen
, Y. F
an
, 
M. c
hen
 & c. z
hang
: the differential transcription network 
between embryo and endosperm in the early developing 
maize seed. Plant Physiol. 162 (2013) 440-455.
Other Papers
2012
n
eumann
,  k., n. S
tein
, a. G
raner
, c. k
lukas
, a. e
ntzian
 & b. k
ilian
: 
non-destructive phenotyping using the high-throughput 
Lemnatec-Scanalyzer 3d platform to investigate drought 
tolerance in barley. Proceedings of the 15
th
 international 
eWac conference, 07.-11.11.2011, novi Sad/Serbia, euro-
pean cereals Genetics co-operative newsletter (2012) 158-
160.
Additional Publications 2011
P
ape
, J.-M.: automatische erkennung und Quantifizierung von 
phänotypischen Pflanzen merkmalen und Strukturen. (ba-
chelor thesis) otto-von-Guericke-universität Magdeburg, 
Fakultät für informatik, Magdeburg (2011) 67 pp.

Abteilung Molekulare Genetik/
Department of Molecular Genetics
118
and remobilization types and (c) transgenic plants with modi-
fied abscisic acid (aba) homeostasis using drought-induced 
promoters active during the generative phase. the above said 
genetic material is used to understand mechanisms of spikelet 
fertility influencing grain number as well reaching enhanced 
yield stability and uncompromised seed quality during grain 
filling under drought stress.
For the investigation of the drought stress response in the 
context of grain number it is of importance to understand the 
mechanism controlling the development of spike architecture. 
the spike architecture (row phenotype) of barley is controlled 
by VRS1, an hd-ziP i family transcription factor 1. Vrs1 (HvHox1) 
is a paralog of HvHox2 and both were generated by duplication 
of an ancestral gene. While the 2-rowed phenotype is associ-
ated with expression of a functional VRS1, in several 6-rowed 
barley accessions the expression of functional VRS1 is abolished. 
With the help of natural mutants and transgenic constructs we 
are analysing the different layers of molecular regulation that 
lead to a change in the fertility of the lateral floral meristems 
in barley. dna methylation of the HvHox1 promotor was identi-
fied after first indications from small Rna sequencing of barley. 
the dna methylation in the HvHox1 promotor region via Rna 
directed dna methylation is indicative for transcriptional gene 
suppression. utilising microarray technology for transcriptome 
analysis we identified downstream target genes that are differ-
entially expressed in the lateral meristem (t. Venkatasubbu).
the phytohormone abscisic acid (aba) is a central regulatory 
factor of the plant’s response to drought stress. the compara-
tive analysis of the “stay-green” versus “senescing” line reveals 
that high accumulation of aba under long-term drought stress 
is negative for assimilate productivity. once a plant fails to 
cope with long-term water stress, a final senescent response 
is mounted based on high aba levels. the analysis of the two 
breeding lines of barley has been extended to transgenic 
plants that either overexpress NCED6 or repress aba hydroxy-
lase gene (using a drought-induced promoter), leading to aba 
flux alterations. transgenic barley lines that overexpress NCED6 
(in an inducible manner) do show enhanced water use effi-
ciency compared to wild type. the manipulation of aba levels 
via a drought-induced promoter that drives expression of a 
key aba biosynthetic gene positively coordinate assimilation 
and transpiration under drought stress due to differential aba 
response of the lines to short- and long-duration stresses (V.t. 
harshavardhan, c. Seiler).
the  identification of the regulatory factors and structural 
genes influencing malting quality during seed germination 
from the seed pool grown under challenging environments 
Research Group:  Stress Genomics 
(till 30.04.2013)
 
Abiotic Stress Genomics 
(since 01.05.2013)
head:   dr. nese Sreenivasulu 
(till 31.03.2013)
 
dr. Markus kuhlmann 
(since 01.05.2013)
Scientists
IPK financed
Venkatasubbu, thirulogachandar (0,50)
Polavarapu, bihan kavi kishore, dr. (0,50, 01.11.-29.12.2012)
Grant Positions
Govind, Geetha, dr. (0,75 bMeLV/bLe, till 30.06.2012; 15.10.-
30.11.2012)
harshavardhan, Vokkaliga thammegowda (0,50/1,00 bMeLV/
bLe)
kalladan, Rajesh (0,50/1,00 industry, till 31.12.2012)
kuhlmann, Markus, dr. (bMbF/dLR, 01.01.-31.03.2013; bMbF, 
01.04.-30.04.2013)
Polavarapu, bihan kavi kishore, dr. (0,50 industry, 24.07.-
29.12.2012)
Seiler, christiane, dr. (0,75 bMbF/dLR, till 30.06.2013; 0,75 
bMbF, since 01.07.2013)
Surdonja, korana (0,50 bMbF, since 01.10.2012)
Wang, hongwen (0,50 SaW-Pakt, since 15.10.2012)
Visiting Scientists/Scholars
Sreenivasulu, nese, dr. (self-financed, since 01.04.2013)
Govind, Geetha, dr. (self-financed, 16.07.-30.09.2012)
kalladan, Rajesh (self-financed, 01.01.-31.08.2013)
Strickert, Marc, dr. (iPk, till 30.09.2012)
Palakolanu, Sudhakar Reddy, dr. (Leibniz daad Scholarship, 
till 28.08.2012)
Reddy, Guda Maheedhara, dr. (bMbF, 20.08.-15.11.2012)
Manish, Raorane, dr. (iRRi, Philippines, 06.07.-15.12.2012)
cordoba Jacoste, Javier (self-financed, 13.04.-15.07.2012)
Goals
We are investigating the molecular mechanisms of yield stabil-
ity under terminal drought with focus on altered grain number 
and seed filling efficiency. the aim is to improve the plant per-
formance to achieve stable yield under drought conditions. 
Research Report
to understand the mechanisms of drought resistance, inte-
grative genomics approaches were used to explore (a) natu-
ral genetic variation in barley by studying introgression line 
populations with wild barley accession donor, (b) mapping 
populations created from selected breeding lines of stay-green 

119
S
reenivasulu
, n., V.t. h
arshavardhan
, G. G
ovind
, c. S
eiler
 & a. k
oh
-
li
: contrapuntal role of aba: does it mediate stress toler-
ance or plant growth retardation under long-term drought 
stress? Gene 506 (2012) 265-273.
S
reenivasulu
,  n. & t. S
chnurbusch
: a genetic playground for en-
hancing grain number in cereals. trends Plant Sci. 17 (2012) 
91-101.
2013
a
miteye
,  S., J.M. c
orral
, h. V
ogel
, M. k
uhlmann
, M.F. M
ette
 & t.F. 
S
harbel
: novel microRnas and microsatellite-like small 
Rnas in sexual and apomictic Boechera species. MicroRna 
2 (2013) 46-63.
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
oppolu
, R., n. a
nwar
, S. S
akuma
, a. t
agiri
, u. L
undqvist
, M. P
ourk
-
heirandish
, t. R
utten
, c. S
eiler
, a. h
immelbach
, R. a
riyadasa
, h.M. 
Y
oussef
, n. S
tein
, n. S
reenivasulu
, t. k
omatsuda
 & t. S
chnurbusch
: 
Six-rowed spike4 (Vrs4) controls spikelet determinacy and 
row-type in barley. Proc. natl. acad. Sci. u.S.a. 110 (2013) 
13198-13203.
L
ermontova
,  i., M. k
uhlmann
, S. F
riedel
, t. R
utten
, S. h
eckmann
, M. 
S
andmann
, d. d
emidov
, V. S
chubert
 & i. S
chubert
: Arabidopsis ki-
netochoRe nuLL
2
 is an upstream component for cenh3 
deposition at centromeres. Plant cell 25 (2013) 3389-3404.
M
alik
,  z.a., G. h
ensel
, J.a. Q
ureshi
, S. M
ansoor
, n. S
reenivasulu
,  
J. k
umlehn
 & n.a. S
aeed
: improved agronomic and physiolo-
will remain an important strategy in the era of climate change. 
to attain high quality malt, besides the importance of defined 
parameters of malting process optimized during seed germi-
nation/micromalting, the seed quality parameters determined 
during seed filling are of foremost importance. by employing 
important genomic tools such as expression (e)QtL analysis, 
the underlying genetic factors and favourable alleles influen-
cing grain yield/seed quality/malting quality will be identified 
using double haploid (dh) population generated from a cross 
of staygreen x remobilizing lines. barley infinium array (9k il-
lumina platform) was employed to genotype doubled haploid 
(dh) population and to construct SnP-based linkage maps of 
the parental genomes. during 2012, 100 randomly selected 
dh lines were grown under field conditions at iPk with a rain 
shelter installed at anthesis to prevent natural rainfall. drought 
stress was imposed at one week after anthesis by withholding 
water until maturity. Mature seeds were harvested and ana-
lyzed. Stress treatment led to reduction in yield in more than 
50 % of the lines whereas thousand Grain Weight (tGW) was 
not affected to the same level. Few lines show no reduction in 
yield under stress. the seed material was used for micro-mal-
ting. We aim at calculating QtLs for (a) yield stability, (b) grain 
quality, (c) malting quality, (d) genome-wide expression data 
to identify cis- and trans-effects for uncompromised seed qua-
lity and malting quality under drought and (e) assessing the 
efficiency of genomic selection for the above mentioned traits 
(k. Surdonja, c. Seiler in collaboration with research group Ge-
nome diversity).
From the set of GM-plants with altered ABA level a particular 
subset showed the interesting phenotype of increased tiller 
outgrowth during vegetative growth phase (see Fig. 36). as 
this phenotype is strongly associated with increased yield it is 
of agro-economic importance. the molecular mechanism how 
the increased aba  level during that specific phase of growth 
is positively influencing the tiller outgrowth is under investiga-
tion (h. Wang, collaboration with n. von Wirén, M. hajirezaei, 
research group Molecular Plant nutrition).
Publications
Peer Reviewed Papers
2012
F
riedel
, S., b. u
sadel
, n. 
von
 W
irén
 & n. S
reenivasulu
: Reverse engi-
neering: a key component of systems biology to unravel 
global abiotic stress cross-talk. Front. Plant Sci. 3 (2012) 294.
M
ir
,  R.R., M. z
aman
-a
llah
, n. S
reenivasulu
, R. t
rethowan
 & R.k. 
V
arshney
: integrated genomics, physiology and breeding 
approaches for improving drought tolerance in crops. the-
or. appl. Genet. 125 (2012) 625-645.
R
adchuk
, V., J. k
umlehn
, t. R
utten
, n. S
reenivasulu
, R. R
adchuk
, h. R
ol
-
letschek
, c. h
errfurth
, i. F
eussner
 & L. b
orisjuk
: Fertility in bar-
ley flowers depends on Jekyll functions in male and female 
sporophytes. new Phytol. 194 (2012) 142-157.
Fig. 36
compared to control plants ('Golden Promise', left) the plants with increased 
content of abscisic acid (Lohi, right) show increased tiller outgrowth (h. Wang).

Abteilung Molekulare Genetik/
Department of Molecular Genetics
120
gical performance of cultivar “Punjab-11”-derived transge-
nic wheat under drought stress. Jokull J. 63 (2013) 136-156.
M
au
,  M., J.M. c
orral
, h. V
ogel
, M. M
elzer
, J. F
uchs
, M. k
uhlmann
,  
n. 
de
 S
torme
, d. G
eelen
 & t.F. S
harbel
: the conserved chimeric 
transcript UPGRADE-2 is associated with unreduced pollen 
formation and is exclusively found in apomictic Boechera. 
Plant Physiol. 163 (2013) 1640-1659
.
S
reenivasulu
, n. & u. W
obus
: Seed-development programs: a sys-
tems biology-based comparison between dicots and mo-
nocots. annu. Rev. Plant biol. 64 (2013) 189-217.
Books and Book Chapters
2013
R
eddy
,  P.S. & n. S
reenivasulu
: different omics approaches in ce-
reals and their possible implications for developing a sys-
tem biology approach to study the mechanism of abiotic 
stress tolerance. in: G
upta
, P.k. & R.k. V
arshney
 (eds.): cereal 
Genomics ii. Springer, dordrecht, the netherlands (2013) 
177-214.
Other Papers
2013
k
uhlmann
,  M. & a. J
unker
 (eds.): barlomics –omic approaches 
in the barley field. abstractbook of the 1
st
 iPk Summer 
School 2013. (2013) http://www.ipk-gatersleben.de/index.
php?id=1310.
PhD and Diploma Theses
2013
h
arshavardhan
, V.t.: altering aba levels in leaf and seed tissue 
of barley to study the role of aba on plant performance 
under post-anthesis drought stress using the transgenic 
approach. (Phd thesis) Martin-Luther-universität halle-
Wittenberg, naturwissenschaftliche Fakultät i biowissen-
schaften, halle/S. (2013) 137 pp.
k
alladan
,  R.: understanding terminal drought tolerance in 
barley using ab-QtL analysis and an integrated omics ap-
proach. (Phd thesis) Martin-Luther-universität halle-Wit-
tenberg, naturwissenschaftliche Fakultät i biowissenschaf-
ten, halle/S. (2013) 150 pp.

Abt. 37
Forschungsthemen in der abteilung Physiologie und zellbiologie (n. von Wirén, h.-P. Mock, M. Melzer, J. kumlehn, G. kunze, G.P. bienert).
Fig. 37
Research topics in the department of Physiology and cell biology (n. von Wirén, h.-P. Mock, M. Melzer, J. kumlehn, G. kunze, G.P. bienert).
Abteilung Physiologie und Zellbiologie/
Department of Physiology and Cell Biology

Abteilung Physiologie und Zellbiologie/
Department of Physiology and Cell Biology
122
Department of Physiology  
and Cell Biology
head:  Prof. nicolaus von Wirén
Research Goals
the common aim in the department is the improvement of 
agronomically relevant traits in crops and of biotechnologi-
cal applications by an improved adaptation and regulation of 
metabolic pathways and developmental processes in plants or 
in microbial expression systems.
Developments in 2012 and 2013
in the Physiology and cell biology department four groups 
mainly employ biochemical and physiological methods to in-
vestigate the metabolism and sensing of nutrients by plants 
(Molecular Plant nutrition and Metalloid transport groups) 
as well as the regulation of secondary metabolism and the 
physiological function of primary metabolites under stress 
(applied biochemistry and Systems biology groups). thereby, 
these groups enlarge the methodological scope of physiologi-
cal traits, which are monitored in screening projects within 
and outside the department. the other three research groups 
primarily employ developmental, biotechnological and cell 
biological methods: the Structural cell biology group employs 
light and electron microscopy for structural analysis and visual-
isation of gene products in plant tissues, while the Plant Repro-
ductive biology group characterizes developmental processes 
which are associated with sexual or asexual reproduction for 
the improvement of biotechnological applications. the Yeast 
Genetics group employs different yeast strains as hosts for re-
combinant protein production, as gene donor and biocatalysts 
for new biotechnological products and as microbial compo-
nents in biosensors for environmental monitoring and food or 
feed control. 
after dr. björn Junker was offered a full professorship at the 
university of halle-Wittenberg, the Systems biology group 
moved out. the laboratories have now been adopted by the 
newly established Metalloid transport group, which is headed 
by dr. Patrick bienert and financed by an emmy-noether fel-
lowship of the dFG.
in the past two years the analytical and cell biological plat-
forms in the department have been enlarged. Fully functional 
platforms now encompass mineral element analysis including 
automated sample digestion, icP-oeS, sector-field icP-MS and 
isotope ratio-mass spectrometry (Molecular Plant nutrition), a 
spinning-disc confocal laser scanning microscopy for live-cell 
imaging of dynamic cellular processes (Structural cell biology) 
and a MaLdi-toF system which is used for protein identifica-
tion and MS-based imaging of metabolites and proteins (ap-
plied biochemistry). a uPLc-MS/MS-based platform for phy-
tohormone analysis and a complementary Lc-MS/MS for the 
analysis of primary metabolites have also been set up.