Barley Genetics
Newsletter (2007) 37: 105-153
REPORTS
OF THE COORDINATORS
Overall
coordinator’s report
Udda Lundqvist
Nordic Gene Bank
e-mail: udda@nordgen.org
Since the latest overall coordinator’s report
in Barley Genetics Newsletter Volume 36, some changes of the coordinators have
taken place. I do hope that most of you are willing to continue with this work
and provide us with new important information and literature search in the
future. A replacement was found for Chromosome 4H, namely Arnis Druka, Genetics
Programme at the Scottish Crop Research Institute, Invergowrie,
In this connection I also want to call upon the
barley community to pay attention on the AceDB database for ’Barley Genes and
Barley Genetic Stocks’. It contains much information connected with images and
is useful for barley research groups inducing barley mutants and looking for
new characters. It gets updated continuously and some more images are added to
the original version. The searchable address is: www.untamo.net/bgs
In some months the 10th International Barley
Genetics Symposium will be organized in
List of Barley Coordinators
Chromoosome 1H (5): Gunter Backes, The University of Copenhagen,
Faculty of Life Science, Department of Agricultural Sciences, Thorvaldsensvej
40, DK-1871 Fredriksberg C, Denmark. FAX: +45 3528 3468; e-mail: <guba@life.ku.dk>
Chromosome 2H (2): Jerry. D. Franckowiak, Hermitage Research Station, Queensland Department of Primary Industries and Fisheries, Warwick, Queensland 4370, Australia, FAX: +61 7 4660 3600; e-mail: <Jerome.franckowiak@dpi.qld.gpv.au>
Chromosome 3H (3): Luke Ramsey, Genetics Programme, Scottish Crop
Research Institute, Invergowrie,
Chromosome 4H (4): Arnis Druka, Genetics Programme, Scottish Crop
Research Institute, Invergowrie,
Chromosome 5H (7): George Fedak, Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, ECORC, Ottawa, ON, Canada K1A 0C6, FAX: +1 613 759 6559; e-mail: <fedakga@agr.gc.ca>
Chromosome 6H (6): Duane Falk, Department of Crop Science,
Chromosome 7H (1): Lynn Dahleen, USDA-ARS,
Integration of molecular and morphological marker maps: Andy Kleinhofs, Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA. FAX: +1 509 335 8674; e-mail: <andyk@wsu.edu>
and
Harold Bockelmann, National Small
Grains Collection,
Trisomic and aneuploid stocks: An Hang, USDA-ARS, National Small
Grains Germplasm Research Facility, 1691 S. 2700 W.,
Translocations and balanced tertiary trisomics: Andreas Houben,
List of Barley Coordinators (continued)
Desynaptic genes: Andreas Houben,
Autotetraploids: Wolfgang Friedt,
Disease and pest resistance genes: Brian Steffenson, Department of
Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford
Circle, St. Paul, MN 55108-6030, USA. FAX: +1 612 625 9728; e-mail: <bsteffen@umn.edu>
Eceriferum genes: Udda Lundqvist, Nordic Gene Bank, P.O.
Box 41, SE-230 53 Alnarp, Sweden. FAX:.+46 40 536650; e-mail: < udda@nordgen.org>
Chloroplast genes: Mats Hansson, Department of Biochemistry, University of Lund, Box 124, SE-221 00 Lund, Sweden. FAX: +46 46 222 4534 e-mail: <mats.hansson@biochemistry.lu.se>
Genetic male sterile genes: Mario C. Therrien, Agriculture and Agri-Food Canada, P.O. Box 1000A, R.R. #3, Brandon, MB, Canada R7A 5Y3, FAX: +1 204 728 3858; e-mail: <MTherrien@agr.gc.ca>
Ear morphology genes: Udda Lundqvist, Nordic Gene Bank, P.O. Box
41, SE-230 53 Alnarp,
or
Antonio Michele Stanca: Istituto Sperimentale per la Cerealicoltura, Sezione di Fiorenzuola d’Arda, Via Protaso 302, IT-29017 Fiorenzuola d’Arda (PC), Italy. FAX +39 0523 983750, e-mail: <michele@stanca.it>
Semi-dwarf genes: Jerry D. Franckowiak, Hermitage Research Station,
Queensland Department of Primary Industries and Fisheries, Warwick, Queensland
4370, Australia, FAX: +61 7
4660 3600; e-mail: < Jerome.franckowiak@dpi.qld.gpv.au >
Early maturity genes: Udda Lundqvist, Nordic Gene
Bank, P.O. Box 41 SE-230
53 Alnarp,
Biochemical mutants - Including lysine, hordein and nitrate reductase: Andy Kleinhofs, Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA. FAX: +1 509 335 8674; e-mail: <andyk@wsu.edu>
Barley-wheat genetic stocks: A.K.M.R. Islam, Department of Plant Science, Waite Agricultural Research Institute, The University of Adelaide, Glen Osmond, S.A. 5064, Australia. FAX: +61 8 8303 7109; e-mail: <rislam@waite.adelaide.edu.au>
Coordinator’s Report: Barley
Chromosome 1H (5)
Gunter Backes
The
Faculty of Life Sciences
Department of Agricultural Sciences
Thorvaldsensvej
40
DK-1871 Frederiksberg C, Denmark
guba@life.ku.dk
In
Arabidopsis, HLM1 encodes the cyclic nucleotide-gated ion channel 4. A
mutant plant for this gene shows necrotic lesions and thereby similarities to
the hypersensitive response (HR) to pathogens. Rostoks et al. (2006)
isolated the homolog of this gene from the previously characterized barley
mutant nec1 and localized the gene in the ‘Steptoe’ x ‘Morex’
“minimapper population” to chromosome 1H, Bin9.
In an
attempt to localize transcription factors (TFs ) belonging to the gene family
of C-repeat binding factors (CBF), their regulators and MYB-TFs, altogether
known to regulate plant response to cold and drought stress, Tondelli et al.
(2006) localized several homologs to the respective Arabidopsis genes in
a joined map of the three populations ‘Nure’ ´ ‘Tremois’, ‘Proctor’ ´ ‘Nudinka’ and ‘Steptoe’ ´ ‘Morex’. Further, they compared the
loci of these putative TFs with the position of published QTLs. They localized
9 homologs and assigned two further homologs by wheat-barley addition lines to
the respective chromosomes. On chromosome 1H they localized HvMYB4 to
Bin6, a homolog to AtMyb2 from Arabidopsis and OsMYB4 from
rice, both known to be part of the regulation processes during abiotic
stresses.
In a
similar effort, Skinner et al. (2006) localized the barley homologs of
14 Arabidopsis CBF-TFs and 2 further TFs in the barley populations ‘Steptoe’
´ ‘Morex’ and 88Ab536 ´ ‘Strider’.The authors also tested
the ‘Steptoe’ ´
‘Morex’ population in climatic chambers for cold tolerance and localized QTLs
based on these data. On chromosome 1H, they localized HvZFP16-1, a
homolog to AtZAT12, to Bin4. A further homolog of the same Arabidopsis
gene, HvZFPR16-2 was assigned to 1H by wheat-barley addition lines. A
QTL for cold tolerance was localized on 1H, Bin11, by a LOD score of 5.7. No
co-localization between the QTLs and the TFs localized in this study was found.
Nevertheless, comparison with literature indicated QTLs at the position of two
candidate gene loci on 5H.
The same
group (Szücs et al. 2006) published results describing the localization
of photoreceptor genes and vernalization-related genes together with QTLs for
photoperiod response. Mapping of both, the candidate genes and QTLs, was
carried out in DH populations of the crosses ‘Dicktoe’ ´ ‘Morex’ and ‘Dicktoe’ ´ ‘Kompolti korai’. While none of the
candidate genes was localized on chromosome 1H, two QTL were detected with the
‘Dicktoo’ ´
‘Morex’ population: a major QTL in Bin11 and a further QTL in Bin12.
In order
to localize qualitative and quantitative resistance against rice blast in
barley, Inukai et al. (2006) analyzed a segregating DH population from
the cross ‘Baroness’ ´ BCD47
with two different rice blast isolates in a greenhouse experiment. For one of
the isolates, a qualitative segregation was found and consequently a new
resistance gene, RMo1, was localized on chromosome 1H, Bin2 at or near
the position of the Mla-locus. For the other isolate, a quantitative
segregation was found and a major QTL was detected at the position of RMo1,
while further 3 QTLs were localized on the chromosomes 3H, 4H and 7H.
Jafary et
al. (2006) investigated the inheritance and specificity of plant factors
that determine the degree of basal defence by host- and nonhost pathogens. For
this purpose, they analyzed 152 RILs from the cross ‘Vada’ x ‘SusPtrit’ with 2
rust isolates from barley rusts and 8 isolates from rusts with no
barley-specificity, isolated from cultivated and wild Poaceae.
‘SusPtrit’ is an experimental barley accession selected for susceptibility to
the wheat leaf rust fungus Puccinia triticina. On chromosome 1H, an
R-gene against the fungus Puccinia hordei-secalini was localized. P.
hordei-secalini has no host-specificity for H. vulgare. Furthermore,
three different QTLs were detected. One of them conferred resistance
against P. hordei-murini, one
against P. graminis f.sp. lolii and one against P. graminis
f.sp. tritici. Only the latter has barley-specificity. As the linkage
map for 1H in this analysis purely consisted of AFLP marker, it was not
possible to assign the R-gene or QTLs to the Bin-map.
A new
qualitative resistance gene against spot blotch, Rcs6, caused by Cochliobolus
sativus, was localized on chromosome 1H either proximal on Bin1 or
distal on Bin2 by Bilgic et al. (2006). They tested the DH population
‘Calcuchima-sib’ ´
‘Bowman-BC’ with two different isolates both on seedlings in the greenhouse and
on adult plants in the field. While one isolate identified the above mentioned
resistance gene both in the seedlings and the adult plants, the other isolate
detected different quantitative resistance loci for the greenhouse compared
with the field, none of them on the position of Rcs6.
Rsp2 and Rsp3, originally
designated Sep2 and Sep3, are barley
resistance genes against speckled leaf blotch in barley, caused by Septoria
passerinii. These genes were mapped by Zhong et al. (2006) in an F2:3
population of the cross 'Foster' x 'Clho 4780' based on seedling tests with a
specific isolate. These two genes are either closely linked or allelic and are
localized on chromosome 1H and, as estimated by the flanking markers, more
exactly in Bin3.
Sameri et
al. (2006) localized QTLs for different agronomic traits in an RIL
population derived from a cross between two Japanese barley varieties
‘Azumamugi’ and ‘Kanto Nakate Gold’. ‘Azumamugi’ is an oriental type barley,
while ‘Kanto Nakate Gold’ belongs to the occidental type of barley varieties in
In an F2:4
population from a cross between two wild barleys (H. v. ssp. spontaneum)
from
QTLs for
grain yield (Bin11/12), heading date (Bin7), plant height (Bin14), ear length
(Bin9, Bin13), spikelets/spike (Bin8/9), grain/spike (Bin8/9), spikes/plant
(Bin12) and 1000-grain mass (Bin9, Bin11/12) were detected on chromosome 1H in
an advanced-backcross experiment (Li et al. 2006). The wild barley
parent was the line ‘HS584’, and the recurrent cultivated parent was the
variety ‘Brenda’. The field trials were carried out on 2 locations during four
years. The map positions of the marker were based on the ‘Igri’ ´ ‘Franka’ and ‘Steptoe’ ´ ‘Morex’ SSR maps ((Li et al.,
2003).
In
another advanced-backcross with the wild barley line ‘ISR42-8’ and the
recurrent cultivated parent ‘Scarlett’, von Korff et al. (2005) analyzed
agronomic traits in a field experiments (four locations during two years). On
1H, QTLs were found for ears per m² (Bin14), heading date (Bin13), plant height
(Bin13), harvest index (Bin13, Bin14) and yield (Bin6-8).
References:
Bilgic, H., B. J. Steffenson, and P. M. Hayes.
2006. Molecular
mapping of loci conferring resistance to different pathotypes of the spot
blotch pathogen in barley. Phytopathology 96(7): 699-708.
Inukai, T., M. I. Vales, K. Hori, K. Sato, and
P. M. Hayes. 2006. RMo1
confers blast resistance in barley and is located within the complex of
resistance genes containing Mla, a powdery mildew resistance gene. Mol.
Plant Microbe Interact. 19(9): 1034-1041.
Jafary, H., L. J. Szabo, and R. E. Niks. 2006. Innate nonhost immunity in barley
to different heterologous rust fungi is controlled by sets of resistance genes
with different and overlapping specificities. Mol. Plant Microbe Interact.
19(11): 1270-1279.
Li, J. Z., X. Q. Huang, F. Heinrichs, M. W.
Ganal, and M. S. Roder. 2006. Analysis of QTLs for yield components, agronomic traits, and disease
resistance in an advanced backcross population of spring barley. Genome 49(5): 454-466.
Li, J. Z., T. G. Sjakste, M. S. Röder, and M.
W. Ganal. 2003. Development and genetic mapping of
127 new microsatellite markers in barley. Theor. Appl. Genet. 107(6):
1021-1027.
Rostoks, N., D. Schmierer, S. Mudie, T. Drader,
R. Brueggeman, D. G. Caldwell, R. Waugh, and A. Kleinhofs. 2006. Barley necrotic locus nec1 encodes
the cyclic nucleotide-gated ion channel 4 homologous to the Arabidopsis HLM1.
Mol. Genet. Genom 275(2): 159-168.
Sameri, M., K. Takeda, and T. Komatsuda. 2006. Quantitative trait loci controlling
agronomic traits in recombinant inbred lines from a cross of oriental- and
occidental-type barley cultivars. Breed. Sci. 56(3): 243-252.
Skinner, J. S., P. Szücs, J. von Zitzewitz, L.
Marquez-Cedillo, T. Filichkin, E. J. Stockinger, M. F. Thomashow, T. H. H.
Chen, and P. M. Hayes. 2006. Mapping of barley homologs to genes that regulate low temperature
tolerance in Arabidopsis. Theor. Appl. Genet. 112(5): 832-842.
Szücs, P., I. Karsai, J. von Zitzewitz, K. Meszaros, L. L. D. Cooper, Y. Q. Gu, T. H. H. Chen, P. M. Hayes, and J. S. Skinner. 2006. Positional relationships between photoperiod response QTL and photoreceptor and vernalization genes in barley. Theor. Appl. Genet. 112(7): 1277-1285.
Tondelli, A., E. Francia, D.
Barabaschi, A. Aprile, J. S. Skinner, E. J. Stockinger, A. M. Stanca, and N.
Pecchioni. 2006. Mapping regulatory genes as candidates for
cold and drought stress tolerance in barley. Theor. Appl. Genet. 112(3):
445-454.
Vanhala, T. K. and P. Stam. 2006. Quantitative trait loci for seed
dormancy in wild barley (Hordeum spontaneum c. Koch). Genet. Resour.
Crop. Evol. 53(5): 1013-1019.
von Korff, M., H. Wang, and J. Léon. 2005. AB-QTL analysis in spring barley. I. Detection of resistance genes
against powdery mildew, leaf rust and scald introgressed from wild barley.
Theor. Appl. Genet. 111(3): 583-590.
Zhong, S. B., H. Toubia-Rahme, B. J. Steffenson, and K. P. Smith. 2006. Molecular mapping and marker-assisted selection of genes for septoria speckled leaf blotch resistance in barley. Phytopathology 96(9): 993-999.
Coordinator’s report: Chromosome 2H (2)
Hermitage Research Station
Queensland Department of Primary Industries and Fisheries
e-mail:
jerome.franckowiak@dpi.qld.gpv.au
Komatsuda et al. (2007) cloned the six-rowed spike 1 (vrs1) gene located on chromosome 2HL of
barley. Expression of the Vrs1 was
strictly localized in the lateral-spikelet primordia of immature spikes and
suggests that the VRS1 protein suppresses development of lateral spikelets.
Phylogenetic analysis of the six-rowed cultivars and mutants demonstrated that
six-rowed spike trait originated repeatedly from two-rowed barley, at least
three different origins among domesticated accessions. Also, the DNA sequence
defects in many of vrs1 mutants held
in the Nordic Gene Bank were identified.
When
the DNA sequence of vrs1 was
determined, Pourkheirandish et al. (2007) found that the region around
the vrs1 locus was collinear with
rice chromosome 4. However, the rice orthologue for the vrs1 sequence was found on rice chromosome 7. The authors
speculated that a transposition of the chromosomal segment Vrs1 to chromosome 2H occurred during the evolution of barley.
Pourkheirandish et al. (2007) also reported that the vrs1 locus is a region of suppressed
recombination based on the study of more than 13,000 gametes.
Řepková
et al. (2006) reported on the mapping of four new sources of resistance
to powdery mildew, caused by Blumeria graminis f. sp. hordei,
that were identified in accessions of wild barley, Hordeum vulgare ssp.
spontaneum. Accession PI 466197
was found to have two dominant resistance genes. One is an allelic at the mla
locus and the other was located on chromosome 2HS based on a highly
significant linkage with molecular marker Bmac0134.
Dahleen
and Franckowiak (2006) found that cer-zt
locus is located on chromosome 2HS based on linkage to molecular marker
Bmac0134 in bin 2H-1. The cert-zt.389
mutant has very little surface wax on the spike (Lundqvist and Franckowiak,
1997), but little effect on other agronomic traits except a slightly increased
number of kernels per spike (Dahleen and Franckowiak, 2006).
Based
on the analysis of 134 recombinant chromosome substitution lines (RCLs) from
the BC3 generation of the backcross of wild barley line (OUH602)
into ‘Haurna Nijo’, Hori et al. (2005) found that QTLs for short spike
and lax spike are on chromosome 2HL near the closed flowering (cleistogamy, cly1/Cly2)
locus of Haurna Nijo. In a previous paper, Hori et al. (2003) reported
that these QTLs plus one for short culm were observed in a population of
doubled-haploid lines from a Haurna Nijo/OUH602 cross.
Using
recombinant inbred lines, Yun et al. (2005) found a QTL for resistance
to Septoria speckled leaf blotch (SSLB, caused by Septoria passerinii Sacc.) from H.
vulgare subsp. spontaneum,
located in bins 7 to 11 of chromosome 2H. They examined a recombinant inbred
line (RIL) population developed from a cross between wild barley accession
OUH602 and the two-rowed malting cultivar ‘Harrington’ for reaction to SSLB.
About 40% of the variation in response to SSLB was explained by the QTL on 2H,
named QTL Rsp-2H-7-ll. The mapped disease resistances were validated using an
advanced backcross population (BC2F6:8) from the same
donor parent, but having two more backcrosses to Harrington (Yun et al.,
2006).
A QTL regulating synthesis of cell wall (1,3;1,4)-beta-D-glucans was located between the markers Adh8 bin 6 and ABG019 bin 7 with the peak closer to ABG019 on 2H (Burton et al., 2006). The cellulose synthase-like (CslF) gene cluster in cereals was identified as candidates responsible for mediating cell wall (1,3;1,4)- ß -D-glucan synthesis using of rice synteny and by transforming Arabidopsis (Burton et al., 2006). The research was based on the map location of a major QTL for (1,3;1,4)-ß-D-glucan content of un-germinated barley grains on 2H. This report is believed the first example of a map-based cloning of a QTL in barley.
Korff et
al. (2006) reported on a large number of QTLs for agronomic traits detected
in doubled-haploid lines from the second backcross of ‘Scarlett’ backcrossed to
Hordeum vulgare ssp. spontaneum accession ISR42-8. Using a
population 301 BC2DH in eight environments, they reported detection
of 86 QTLs for nine agronomic traits. The QTLs having large effects that were
associated with chromosome 2H included: ears/m2, days to head (Eam1 or Ppd-H1), plant height (sdw1
from Scarlett), and yield.
Yin et
al. (2005) confirmed that a QTL having an important effect on preflowering
duration in the ‘Apex’/‘Prisma’ population of 94 recombinant inbred lines (RILs)
was located on the long arm of chromosome 2H. The other QTL having a large
effect was located on chromosome 3H at the same position as the sdw1 gene from Prisma.
Dragan et al. (2007) located two members of the nicotianamine synthase (NAS) family of genes on the short arm of chromosome 2H (2HS). Nicotianamine is involved chelation of iron and other heavy metals and their transport in the plant.
The number of molecular markers located on chromosome 2H has been increased by several studies. Beaubien and Smith (2006) placed 7 of the 60 new mapped SSR markers on 2H at bin positions that previously had been identified as being poorly covered by SSR markers currently available. Stein et al. (2007) published an expressed sequence tag (EST)-based map for barley based 200 anchor markers from three previously published maps. The map contained 1,055 loci and a map size of 1,118.3 cM. The map for 2H contained 179 EST loci and a map length of 165.1 cM. Using barley-wheat addition lines and the Barley1 Affymetrix GeneChip probe array, Cho et al. (2006) associated 1,787 of 4,104 transcript accumulation patterns detected in Betzes, but not Chinese Spring, with specific barley chromosomes. Of these 271 were associated with the 2H addition line of Chinese Spring.
Takahashi
et al. (2006) mapped in barley
miniature inverted-repeat transposable elements (MITEs), which represent a
large superfamily of transposons that is moderately to highly repetitive and
frequently found near or within plant genes. To elucidate the organization of
MITEs in the barley genome, MITEs were integrated into the genetic map of
barley using 93 doubled haploid lines from a Haruna Nijo by H. vulgare ssp. spontaneum accession OUH602 cross. They described the use of MITEs
in amplified fragment length polymorphism (AFLP) mapping and demonstrate their
superiority over conventional AFLP mapping. A total of 214 loci covered a total
map distance of 1,165 cM, and 39 were placed on 2H.
References:
Beaubien, K.A., and K. P. Smith. 2006. New SSR markers for barley derived from the EST database. Barley Genet. Newsl. 36:30-36.
Burton, R.A., S.M. Wilson, M. Hrmova, A.J. Harvey, N.J. Shirley, A.
Medhurst, B.A. Stone, E.J. Newbigin, A. Bacic, and G.B. Fincher. 2006. Cellulose synthase-like CslF genes mediate the synthesis of cell
wall (1,3;1,4)-beta-D-glucans. Science 311:1940-1943.
Cho, S., D.F. Garvin, and G.J. Muehlbauer.
2006. Transcriptome analysis and physical mapping
of barley genes in wheat–barley chromosome addition lines. Genetics
172:1277-1285.
Dahleen,
L.S. and J.D. Franckowiak. 2006. SSR linkages to eight additional morphological marker traits. Barley
Genet. Newsl. 36:12-16.
Dragan Perovic, D., P. Tiffin, D. Douchkov, H. Bäumlein, and A. Graner. 2007. An integrated approach for the comparative analysis of a multigene family: The nicotianamine synthase genes of barley. Funct. Integr. Genomics 7:169-179.
Hori, K., T. Kobayashi, A. Shimizu, K.
Sato, K. Takeda, and
Hori, K., K.
Sato, N. Nankaku, and K. Takeda. 2005. QTL analysis
in recombinant chromosome substitution lines and doubled haploid lines derived
from a cross between Hordeum vulgare ssp. vulgare and Hordeum
vulgare ssp. spontaneum. Mol.
Breeding 16(4):295-311.
Komatsuda,
T., M. Pourkheirandish, C. He, P. Azhaguvel, H. Kanamori, D. Perovic, N. Stein,
A. Graner, T. Wicker, A. Tagiri, U. Lundqvist, T. Fujimura, M. Matsuoka, T.
Matsumoto, and M. Yano. 2007. Six-rowed barley originated from a mutation in a
homeodomain-leucine zipper I-class homeobox gene. PNAS 104:1424-1429.
von Korff, M., H. Wang, J. Léon, and K. Pillen. 2006. AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor. Appl. Genet. 112:1221-1231.
Lundqvist, U., and J.D. Franckowiak. 1997. BGS 437, Eceriferum-zt, cer-zt. Barley Genet Newsl. 26:389
Pourkheirandish, M., T. Wicker, N. Stein, T. Fujimura, and T. Komatsuda. 2007. Analysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of the rice-barley micro collinearity by a transposition. Theor. Appl. Genet. 114:1357-1365.
Řepková,
J., A. Dreiseitl, P. Lízal, Z. Kyjovská, K. Teturová, R. Psotková, and A.
Jahoor. 2006. Identification of
resistance genes against powdery mildew in four accessions of Hordeum
vulgare ssp. spontaneum. Euphytica 151:23-30.
Stein, N., M.
Prasad, U. Scholz, T. Thiel, H. Zhang, M. Wolf, R. Kota, R.K. Varshney, D.
Perovic, I. Grosse, and A. Graner. 2007.
A 1,000-loci transcript map of the barley genome: new anchoring points for
integrative grass genomic. Theor. Appl. Genet. 114:823-839.
Takahashi, H., H. Akagi, K. Mori, K. Sato, and K. Takeda. 2006. Genomic distribution of MITEs in barley
determined by MITE-AFLP mapping. Genome 49:1616- 1618.
Yin, X., P.C.
Struik, F.A. van Eeuwijk, P. Stam, and J. Tang. 2005. QTL analysis and QTL-based prediction of flowering
phenology in recombinant inbred lines of barley J. Exp. Bot. 56 (413):967-976.
Yun, S.J., L.
Gyenis, E. Bossolini, P.M. Hayes, I. Matus, K.P. Smith, B.J. Steffenson, R.
Tuberosa, and G.J. Muehlbauer. 2006. Validation of quantitative
trait loci for multiple disease resistance in barley using advanced backcross
lines developed with a wild barley. Crop Sci. 46:1179-1186.
Yun, S.J., L.
Gyenis, P.M. Hayes,
Coordinator’s Report: Barley Chromosome
3H
L. Ramsay
Genetics Programme
Scottish Crop Research Institute
Invergowrie, Dundee, DD2
5DA, Scotland, UK.
e-mail:
Luke.Ramsay@scri.ac.uk
Over the last year there have been a number of publications reporting the mapping of genes and QTL on barley chromosome 3H. One of the highlights of this reporting period was the genetic mapping of over 1000 genes, including 179 on 3H, by Stein et al. (2007). This worked confirmed the syntenic relationship of 3H to rice chromosome 1 and importantly put the detailed EST information underlying this and previous reports in the public domain. This includes the details of which genes are represented by the EST derived microsatellites reported by Varshney et al. (2006) that included 35 that map to 3H. Another report of EST derived microsatellites with the associated EST information, including 11 on 3H, was that of Beaubien and Smith (2006).
Another important general mapping paper was the development of a consensus map derived from DArT marker loci (Wenzl et al, 2006) that opens up the possibility of using loci derived from this technology as proxies for more expensive genic markers. Also of importance is the detailed consensus map presented by Marcel et al. (2007) which brings together standard AFLP, microsatellite and RFLP loci and that will allow additional alignment of past work with the positions of genic loci.
A range of QTL on chromosome 3H were again reported this year. In a RIL population derived from a cross between Azumamugi and Kanto Nakate Gold studied by Sameri et al. (2006) QTL were found on 3H for a range of agronomic characters including plant height, spike length and awn length. The position of the QTL found indicates that they are due to the segregation of uzu in the population. Li et al. (2006) reported the positions of QTL for a range of agronomic traits using recombinant chromosome substation lines derived from a Hordeum vulgare subsp. vulgare (cltv. Brenda) by Hordeum vulgare subsp. spontaneum (accession HS584) cross to delineate association with genomic regions. The QTL found on 3H included those for yield and components such as spikelet no. per spike, grain no. per spike, thousand-grain mass as well as other traits such as heading date, plant height, ear length, leaf length and leaf area. A QTL for resistance on 3H was also found to leaf rust in two trials which may relate to the two QTL for leaf rust resistance found on chromosome 3H in a consensus map by Marcel et al. (2007) in a summary of work on six mapping populations. One of the populations used in the construction of this consensus map, L94 x Vada, was also tested for mildew and scald resistance and a novel powdery mildew resistance QTL designated Rbgq2 was detected on 3H which did not map to a region where a major gene for powdery mildew has previously been reported (Shtaya et al. 2006). Another of the populations included in the report of Marcel et al. 2007 was that derived from a cross between an experimental line SusPrit and Vada to study the inheritance of non-host immunity to rusts (Jafary et al. 2006). This work found three QTL on 3H associated with host and non-host resistance to Puccinia spp. Other disease QTL reported on 3H included the improved resolution of spot blotch resistance QTL on the Calicuchima-sib / Bowman BC population by Bilgic et al. (2006) and a scald resistance QTL on the long arm of 3H identified using a partial map of a doubled haploid population derived from a Mundah/Keel cross (Cheong et al., 2006).
References:
Beaubien, K.A. and K.P. Smith. 2006 New SSR markers for barley derived from the EST database. Barley Genetics Newsletter 36: 30-43.
Bilgic, H., B.J. Steffenson, and P.M. Hayes. 2006. Molecular mapping of loci conferring resistance to different pathotypes of the spot blotch pathogen in barley. Phytopathology 96: 699-708.
Cheong, J., K. Williams, and H. Wallwork, 2006. The identification of QTLs for adult plant resistance to leaf scald in barley. Australian Journal of Agricultural Research 57: 961-965.
Jafary, H., L.J. Szabo, and R.E. Niks, 2006. Innate nonhost immunity in barley to different heterologous rust fungi is controlled by sets of resistance genes with different and overlapping specificities. Molecular Plant-Microbe Interactions 19: 1270-1279.
Li, J.Z., X.Q. Huang, F. Heinrichs, M.W. Ganal, and M.S. Roder, 2006. Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley. Genome 49: 454-466.
Marcel, T.C.,
R.K. Varshney, M. Barbieri, H. Jafary, M.J.D. de Kock, A. Graner and R.E.
Niks, 2007. A high-density consensus map of barley to
compare the distribution of QTLs for partial resistance to Puccinina hordei and of defence gene homologues. Theor Appl. Genet 114:
487-500.
Samuri, M., K. Takeda and Komatsuda, T. 2006. Quantitative trait loci controlling agronomic traits in recombinant inbred lines from a cross of oriental- and occidental-type barley cultivars. Breeding Science 56: 243-252.
Shtaya, M.J.Y., T.C. Marcel, J.C. Sillero, R.E. Niks, and D. Rubiales, 2006. Identification of QTLs for powdery mildew and scald resistance in barley. Euphytica 151: 421-429.
Stein, N., M. Prassa, U. Scholz, T. Thiel, H. Zhang, M. Wolf, R. Kota, R.K. Varshney, D. Perovic, I. Grosse and A. Graner, 2007. A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet on-line preprint DOI 10.1007/s00122-006-0480-2
Varshney, R.K., I. Grosse, U. Hahnel, R. Siefken, M. Prasad, N. Stein, P. Langridge, L. Altschmied, and A. Graner, 2006. Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor Appl Genet 113: 239-250.
Wenzl, P., H.B. Li, J. Carling, M.X. Zhou, H. Raman, E. Paul, P. Hearnden, C. Maier, L. Xia, V. Caig, J. Ovesna, M. Cakir, D. Poulsen, J.P. Wang, R. Raman, K.P. Smith, G.J. Muehlbauer, K.J. Chalmers, A. Kleinhofs, E. Huttner, and A. Kilian, 2006. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7:206.
Coordinator’s Report: Chromosome 4H
Arnis Druka
Genetics Programme
Scottish Crop Research Institute
Invergowrie,
e-mail: adruka@scri.sari.ac.uk
Several papers that relate to the
genes on chromosome 4H have been published in 2006 - 2007. At least four of
them combine mRNA abundance analyses with phenotypic trait genetic analyses
clearly showing added value of such approach (Malatrasi et al., 2006;
Zhang et al., 2006; Wang et al., 2007 and Walia et al.,
2007).
The HvMATE gene, encoding a multidrug and toxic compound extrusion protein has been identified as a candidate controlling aluminium (Al) tolerance in barley. The gene itself was found not to be polymorphic between Al-tolerant and sensitive cultivars, but it accumulates mRNA 30 times more in the Al tolerant cultivar. HvMATE mRNA accumulation was measured in the F(2:3) families and was found significantly correlated with the Al tolerance and Al-activated citrate efflux phenotypes that have been mapped on the long arm of chromosome 4H (Wang et al., 2007).
A different study addressed the salt tolerance in barley by analysing single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs) in the salt tolerant cultivar Golden Promise and intolerant cultivar Maythorpe. Golden Promise has been generated by inducing mutation in the cultivar Maythorpe. The transcriptome analysis indicates that the response of the two genotypes to the salinity stress is quite different.. This study identified 3 haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H suggesting that Golden Promise is not isogenic (Walia et al., 2007).
A gene encoding the branched-chain amino acid aminotransferase (HvBCAT-1) that mapped on chromosome 4H, was identified by using differential mRNA display applied to ABA, drought and cold treated barley seedling shoots. Transcript levels of Hvbcat-1 increased in response to drought stress. The complementation of a yeast double knockout strain revealed that HvBCAT-1 can function as the mitochondrial (catabolic) BCATs in vivo. This allowed to put forward the hypothesis, that under drought stress conditions, one of the detoxification mechanisms could be associated with degradation of the branched-chain amino acids (Malatrasi et al., 2006).
Zhang et al. (2006) have reported a novel locus that is required for Rpg1 gene mediated resistance to the stem rust (Puccinia graminis f. sp. tritici) fungus. It was identified by inducing the irradiation mutations in the resistant barley cultivar and selecting for susceptible individuals in the M2 progeny. Rpg1 gene in one such susceptible mutant plants was found to be intact and the following mutation mapping identified a locus on chromosome 4H, that was named Rpr1 (Required for P. graminis resistance). Several candidate genes or novel markers for this locus were identified by using large scale parallel transcript profiling approach.
Other papers that related to chromosome 4H were describing either characterization and mapping gene families and the candidate genes for certain QTLs (Brueggeman et al., 2006; Skinner et al., 2006) or mapping novel QTLs (Friesen et al., 2006; Richardson et al., 2006; Yan and Chen 2006; von Korff et al., 2006).
Thus, Brueggeman et al. (2006) reported mapping of members of the serine/threonine kinase-like protein family that encode at least one predicted catalytically active kinase domain. One of them was localized to chromosome 4H. In a different study, allelic nature and map locations of barley homologs to three classes of Arabidopsis low temperature regulatory genes-CBFs, ICE1, and ZAT12 were investigated for associations with the LT tolerance QTLs. In the same study, phenotyping of the Dicktoo x Morex (DxM) mapping population under controlled freezing conditions identified three new low temperature tolerance (LT) QTLs on 1H-L, 4H-S, and 4H-L in addition to the previously reported 5H-L Fr-H1 QTL. (Skinner et al., 2006).
Barley interaction with the net blotch fungi, Pyrenophora teres f. teres (net-type net blotch (NTNB)) and Pyrenophora teres f. maculata (spot-type net blotch (STNB)) was studied using a doubled-haploid population derived from the lines SM89010 and Q21861. Major QTLs for NTNB and STNB resistance were located on chromosomes 6H and 4H, respectively (Friesen et al., 2006).
Barley and the stripe rust fungus (Puccinia striiformis f. sp. hordei) interaction phenotypes, such as latency period, infection efficiency, lesion size and pustule density were mapped using i-BISON lines (intermediate barley near-isogenic lines). The (i-BISON) lines represented disease resistance QTL combined in one-, two-, and three-way combinations in a susceptible background. The 4H QTL allele had the largest effect followed by the alleles on chromosomes1H and 5H (Richardson et al., 2006).
In a different study Yan and Chen (2006) reported population of 182 recombinant inbred lines (RILs) (F8) derived from cultivars Steptoe and GZ that was generated to map the resistance to two barley stripe rust fungus strains on the long arm of barley chromosome 4H.
The BC2DH population derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum) was developed to evaluate nine agronomic traits. Favourable ISR42-8 alleles were detected for the yield-related traits that have QTLs on the long arm of chromosome 4H (von Korff et al., 2006).
References:
Brueggeman R. T. Drader, and A. Kleinhofs 2006. The barley serine/threonine kinase gene Rpg1 providing
resistance to stem rust belongs to a gene family with five other members
encoding kinase domains. Theor. Appl. Genet. 113(6):1147-1158.
Friesen T.L., J.D. Faris, Z. Lai, and B.J. Steffenson. 2006. Identification and chromosomal location of major genes
for resistance to Pyrenophora teres
in a doubled-haploid barley population. Genome 49(7):855-859.
Malatrasi M., M. Corradi, J.T.
Svensson, T.J. Close, M. Gulli, and N. Marmiroli 2006. A
branched-chain amino acid aminotransferase gene isolated from Hordeum vulgare is differentially
regulated by drought stress. Theor. Appl. Genet. 113(6):965-976.
Skinner J.S., P. Szucs, J. von Zitzewitz, L.
Marquez-Cedillo, T. Filichkin, E.J. Stockinger, M.F. Thomashow, T.H. Chen, and
P.M. Hayes. 2006. Mapping of barley
homologs to genes that regulate low temperature tolerance in Arabidopsis. Theor. Appl. Genet.
112(5):832-842.
von Korff M., H. Wang, J. Léon, and K. Pillen. 2006. AB-QTL analysis in spring barley: II. Detection of
favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor.
Appl. Genet. 112(7):1221-1231.
Walia H., C. Wilson, P. Condamine, A.M. Ismail, J. Xu, X.
Cui, and T.J. Close. 2007. Array-based
genotyping and expression analysis of barley cv. Maythorpe and Golden Promise. BMC
Genomics. Mar 30; 8:87.
Wang J., H. Raman, M. Zhou, P.R. Ryan, E. Delhaize, D.M.
Hebb, N. Coombes, and N. Mendham. 2007.
High-resolution mapping of the Alp
locus and identification of a candidate gene HvMATE controlling aluminium tolerance in barley (Hordeum vulgare L.). Theor. Appl. Genet.
Jun 6 [Epub ahead of print].
Yan G.P. and X.M. Chen.
Molecular mapping of a recessive gene for resistance to stripe rust in barley.
Theor. Appl. Genet. 2006 113(3):529-537.
Zhang L., T.
Fetch, J. Nirmala, D. Schmierer, R. Brueggeman, B. Steffenson, and A.
Kleinhofs. 2006.
Rpr1, a gene required for Rpg1-dependent resistance to stem rust
in barley. Theor. Appl. Genet. 113(5):847-855.
Coordinator’s Report: Chromosome 5H
George Fedak
Eastern Cereals and Oilseeds Research Centre
Agriculture and
e-mail: fedakga@agr.gc.ca
The grain hardness locus (Ha) of barley consists of a cluster of genes located on the short arm of 5H designated as Hina, Hinb-1, Hinb-2 and GSP. Eighty diverse barley genotypes were screened for kernel hardness, ruminant digestibility and haplotypes of the four alleles. The highest level of genetic variation was obtained with GSP followed by Hina, Hinb-2. Hina was significantly related to grain hardness while Hinb-1 and Hinb-2 were significantly associated with dry water digestibility. (Turuspekov et al., 2007).
Using the Nure (winter) x Tremois (spring) mapping population, two low temperature QTL were located on the long arm of chromosome 5H. FrHi was located in a distal position and Fr-H2 in a proximal location. The location of the latter coincided with the location of a QTL regulating the accumulation of two COR proteins; COR14b and TMC-Ap3. Six barley genes for the CBF transcription factor have been mapped in a single cluster in this region and they represent candidate genes for Fr-H2. (Francia et.al., 2007)
In a related study, Lombda phage libraries were constructed from 2 spring (Morex and Tremois) and two winter (Dicktos, Nure) cultivars. Clones containing CBF genes were sequenced. It was found that the winter varieties have a large duplication at the Fr-H2 gene resulting in an increased number of CBF genes at this locus. The spring barley Tremois, however, has a significant deletion at this locus. This suggests that the relative numbers of CBF in the cluster contributes to different levels of winterhardiness (Knox et.al.,2007).
References:
Francia, E., D. Baraboschi, A. Tondelli, G.
Laido, A.M. Stanca, E. Stockinger and N. Pecchioni, 2007. Fine mapping of a
Hv CBF gene cluster, at Fr-H2, a QTL controlling frost resistance in barley. PAG - XV Poster
331. Plant and Animal Genomes XV Conference, Jan 13-17, 2007.
Knox, A.K., H. Chang . and E.I. Stockinger,
2007. Comparative Sequence analysis of CBF genes at the Fr-H2 locus in four barley
cultivars. PAG – XV Poster 321. Plant and Animal Genomes XV Conference, Jan
13-17, 2007.
Turuspekov Y., B. Beecher, Y. Darlington,
J. Bowman, T. Blake and M. Gioux. 2007.Genetic variation of hardness locus
in barley. PAG-XV Poster 329. Plant and Animal Genomes XV Conference, Jan
13-17, 2007,
Coordinator’s Report: Chromosome 7H
USDA-Agricultural Research Service
e-mail: DAHLEEN@fargo.ars.usda.gov
Barley gene mapping in 2006 showed a greater emphasis on using candidate gene approaches in addition to standard qualitative and quantitative trait mapping. Increased use of public EST and BAC libraries was evident, providing tools to better understand the barley genome.
Efforts to map morphological genes have continued. Roder et al. (2006) mapped the shrunken endosperm gene seg8 to a 4.6 cM interval near the centromere of chromosome 7H, while Taketa et al. (2006) developed a fine map of the naked caryopsis nud locus, placing it in a 0.66 cM region. Rostoks et al. (2006) found that the barley homolog of the Arabidopsis HLM1 gene corresponded to the nec1 locus on chromosome 7H. Allelic variation was uncovered at the locus that causes necrotic spotting of nec1 plants. Rossini et al. (2006) examined candidate rice genes in regions syntenous with markers linked to various barley morphological mutants. On chromosome 7H they found brh1 candidate genes on rice chromosome 6 and candidates for suKF-76, suKE-74 (suppressors of Hooded) and sld4 on rice chromosomes 6 and 8. The low resolution of the barley maps in this region resulted in selection of rather large rice regions and numerous candidate genes. Yan et al. (2006) identified the AtFT flowering locus as an ortholog of the barley and wheat vernalization gene VRN3. The barley gene VRN-H3 was located on the short arm of chromosome 7H, not chromosome 1H as previously thought based on loose linkage with BLP. Szucs et al. (2006) mapped genes for photoreceptor gene families and vernalization regulation, and compared their locations to QTL for photoperiod response. The barley ortholog to a wheat flowering repressor, HvVRT-2 mapped to the short arm of chromosome 7H. This locus coincided with a photoperiod QTL with small effects mapped in the Dicktoo x Morex population. Tondelli et al. (2006), using a similar approach, mapped candidate genes for cold or drought response based on sequences identified in other plants. Two orthologs of Arabidopsis genes (AtFRY1 and AtICE1) that have a prominent role in cold acclimation were identified on chromosome 7H.
QTL analyses for a variety of traits were reported this year. Chloupek et al. (2006) mapped root system size traits in a population segregating for two semidwarf genes, sdw1 and ari-e.GP. On chromosome 7H, they identified a region associated with height, and another region associated with harvest index, plant weight, root system size at grain filling and total root system size. Advanced backcross QTL analysis continued, with von Korff et al. (2006) detecting favorable alleles from wild barley in crosses with Scarlett. Out of the 86 QTL identified for 9 traits, the H. spontaneum alleles improved performance for 31. QTL for height, heading date, harvest index, lodging at flowering, vegetative dry biomass, thousand grain weight, brittleness and yield were located on chromosome 7H. Li et al. (2006), in a similar study of a wild barley x Brenda advanced backcross, found 100 QTL. Chromosome 7H QTL included yield, heading date, height, ear length, spikelets per spike, seed per spike, spikes per plant, thousand grain weight, leaf length, and leaf area loci. Yun et al. (2006) also used advanced backcross lines from a cross of H. spontaneum with Harrington to validate QTLs for disease resistance loci. A QTL for spot blotch resistance previously identified in a RIL population was confirmed to be located on chromosome 7H.
Additional disease resistance genes were located in several stud