Gen om e d iver si ty

PhD and Diploma Theses
2012
a
thmer
, b.: differentielle Genexpression in Roggen, Weizen und 
Gerste während der kälteakklimatisierung und ihr bezug zur 
Frosttoleranz. (Phd thesis) Martin-Luther-universität halle-
Wittenberg, institut für agrar- und ernährungswissenschaf-
ten der naturwissenschaftlichen Fakultät iii, halle/S. (2012) 
199 pp.
P
asam
,  R.k.: development of stratified barley populations for 
association mapping studies. (Phd thesis) Martin-Luther-
universität halle-Wittenberg, institut für agrar- und ernäh-
rungswissenschaften der naturwissenschaftlichen Fakultät 
iii, halle/S. (2012) 167 pp.
P
oursarebani
, n.: a genetically anchored physical map of barley 
chromosome 2h. (Phd thesis) Martin-Luther-universität 
halle-Wittenberg, institut für agrar- und ernährungs-
wissenschaften der naturwissenschaftlichen Fakultät iii, 
halle/S. (2012) 106 pp.
2013
S
harma
,  R.: Genome-wide association studies in diverse gene 
pools of barley. (Phd thesis) Martin-Luther-universität 
halle-Wittenberg, institut für agrar- und ernährungswissen-
schaften der naturwissenschaftlichen Fakultät iii, halle/S. 
(2013) 167 pp.
k
uon
, J.e.: identification of a many-noded-dwarf gene by using 
a cloning-by-sequencing approach in barley. (Master thesis) 
institut für Pflanzenzüchtung, Saatgutforschung und Popu-
lationsgenetik, universität hohenheim (2013) 55 pp.
S
akuma
, S., M. P
ourkheirandish
, G. h
ensel
, J. k
umlehn
, n. S
tein
, a. t
agi
-
ri
, n. Y
amaji
, J.F. M
a
, h. S
assa
, t. k
oba
 & t. k
omatsuda
: divergence 
of expression pattern contributed to neofunctionalization 
of duplicated hd-zip i transcription factor in barley. new 
Phytol. 197 (2013) 939-948.
t
ondelli
, a., X. X
u
, M. M
oragues
, R. S
harma
, F. S
chnaithmann
, c. i
n
-
gvardsen
, o. M
anninen
, J. c
omadran
, J. R
ussell
, R. W
augh
, a.h. 
S
chulman
, k. P
illen
, S.k. R
asmussen
, b. k
ilian
, L. c
attivelli
, W.t.b. 
t
homas
 & a.J. F
lavell
: Structural and temporal variation in ge-
netic diversity of european spring 2-row barley cultivars and 
association mapping of quantitative traits. Plant Genome 6 
(2013) 1-14.
Y
ang
, P., d. P
erovic
, a. h
abekuss
, R. z
hou
, a. G
raner
, F. o
rdon
 & n. 
S
tein
: Gene-based high-density mapping of the gene rym7 
conferring resistance to Barley mild mosaic virus (baMMV). 
Mol. breed. 32 (2013) 27-37.
Books and Book Chapters
2012
k
ilian
,  b., h. Ö
zkan
, S. S
haaf
, S. h
übner
, R.k. P
asam
, R. S
harma
, k. 
n
eumann
, W. W
eissgerber
, F.a. k
onovalov
, J. k
eilwagen
, S. F
riedel
, 
h. k
nüpffer
, M. 
von
 k
orff
, G. c
oupland
 & a. G
raner
: comparing 
genetic diversity within a crop and its wild progenitor: a case 
study for barley. in: M
axted
, n., M.e. d
ulloo
, b.V. F
ord
-L
loyd
, 
L. F
rese
, J.M. i
riondo
 & M.a.a. P
inheiro
 
de
  c
arvalho
 (eds.): ag-
robiodiversity conservation: Securing the diversity of crop 
Wild Relatives and Landraces. cabi Publishing, Wallingford 
(2012) 186-192.
2013
P
erovic
, d., d. k
opahnke
, b.J. S
teffenson
, J. F
örster
, J. k
önig
, b. k
ili
-
an
, J. P
lieske
, G. d
urstewitz
, V. k
orzun
, i. k
raemer
, a. h
abekuss
, P. 
J
ohnston
, R. P
ickering
 & F. o
rdon
: Genetic fine mapping of a 
novel leaf rust resistance gene and a barley yellow dwarf vi-
rus tolerance (bYdV) introgressed from Hordeum bulbosum 
by the use of the 9k iSelect chip. in: z
hang
, G., c. L
i
 & X. L
iu
 
(eds.): advance in barley Sciences. Proceedings of 11
th
 inter-
national barley Genetics Symposium. Springer and zhejiang 
university Press (2013) 269-284.
Other Papers
2012
acatech
 – d
eutsche
 a
kademie
 
der
 t
echnikwissenschaften
, d. a
meling
, b. 
b
ajorat
, j. 
von
 b
raun
, w. b
rinker
, r. b
urger
, h.j. c
ramer
, k. 
von
 
d
ohnanyi
,  h.  f
erkel
,  a.  g
edaschko
,  g.  g
latzel
,  a.  g
raner
,  p. 
zu
 
g
uttenberg
, p. h
erzig
, b. h
orsfield
, m. h
üther
, r. h
üttl
, m. j
äger
, 
k.  k
onrad
,  k.  k
ornwachs
,  c.  k
ratz
,  k.  l
ochte
, v.  m
osbrugger
,  b. 
m
üller
, h.h. n
acke
, l. r
eisch
, m. s
titt
, r. 
van
 
der
 m
eer
, f. v
ahren
-
holt
, a. v
oss
, c.c. 
von
 w
eizsäcker
, c. w
itt
 & h. z
eiss
 (eds.): an-
passungsstrategien in der klimapolitik (acatech PoSition). 
Springer-Verlag, heidelberg et al. (2012) 38 pp.

35
Integration of IPK data in information networks. Passport 
data of genebank accessions were repeatedly exported and 
submitted to the German national inventory of PGR (PGRdeu), 
the european central PGR Search catalogue (euRiSco), and nu-
merous ecPGR european central crop databases. GbiF (Global 
biodiversity information Facility) is accessing iPk’s passport 
data via a web service. 
Since September 2012, a dFG-funded project on Herbarium 
Digitization is being carried out, in cooperation with the re-
search group experimental taxonomy (k. Pistrick). the her-
barium images are scanned with high resolution and visualised 
using the djatoka image server. Label data are documented 
using the JacQ software developed by the herbarium of the 
university of Vienna, austria, within the project Virtual her-
baria. this ensures standardised data recording as well as the 
searchability of digitized iPk herbarium data jointly with other 
those of herbaria participating in the Virtual herbaria project. 
the group is developing software to connect images with 
gene bank accessions via accession numbers and other identi-
fiers with the aim of integrating herbarium images and other 
images (e.g. scanned card files) into the GbiS specimen man-
agement system (see above) (cong khac dung, c. dittmann,  
M. oppermann).
the group is hosting the European Barley Database (ebdb), 
the European Poa Database, and the European Allium Da-
tabase (since 2012) of the european cooperative Programme 
for Plant Genetic Resources (ecPGR), the latter two in coopera-
tion with e. Willner (Satellite collections north) and J. keller (re-
search group In vitro Storage and cryopreservation). in collabo-
ration with the research group bioinformatics and information 
technology (u. Scholz) a bid was won for hosting and further 
develop, from 2014 on, the european Search Portal for Plant 
Genetic Resources (EURISCO). Preparation for the transfer to 
iPk started already in the second half of 2013.
the group is also maintaining other databases: Mansfeld’s 
World Database of Agricultural and Horticultural Crops 
(http://mansfeld.ipk-gatersleben.de) and the in-house Data-
base for Checklists of Cultivated Plants (not online) (M. op-
permann, h. knüpffer).
in addition, the automatic IPK weather stations in Gatersle-
ben and Malchow are operated by the group, and the data 
generated are made publicly accessible via the iPk website (M. 
oppermann).
Research Group: Genebank Documentation
head:  dr. helmut knüpffer
Scientists
IPK financed
dittmann, claudia
oppermann, Markus 
Grant Positions
cong, khac dung, dr. (dFG, since 01.09.2012)
Visiting Scientists/Scholars
Filatenko, anna, dr. (iPk/Gemeinschaft zur Förderung der kul-
turpflanzenforschung Gatersleben e.V., 22.03.-12.04.2013)
kywan, khouloud (self-financed, 08.10.2012-30.06.2014)
Goals
development and maintenance of information systems for 
plant genetic resources (PGR) with the aim to provide informa-
tion to researchers, breeders and other users, and to support 
the conservation management.
Research Report
the group’s activities focused on the continuous maintenance, 
development and extension of the Genebank Information Sys-
tem (GBIS). GbiS is being developed in an oracle environment. 
(1) GBIS/M, the internal genebank management system, offers 
numerous functions supporting the day-to-day genebank ac-
tivities. it has been operational since 2006. the in vitro storage 
module and the full integration of the Groß Lüsewitz potato 
collection in GbiS were completed in 2013 (c. dittmann, M. 
oppermann, cooperation with J. keller, research group In vitro 
Storage and cryopreservation, and k. dehmer, research group 
Satellite collections north). in 2013, the development of the 
specimen management system (e.g. herbarium images) was 
started (c. dittmann, M. oppermann). 
the developers’ (technical) documentation for GbiS/M and the 
user manual are updated annually. bug-fixing, the implementa-
tion of change requests, and improving the user-friendliness of 
GbiS are continuously carried out. the data base was increased 
and further consolidated, and the data quality was improved 
(M. oppermann, h. knüpffer). 
(2) GBIS/I, the internet portal for searching and ordering gene-
bank accessions (http://gbis.ipk-gatersleben.de/gbis_i/), pro-
vides online access to 151,000 accessions of the iPk Genebank 
collections at Gatersleben, Malchow and Groß Lüsewitz. it was 
adapted to the new oracle Weblogic server technology in 2013. 
it has been used for material requests by more than 70 % of the 
users in 2012-2013 (cf. diagram in Fig. 11 b, p. 36).

Abteilung Genbank/
Department of Genebank
36
Publications
Peer Reviewed Papers
2012
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.
e
ndresen
,  d.t.F. & h. k
nüpffer
: the darwin core extension for 
gene banks opens up new opportunities for sharing germ-
plasm data sets. biodiversity informatics 8 (2012) 12-29.
h
anelt
, P., h. k
nüpffer
 & k. h
ammer
: erna bennett (5 august 1925- 3 
January 2012). Genet. Resour. crop evol. 59 (2012) 967-970.
t
homas
,  k., R. t
hanopoulos
, h. k
nüpffer
 & P.J. b
ebeli
: Plant gene-
tic resources of Lemnos (Greece), an isolated island in the 
northern aegean Sea, with emphasis on landraces. Genet. 
Resour. crop evol. 59 (2012) 1417-1440.
V
incent
, h., R. 
von
 b
othmer
, h. k
nüpffer
, a. a
mri
, J. k
onopka
 & n. M
ax
-
ted
: Genetic gap analysis of wild Hordeum taxa. Plant Genet. 
Resour. 10 (2012) 242-253.
Fig. 11
a) Genebank accessions by country of origin. b) distributed samples in 2006-2013 by institution type. c) numbers of new accessions per year (1945-2013), reflecting the 
sources of material. d) utilization of GbiS/i for requesting genebank material: percentage of distributed samples (source: M. oppermann).
2013
R
odriguez
, M., d. R
au
, S.a. a
ngioi
, e. b
ellucci
, e. b
itocchi
, L. n
anni
, h. 
k
nüpffer
, V. n
egri
, R. P
apa
 & G. a
ttene
: european Phaseolus coc-
cineus L. landraces: Population structure and adaptation, as 
revealed by cpSSRs and phenotypic analyses. PLoS one 8 
(2013) e57337.
t
homas
, k., R. t
hanopoulos
, h. k
nüpffer
 & P.J. b
ebeli
: Plant genetic 
resources in a touristic island: the case of Lefkada (ionian 
islands, Greece). Genet. Resour. crop evol. 60 (2013) 2431-
2455.
Books and Book Chapters
2012
k
ilian
, b., h. Ö
zkan
, S. S
haaf
, S. h
übner
, R.k. P
asam
, R. S
harma
, k. n
eu
-
mann
, W. W
eissgerber
, F.a. k
onovalov
, J. k
eilwagen
, S. F
riedel
, h. 
k
nüpffer
, M. 
von
 k
orff
, G. c
oupland
 & a. G
raner
: comparing 
genetic diversity within a crop and its wild progenitor: a 
case study for barley. in: M
axted
, n., M.e. d
ulloo
, b.V. F
ord
-
L
loyd
, L. F
rese
, J.M. i
riondo
 & M.a.a. P
inheiro
 
de
 c
arvalho
 (eds.): 
agrobiodiversity conservation: Securing the diversity of 
crop Wild Relatives and Landraces. cabi Publishing, Wal-
lingford (2012) 186-192.

37
(Hordeum vulgare L.), which bears one to three single-flowered 
spikelets at each rachis internode. a triple spikelet meristem 
is one of the unique features of barley spikes, in which three 
spikelets (one central and two lateral spikelets) are produced 
at each rachis internode. Fertility of the lateral spikelets at trip-
le spikelet meristem gives row-type identity to barley spikes. 
Six-rowed spikes show fertile lateral spikelets and produce 
increased grain yield per spike, compared with two-rowed 
spikes with sterile lateral spikelets. in the present study, we 
isolated Six-rowed spike4 (Vrs4), a barley ortholog of the maize 
(Zea mays L.) inflorescence architecture gene RAMOSA2 (RA2). 
eighteen coding mutations in barley RA2 (HvRA2) were specifi-
cally associated with lateral spikelet fertility and loss of spikelet 
determinacy (koppolu et al., PnaS 110 (2013) 13198-13203). 
expression analyses through mRna in situ hybridization and 
microarray showed that Vrs4 controls the row-type pathway 
through  Vrs1  (Fig. 13). Furthermore, Vrs4 controls transcripts 
of genes belonging to the trehalose biosynthesis pathway; 
i.e. barley trehalose-6-phosphate synthase (tPS1), and barley 
SISTER OF RAMOSA3 (HvSRA), a putative trehalose-6-phosphate 
phosphatase (tPP), both involved in trehalose-6-phosphate 
(t6P) homeostasis implicated to control spikelet determinacy. 
Most importantly, the obtained picture of regulation for inflo-
rescence development in barley appeared to be quite different 
compared to previously published models of maize and the 
corresponding RaMoSa pathway (kellogg, curr. opin. Plant 
biol. 10 (2007) 26-31), clearly suggesting that barley along with 
other triticeae species including wheat, possess distinct gene 
regulatory networks during inflorescence development (see 
Fig. 13, p. 38). in summary, our vrs4 work has shown that spike-
let and floret development lies at the heart of increasing grain 
number in barley, and that fundamental discoveries in this im-
portant area may provide new avenues for crop improvement 
and breeding.
A circadian clock-related gene underlies Eps-3A
m
 in ein-
korn wheat
the circadian clock is an intrinsic regulator of biological proces-
ses oscillating with about a 24-hour period. it is considered to 
be the main mechanism by which plants recognize the optimal 
photoperiod for seasonal flowering. transcriptional regulation 
of the circadian clock has been well described in Arabidopsis 
(Pokhilko et al., Mol. Syst. biol. 8 (2012) with the latest model 
emphasizing the importance of the evening complex (ec) com-
posed of eaRLY FLoWeRinG 3, eaRLY FLoWeRinG 4 and LuX 
aRRhYthMo/PhYtocLock 1 (eLF3, eLF4, LuX/ PcL1) prote-
ins. in our dFG-funded project (P. Gawroński) a high-resolution 
mapping approach combined with mutant analysis revealed 
a cereal ortholog of Arabidopsis thaliana LuX aRRhYthMo/ 
PhYtocLock 1 (LuX/ PcL1) as a promising candidate for the 
earliness per se 3 (Eps-3A
m
) locus in einkorn wheat (Triticum mo-
nococcum L.). using delayed fluorescence (dF) measurements 
Research Group: Plant Architecture
head:  dr. thorsten Schnurbusch
Scientists
IPK financed
alqudah, ahmad Mohammad (0,50, since 28.09.2013)
Gawroński, Piotr (0,50, 15.09.-31.12.2012) 
Guo, zifeng (0,50, 16.07.-30.09.2012)
koppolu, Ravi (0,50, since 16.03.2013)
Seidensticker, tina (0,50, till 31.08.2012;01.03.-
31.05.2013;01.09.-30.11.2013)
thiel, Johannes, dr. (0,25, 01.09.-31.12.2013)
Grant Positions
alqudah, ahmad Mohammad (0,65 dFG, till 27.09.2013)
Gawroński, Piotr (0,50 dFG, till 14.09.2012) 
koppolu, Ravi (0,50 dFG, till 15.03.2013)
Poursarebani, naser, dr. (0,50/1,00 bMbF)
Wolde, Gizaw Metafei (0,50 SaW-Leibniz Graduate School 
Gatersleben, since 01.11.2012)
Youssef, helmy Mohamed, dr. (0,50 eu, since 01.03.2012)
Visiting Scientists/Scholars
Gawroński, Piotr (self-financed, 01.01.-31.12.2013) 
Seidensticker, tina (self-financed, 01.09.2012-
28.02.2013;12.06.-31.08.2013; since 01.12.2013)
zifeng, Guo (china Scholarship council – cSc, since 
01.10.2012)
Goals
elucidating the developmental and molecular mechanisms of 
spike development in small grain cereals wheat and barley.
Research Report
Discovery of the genetic basis for the triple spikelet meris-
tem in barley
the appearance of the six-rowed spike phenotype in barley is 
one of the important developmental processes that promoted 
barley domestication owing to its increased grain yield. until 
today, five different loci have been identified which can convert 
two-rowed into six-rowed barley; they include vrs1 (2hL), vrs2 
(5hL), vrs3 (1hL), vrs4 (3hS) and int-c (5hS) (for phenotypes see 
Fig. 12, p. 38). komatsuda et al. (PnaS 104 (2007) 1424-1429) 
identified the Vrs1 gene as being an hd ziP transcription factor 
and recently Ramsay et al. found int-c as the barley orthologue 
of maize Teosinte Branched1 (nat. Genet. 43 (2011) 169-172). 
among other vrs loci (vrs2 and vrs3) vrs4 is known to produce 
a prominent six-rowed phenotype with many fully fertile, long 
awned lateral spikelets. in our previous dFG-funded project (R. 
koppolu) we examined the inflorescence architecture of barley 

Abteilung Genbank/
Department of Genebank
38
it was shown that Eps-3A
m
 containing einkorn wheat accession 
kt3-5 had a distorted circadian clock (Gawroński and Schnur-
busch, Mol. breed. 30 (2012) 1097-1108; Gawroński et al. 2013, 
Genetics doi10.1534/genetics.113.158444). the hypothesis was 
subsequently confirmed by performing a time course study on 
central and output circadian clock genes, which showed ar-
rhythmic transcript patterns in the kt3-5 mutant under cons-
tant ambient conditions, i.e. constant light and temperature. it 
was also demonstrated that variation in spikelet number bet-
ween Wt and mutants is sensitive to temperature, becoming 
negligible at 25 °c. these observations lead us to propose that 
the distorted clock is causative for both early flowering, and 
variation in spike size and spikelet number, and that having a 
dysfunctional LuX could have neutral, or even positive, effects 
in warmer climates. to test the latter hypothesis we ascertai-
ned sequence variation of LuX in a range of wheat germplasm. 
We observed a higher variation in the LuX sequence among 
accessions coming from the warmer climate and a unique in-
frame mutation in early-flowering chinese T. turgidum cultivar 
tsing hua no. 559. in this study on LuX aRRhYthMo in einkorn 
wheat, we have provided further justification for circadian clock 
research in modern crops and a clear link to environmental ad-
aptation and yield optimization. We have also shown that the 
most efficient route to follow can be screening for clock mu-
tants by using the dF measurements and subsequently confir-
ming putative mutations with the time course Rt-qPcR. Further 
investigations are required, including those at the protein level, 
to bring more direct evidence for the existence and molecular 
function of an evening complex (ec) in cereal crops.
Fig. 12
Six-rowed spike phenotypes of 
different vrs mutants (koppolu  
et al., PnaS 2013).
Fig. 13
Working model showing putative targets of Vrs4/HvRA2 (koppolu et al., PnaS 
2013).
Publications
Peer Reviewed Papers
2012
b
ennett
, d., a. i
zanloo
, J. e
dwards
, h. k
uchel
, k. c
halmers
, M. t
ester
, 
M. R
eynolds
, t. S
chnurbusch
 & P. L
angridge
: identification of 
novel quantitative trait loci for days to ear emergence and 
flag leaf glaucousness in a bread wheat (Triticum aestivum 
L.) population adapted to southern australian conditions. 
theor. appl. Genet. 124 (2012) 697-711.
b
ennett
,  d., a. i
zanloo
, M. R
eynolds
, h. k
uchel
, P. L
angridge
 & t. 
S
chnurbusch
: Genetic dissection of grain yield and physical 
grain quality in bread wheat (Triticum aestivum L.) under 
water-limited environments. theor. appl. Genet. 125 (2012) 
255-271.
b
ennett
, d., M. R
eynolds
, d. M
ullan
, a. i
zanloo
, h. k
uchel
, P. L
angridge
 
& t. S
chnurbusch
: detection of two major grain yield QtL in 
bread wheat (Triticum aestivum L.) under heat, drought and 
high yield potential environments. theor. appl. Genet. 125 
(2012) 1473-1485.
b
owne
, J.b., t.a. e
rwin
, J. J
uttner
, t. S
chnurbusch
, P. L
angridge
, a. b
acic
 
& u. R
oessner
: drought responses of leaf tissues from wheat 
cultivars of differing drought tolerance at the metabolite 
level. Mol. Plant 5 (2012) 418-429.
G
awroński
, P. & t. S
chnurbusch
: high density-mapping of the earli-
ness per se-3A
m
 (Eps-3A
m
) locus in diploid einkorn wheat and 
its relation to the syntenic regions in rice and Brachypodium 
distachyon L. Mol. breed. 30 (2012) 1097-1108.
M
iedaner
, t., P. R
isser
, S. P
aillard
, t. S
chnurbusch
, b. k
eller
, L. h
artl
,  
J. h
olzapfel
, V. k
orzun
, e. e
bmeyer
 & h.F. u
tz
: broad-spectrum re-
sistance loci for three quantitatively inherited diseases in two 

39
winter wheat populations. Mol. breed. 29 (2012) 731-742.
S
reenivasulu
,  n. & t. S
chnurbusch
: a genetic playground for en-
hancing grain number in cereals. trends Plant Sci. 17 (2012) 
91-101.
Y
oussef
, h.M., R. k
oppolu
 & t. S
chnurbusch
: Re-sequencing of vrs1 
and  int-c loci shows that labile barleys (Hordeum vulgare 
convar. labile) have a six-rowed genetic background. Genet. 
Resour. crop evol. 59 (2012) 1319-1328.