overall coordinator’s reportwheat.pw.usda.gov/ggpages/bgn/40/coordinators.pdfbarley genetics...

Barley Genetics Newsletter (2010) 40:2-44

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Overall coordinator’s report

Udda Lundqvist

Nordic Genetic Resource Center (Nordgen) P.O. Box 41, SE 230 53 Alnarp, Sweden

e-mail:

[email protected]

Since the latest overall coordinator’s report in Barley Genetics Newsletter Volume 39 not any changes of the coordinators took place. Most of the coordinators are continueing and delivered their reports, and I hope they also will do so in the future. To-day it is very important to let us know the newest research results as especially the genome investigations are increasing rapidly. We do not only need the to-days information but also publications and informations from the last century. Several research groups world-wide are working with Single Nucleotide Polymorphism (SNP) genotyping and are using induced mutants from different Gene Banks. Good results have already been published in many publications as different reports are dealing with. About 950 different near isogenic lines (NIL) that are established by J.D. Franckowiak, now working in Australia, are an extraordinary source for this genotyping. During the summer of 2010 about 500 of these lines have been increased and propagated in Sweden in order to incorporate them in the Nordic Genetic Resource Center (Nordgen), Alnarp, Sweden. The Male Sterile Genetic lines will be increased during the summer of 2011 in Sweden for incorporation in the Gene Bank. It has been decided to establish an International Centre for Barley Genetic Stocks at Nordgen, Sweden. Unhappily, I also have to inform the barley community with a sad message: Professor Arne Hagberg, Sweden, passed away 91 years old on January 18, 2010. He was one of the large Swedish barley researchers, geneticists and plantbreeders and contributed with not only breeding, developed several Swedish cultivars, but also very important genetic barley research. For instance he developed many different barley translocation and duplication lines that are incorporated in the Nordic Genetic Resource Center. He also was one of thr initiators to establish ‘The International Barley Genetics Symposia’ and proposed the establishment of ‘Barley Genetics Newsletter’. We all will miss him enormously.

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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: <

[email protected]>

Chromosome 2H (2): Jerry. D. Franckowiak, Hermitage Research Station, Agri-science Queensland, Department of Employment, Economic Development and Innovation, Warwick, Queensland 4370, Australia, FAX: +61 7 4660 3600; e-mail: <[email protected]

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Chromosome 3H (3): Luke Ramsey, Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom. FAX: +44 1382 562426. e-mail: <[email protected]

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Chromosome 4H (4): Arnis Druka, Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom. FAX: +44 1382 562426. e-mail: <[email protected]

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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: <[email protected]

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Chromosome 6H (6): Victoria Carollo Blake, Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA. e-mail: <[email protected]

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Chromosome 7H (1): Lynn Dahleen, USDA-ARS, State University Station, P.O. Box 5677, Fargo, ND 58105, USA. FAX: + 1 701 239 1369; e-mail: <[email protected]

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Integration of molecular and morphological marker maps: David Marshall, Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom. FAX: 44 1382 562426. e-mail: <[email protected]

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Barley Genetics Stock Center: Harold Bockelman, USDA-ARS, National Small Grains Germplasm Research Facility, 1691 S. 2700 W., Aberdeen, ID 83210, USA. FAX: +1 208 397 4165; e-mail: <[email protected]

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Trisomic and aneuploid stocks: Harold Bockelman, USDA-ARS, National Small Grains Germplasm Research Facility, 1691 S. 2700 W., Aberdeen, ID 83210, USA. FAX: +1 208 397 4165; e-mail: <[email protected]

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List of Barley Coordinators (continued)

Translocations and balanced tertiary trisomics: Andreas Houben, Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, DE-06466 Gatersleben, Germany. FAX: +49 39482 5137; e-mail: <[email protected]

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Desynaptic genes: Andreas Houben, Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, DE-06466 Gatersleben, Germany. FAX: +49 39482 5137; e-mail: <

[email protected]>

Autotetraploids: Wolfgang Friedt, Institute of Crop Science and Plant Breeding, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, DE-35392 Giessen, Germany. FAX: +49 641 9937429; e-mail: <[email protected]

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Disease and pest resistance genes: Frank Ordon, Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Strasse 27, DE-06484 Quedlinburg, Germany. e-mail: <[email protected]> Eceriferum genes: Udda Lundqvist, Nordic Genetic Resource Center, P.O. Box 41, SE-230 53 Alnarp, Sweden. FAX:.+46 40 536650; e-mail: < [email protected]

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Chloroplast genes: Mats Hansson, Carlsberg Research Center, Gamle Carlsberg vej 10, DK-2500 Valby, Copenhagen Denmark. FAX: +45 3327 4708; e-mail: <[email protected]

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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: <[email protected]

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Ear morphology genes: Udda Lundqvist, Nordic Genetic Resource Center, P.O. Box 41, SE-230 53 Alnarp, Sweden. FAX: +46 40 536650; e-mail: <or

[email protected]>

Antonio Michele Stanca: Faculty of Agricultural Science, UNIMORE, Reggio Emilia, Italy. FAX +39 0523 983750, e-mail: <[email protected]

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Semi-dwarf genes: Jerry D. Franckowiak, Hermitage Research Station, Agri-science Queensland, Department of Employment, Economic Development and Innovation, Warwick, Queensland 4370, Australia, FAX: +61 7 4660 3600; e-mail: < [email protected]

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Early maturity genes: Udda Lundqvist, Nordic Genetic Resource Center, P.O. Box 41, SE-230 53 Alnarp, Sweden. FAX: +46 40 536650; e-mail: <[email protected]

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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: [email protected]

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Coordinator’s Report: Barley Chromosome 1H (5)

Gunter Backes

The University of Copenhagen Faculty of Life Sciences

Department of Agriculture and Ecology

Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark

e-mail:

[email protected]

Sato et al., (2009) developed 2,948 EST-based markers on the background of nine cDNA libraries from the two cultivars ‘Haruna Nijo’, ‘Akashinriki’ and the wild barley line ‘H602’. These markers were mapped together with 58 anchor markers in 93 doubled haploid lines from the cross ‘Haruna Nijo’ × ‘H602’. Chromosome 1H was covered by 388 markers, including 3 anchor markers and covered 383 cM. Three analogues for the Arabidopsis FT-gene that promotes flowering and is characterized by a unique phosphatidylethanolamine-binding domain, were found in barley by Kikouchi et al., (2009). They localized the analogues in the ‘Steptoe’ × ‘Morex’ population (Kleinhofs et al., 1993). One of them, HvFT3, localized to 1H bin 11/12, where Ppd-H2, a major QTL for heading date was previously described (Laurie et al., 1995). ‘Steptoe’ has lost a major part of the gene and is not able to express it, while the full sequence can be found in ‘Morex’. Six copies of the gene P23k, which was suggested to play an essential role in sugar translocation in the germinating scutellum, where found in barley (Kouzaki et al., 2009). Two copies were tandem arranged on chromosome 1H, one on 2H and 3 tandem-arranged on 3H, while only one homologous gene was detected in wheat on 3A. The two copies on 1H, named HT-P23k-1H.1 and HT-P23k-1H.2, were localized to bin-1, with a distance of 0.7 cM to each other, using 150 doubled haploid lines from the cross ‘Harrington’ × ‘TR-306’ (Kasha et al., 1994). The gene HvHDAC2-1, which codes for a protein that deacetylases histones and thereby induces transcriptional depression of the DNA sequence, the respective histones bind to, was localized to chromosome 1H of barley, bin 14, in a very distal position (Demetriou et al., 2009). The localization was carried out in 94 doubled haploid lines of the Oregon Wolfe Barley population (Costa et al., 2001). In the same population, reduced to 89 individuals and in 89 doubled haploid lines of the ‘Steptoe’ × ‘Morex’ population (Kleinhofs et al., 1993). Pietsch et al., (2009) localized 66 candidates of regulators for seed development (kinases and transcription factors). They tried to annotate the candidates based on blasts to Arabidopsis and rice. Six of those candidates mapped to chromosome 1H: a GSK-like kinase to bin 8, an MCB1 protein to bin 8/9, an ethylene responsive binding factor to bin-9 and three further, not annotated candidates to bin-2/3, bin 9 and bin 14.


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Bovill et al., (2009) localized QTLs for recombination frequency, based on the frequency of recombinations per individual line from existing marker data in wheat, barley and rice. In barley, they used five different segregating populations and detected 14 QTLs on all chromosomes beside 4H. On 1H they found a QTL in a RI-population of 153 lines from the cross ‘WI2875’ × ‘Alexis’ (Barr et al., 2003). It localized to bin 3/4 and explained 7% of the phenotypic variance for recombination frequency in this cross. Using both a segregating population of 94 doubled haploid lines from the cross ‘BCD47’ (rice-blast susceptible) × ‘Baroness’ (rice-blast resistant) and a set of isogenic lines with introgressions of ‘BCD47’ and ‘BCD12’ in a ‘Baroness’-background, Kongprakhon et al., (2009) confirmed a rice-blast resistance on 1H near the Mla-locus (bin 2). The doubled haploid lines were genotyped with 71 SSR markers and the isogenic lines had been characterized by 4,608 SNPs. A QTL analysis for zinc uptake and distribution in plants was carried out by Lonergan et al., (2009) in 150 doubled lines from the cross ‘Clipper’ × ‘Sahara’ (Karakousis et al., 2003). The experiment was carried out in growth chambers under controlled conditions and three QTL were found on chromosome 1H: in bin 4 and in bin 8 a QTL affecting the Zn content and the Zn concentration in seed, respectively, and in bin 12 a QTL with effect on the shoot Na concentration. Xue et al., (2009) localized QTLs for salinity tolerance in late growth stages of barley. They grew 93 doubled haploid lines of a cross between the salt-tolerant line ‘CM72’ and the salt-sensitive variety ‘Gairdner’ with and without salt stress. Their linkage map was based on 48 SSR markers and 284 DArT markers. On chromosome 1H, they detected four QTLs: one on bins 1-3 for the number of spikes per plant under salinity conditions, one on bins 3-4 for the Na:K ratio in the plant shoot and for the spikes per plant under control conditions, one on bins 5-6 for the spikes per line under control conditions and one on bin 2 22-23 for Na concentration in the plant shoot under control conditions. In 80 ‘recombinant chromosome substitution lines’ (BC2F6) from a cross between the wild barley (H. vulgare, ssp. spontaneum) ‘Caeserea 26-24’ and the variety ‘Harrington’, characterized by 25 SSR lines, Inostroza et al., (2009) analyzed QTLs for plant height, yield and yield stability. The plants were grown in the field at six environments with two replicates each. On chromosome 1H they detected an environment dependent QTL for grain yield in bin 3 and an environment-independent QTL for plant height in bin 12. A similar population of 39 BC2DH lines from a cross between the wild barley line ‘S42’ and the variety ‘Scarlett’, was analyzed for both agronomic traits (Schmalenbach et al., 2009) and malting-quality related traits (Schmalenbach and Pillen, 2009). Each line had a single marker-defined introgression of ‘S42’ in the ‘Scarlett’-background and the plants were grown on three locations with three repeats each. Two fragments of ‘S42’ on chromosome 1H changed significantly the agronomic traits: a fragment covering bins 7 to 9 resulted in earlier heading date, higher plants and higher lodging, while a fragment stretching from bins 5 to 7 resulted in a later heading date. Four ‘S42’ introgression fragments on 1H changed the malting quality related traits. A fragment in bins 1 to 2 lowered the α-amylase activity; a fragment in bin 6 -7 lowered the fine grind extract and the sieving fraction; lines showing an ‘S42’ fragment from bin 7


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showed a lower α-amylase activity, a lower friability, a lower Kolbach index and a higher viscosity and a fragment covering bins 7 to 9 resulted in higher grain protein. In total, for six of the 40 QTL that were detected with these lines, the wild barley introgression improved the trait. Malting quality QTLs were also detected by Laido et al., (2009). They used a population of 207 doubled haploid lines from the cross ‘Nure’ × ‘Tremois’, genotyped with 104 markers (RFLP, STS, SSR). All lines were grown in a field experiment in two years and two locations (three replications) and analyzed for malting-quality traits, but in the analysis, the data of 129 lines were used for detection, while 78 lines were used for QTL validation. On chromosome 1H, five QTLs were detected: on bin 3 for acrospire growth, on bin 6 for grain β-glucans, friability, wort viscosity, hot water extract and a quality score, on bin 7 for quality score, on bin 9 for grain β-glucans, hot water extract and quality score and on bin 10 for grain protein content. Siahsar et al., (2009) detected QTLs for forage quality of barley shoots in 72 doubled haploid lines from the ‘Steptoe’ × ‘Morex’ population (Kleinhofs et al., 1993). Their field experiment included two locations with two replicates each and the traits were measured using NIR on dried samples taken at dough stage, milled and sieved. On chromosome 1H, they detected three different QTLs: in bins 5 to 6 a QTL affecting neutral detergent fiber and acid detergent lignin, in bins 7 to 8 a QTL affecting dry matter digestibility, acid detergent fiber, crude fiber, crude protein and ash content and in bin 11 a QTL affecting dry matter digestibility. A virtual map of chromosome 1H, based on flow-cytometric sorting, 545-sequencing with 1.3 × coverage and on the synteny between barley, sorghum and rice was presented by Mayer et al., (2009). The authors claim to have covered 90% of all genes on chromosome 1H. Between 74.5% and 77.5% of the sequences consists of repetitive elements. The authors estimate the number of genes in chromosome 1H to between 4,600 and 5,800 and to between 38,000 and 48,000 in the whole barley genome. References: Barr, A.R., S.P. Jefferies, S. Broughton, K.J. Chalmers, J.M. Kretschmer, J.R. Boyd, H.M.

Collins, S. Roumeliotis, S.J. Logue, S. Coventry, D.B. Moody, B.J. Read, D. Poulsen, R.C.M. Lance, G.J. Platz, R.F. Park, J.F. Panozzo, A. Karakousis, P. Lim, A.P. Verbyla, and P.J. Eckermann, 2003. Mapping and QTL analysis of the barley population Alexis × Sloop. Aust. J. Agr. Res. 54: 1117-1123.

Bovill, W.D., P. Deveshwar, S. Kapoor, and J.A. Able, 2009. Whole genome approaches to

identify early meiotic gene candidates in cereals. Funct. Integr. Genomics 9: 219-229. Costa, J.M., A. Corey, P.M. Hayes, C. Jobet, A. Kleinhofs, A. Kopisch-Obusch, S.F.

Kramer, D. Kudrna, M. Li, O. Riera-Lizarazu, K. Sato, P. Szucs, T. Toojinda, M.I. Vales, and R.I. Wolfe, 2001. Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population. Theor. Appl. Genet. 103: 415-424.


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Demetriou, K., A. Kapazoglou, A. Tondelli, E. Francia, M.A. Stanca, K. Bladenopoulos, and A.S. Tsaftaris, 2009. Epigenetic chromatin modifiers in barley: I. Cloning, mapping and expression analysis of the plant specific HD2 family of histone deacetylases from barley, during seed development and after hormonal treatment. Physiol. Plantarum 136: 358-368.

Inostroza, L., A. Pozo, I. Matus, D. Castillo, P. Hayes, S. Machado, and A. Corey, 2009.

Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol. Breed. 23: 365-376.

Karakousis, A., A.R. Barr, J.M. Kretschmer, S. Manning, S.P. Jefferies, K.J. Chalmers,

A.K.M. Islam, and P. Langridge, 2003. Mapping and QTL analysis of the barley population Clipper × Sahara. Aust. J. Agr. Res. 54: 1137-1140.

Kasha, K.J., A. Kleinhofs, and N.A.B.G. Project, 1994. Mapping of the Barley Cross

Harrington × TR306. Barley Genet. Newsl. 23: 65-69. Kikuchi, R., H. Kawahigashi, T. Ando, T. Tonooka, and H. Handa, 2009. Molecular and

functional characterization of PEBP genes in barley reveal the diversification of their roles in flowering. Plant Physiol. 149: 1341-1353.

Kleinhofs, A., A. Kilian, M.A.S. Maroof, R.M. Biyashev, P.M. Hayes, F.Q. Chen, N.

Lapitan, A. Fenwick, T.K. Blake, V. Kanazin, E. Ananieve, L. Dahleen, D. Kudrna, J. Bollinger, S.J. Knapp, B. Liu, M.E. Sorrells, M. Heun, J.D. Franckowiak, D. Hoffman, R. Skadsen, and B.J. Steffenson, 1993. A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor. Appl. Genet. 86: 705-712.

Kongprakhon, P., A. Cuesta-Marcos, P.M. Hayes, K.L. Richardson, P. Sirithunya, K. Sato,

B. Steffenson, and T. Toojinda, 2009. Validation of rice blast resistance genes in barley using a QTL mapping population and near-isolines. Breed. Sci. 59: 341-349.

Kouzaki, H., S.-I. Kidou, H. Miura, and K. Kato, 2009. Genomic diversity of germinating

scutellum specific gene P23k in barley and wheat. Genetica 137: 233-242. Laido, G., D. Barabaschi, A. Tondelli, A. Gianinetti, A.M. Stanca, O.L.D. Nicosia, N. Di

Fonzo, E. Francia, and N. Pecchioni, 2009. QTL alleles from a winter feed type can improve malting quality in barley. Plant Breed. 128: 598-605.

Laurie, D.A., N. Pratchett, J.H. Bezant, and J.W. Snape, 1995. RFLP mapping of 5 major

genes and 8 quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. Genome 38: 575-585.


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Lonergan, P.F., M.A. Pallotta, M. Lorimer, J.G. Paull, S.J. Barker, and R.D. Graham, 2009. Multiple genetic loci for zinc uptake and distribution in barley (Hordeum vulgare). New Phytologist 184: 168-179.

Mayer, K.F.X., S. Taudien, M. Martis, H. Simkova, P. Suchankova, H. Gundlach, T.

Wicker, A. Petzold, M. Felder, B. Steuernagel, U. Scholz, A. Graner, M. Platzer, J. Dolezel, and N. Stein, 2009. Gene Content and Virtual Gene Order of Barley Chromosome 1H. Plant Physiol. 151: 496-505.

Pietsch, C., N. Sreenivasulu, U. Wobus, and M.S. Röder, 2009. Linkage mapping of putative

regulator genes of barley grain development characterized by expression profiling. Bmc Plant Biology 9: 11.

Sato, K., N. Nankaku, and K. Takeda, 2009. A high-density transcript linkage map of barley

derived from a single population. Heredity 103: 110-117. Schmalenbach, I., J. Léon, and K. Pillen, 2009. Identification and verification of QTLs for

agronomic traits using wild barley introgression lines. Theor. Appl. Genet. 118: 483-497. Schmalenbach, I. and K. Pillen, 2009. Detection and verification of malting quality QTLs

using wild barley introgression lines. Theor. Appl. Genet. 118: 1411-1427. Siahsar, B.A., S.A. Peighambari, A.R. Taleii, M.R. Naghavi, A. Nabipour, and A. Sarrafi,

2009. QTL Analysis of Forage Quality Traits in Barley (Hordeum vulgare L.). Cereal Res. Comm. 37: 479-488.

Xue, D.W., Y.Z. Huang, X.Q. Zhang, K. Wei, S. Westcott, C.D. Li, M.C. Chen, G.P. Zhang,

and R. Lance, 2009. Identification of QTLs associated with salinity tolerance at late growth stage in barley. Euphytica 169: 187-196.


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Coordinator’s report: Chromosome 2H (2)

J.D. Franckowiak

Hermitage Research Station Agri-science Queensland

Department of Employment, Economic Development and Innovation Warwick, Queensland 4370, Australia

e-mail: [email protected]

Saisho et al. (2009) found considerable sequence variability in the six-rowed spike 1 (vrs1) locus, which is the main locus controlling spike type in barley. A target 2.1 kb fragment including HvHox1 region of the vrs1 locus was re-sequenced in a large of domesticated and wild barley accessions. Only certain sequence variants were associated with changes in the fertility and morphology of lateral spikelets. The six-rowed variants (vrs1.a1, vrs1.a2 and vrs1.a3) and the deficiens variant (Vrs1.t) had isoforms at the vrs1 locus that were different from those of wild and two-rowed barleys. The isoforms present in domesticated two-rowed barleys were among those present in Hordeum vulgare ssp. spontaneum accessions. Using association mapping and a large collection of Hordeum vulgare ssp. spontaneum accessions, Roy et al. (2010) detected a large number of positive associations between reactions to spot blotch, caused by Cochliobolus sativus, and molecular markers, DArTs and SNPs. Associations were reported for all chromosomes expect 6H. In chromosome 2H, the association localized in bin 08 was much stronger than the association in bin 01. Vu et al. (2010) attempted to locate the gene for a gibberellin-insensitivity using the semidwarf mutant, sdw3. The sdw3 gene was mapped to a 0.04 cM region of the short arm of chromosome 2H near the centromere, in bin 07. Orthologous regions in rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium sylvaticum were identified and barley BACs were used to identify four candidate genes for sdw3. Taketa et al. (2010) mapped two polyphenol oxidase genes (PPO1 and PPO2) on 2HL at the same position as the phenol reaction (Phr) gene, which was described by Takeda and Chang (1996) as a an inhibitor of the staining of awn in response treatment with a 1% phenol solution. The recombination estimates reported by Takeda and Chang (1996) were 24.7 ± 2.6 for vrs1 (six-rowed spike 1) to Phr1 and 22.2 ± 4.7 for Phr1 to lig1 (liguleless 1). Taketa et al. (2010) place the PPO1/PPO2 loci between molecular markers MWG882 and Bmac415, likely in 2HL bin 12. The observations of Taketa et al. (2010) demonstrated that PPO1 is the major determinant controlling the phenol reaction of awns. Comparisons of PPO1 single mutants and the PPO1PPO2 double mutant indicated that PPO2 partially controls the phenol reaction in the crease on the ventral side of caryopses in naked barley. This region of 2HL may be where March et al. (2008) mapped one of three QTL for black point. Deficiency of the micronutrient zinc is a critical problem in soils of many areas of the world. Selection for Zn-dense seeds is a goal of breeding programs for many crops. Using 150 doubled



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haploid lines from a Clipper/Sahara 3771 cross, Sadeghzadeh et al. (2010) mapped QTL for Zn accumulation from Sahara 3771. The closest molecular marker to the QTL located in 2HS was reported to be bcd175, likely in 2H bin 03. A closely linked dominant PCR-based marker, SZnR1, was developed and mapped about 12 cM distal from bcd175. Yu et al. (2010a) reported a QTL for resistance to Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, from the North Dakota breeding line PI 643302 located in 2HL. The resistance level conferred by the 2HL QTL (QrSp-2H) following seedling inoculations to S. passerinii were less than that associated with a QTL located in 1HS (QrSp-1H), presumably the Rsp2 locus. The estimated position of QrSp-2H was in 2H bin 13. A QTL for partial resistance to Fusarium head blight (FHB), caused by Fusarium graminearum, was identified in 6 of 6 environments (9 to 18% of the variability) between DArT markers bPb-5755 and bPb-1181 with a peak at bPb-5460 in 2HL, likely in bin 14 (Yu et al. 2010b). The resistant allele was from the PI 643302 (ND16092) parent of the single seed descent population. In the same population, Yu et al. (2010c) identified a QTL for reduced rachis internode length, dense or close placement of spikelets on the spike, in 2HL between DArT markers bPb-6055 and bPb-4691 with a peak at bPb-5755. Zhenongda 7 was the donor of dense spike trait and the peak of the QTL was slightly proximal from the QTL for FHB resistance, likely in bin 13. The QTL from the Chinese cultivar Zhenongda 7 explained 66% of the phenotypic variation in spike density. Hassan et al. (2010) used suppression subtractive hybridization on root cDNA from boron tolerant and intolerant doubled haploid lines from a Clipper/Sahara-3771 cross to identify genes associated with boron tolerance. Nine of the 111 clones for know proteins that were up-regulated were mapped near previously reported QTL for boron tolerance. These include a clone identical to the boron transporter gene Bot1 and a clone coding for a bromo-adjacent homology domain-containing a protein mapping to the 6H boron tolerance locus. A third clone mapped to the 2H QTL region and encoded for an S-adenosylmethionine decarboxylase precursor. In a doubled haploid population from a Triumph/Morex cross, Elía et al. (2010) demonstrated that significant differences in malting quality between European and North American barley cultivars was associated with the six-rowed spike 1 (vrs1) locus in 2HL. At least one QTL for each trait studied was located near the vrs1 locus.

Peroxidases (Prx) appear to be associated with plant disease resistance based on observations on Prx induction during disease challenge (González et al., 2010). Despite these associations, there is no evidence that allelic variation of peroxidases directly determines levels of disease resistance. Using Prx-Profiling, González et al. (2010) showed that a large number of peroxidase genes can be mapped in the barley genome. Based on their examinations of the associations between the Prx map positions and QTL for resistance leaf rust and powdery mildew, they reported about 60% co-localize, including Prx based markers present in clusters on 2H.

Cheung et al. (2010) located a QTL for resistance to bird cherry-oat aphid (Rhopalosiphum padi) in 3HL from the susceptible parent, Lina. This QTL was not as strong as the 2H QTL for resistance to R. padi from Hordeum vulgare spp. spontaneum (unpublished data), which was


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reported to be located at the same position in 2H as the QTL for Russian wheat aphid (Diuraphis noxia) resistance located by Mittal et al. (2008).

References: Cheung, W.Y., L. Di Giorgio, and I. Åhman. 2010. Mapping resistance to the bird cherry-oat

aphid (Rhopalosiphum padi) in barley. Plant Breed. 129:637-646. Elía, M., J.S. Swanston, M. Moralejo, A. Casas, A.-M. Pérez-Vendrell, F.J. Ciudad, W.T.B.

Thomas, P.L. Smith, S.E. Ullrich, and J.-L. Molina-Cano. 2010. A model of the genetic differences in malting quality between European and North American barley cultivars based on a QTL study of the cross Triumph x Morex. Plant Breed. 129:280-290.

González, A.M., T.C Marcel, Z. Kohutova, P. Stam, C. G. van der Linden, and R.E Niks.

2010. Peroxidase profiling reveals genetic linkage between peroxidase gene clusters and basal host and non-host resistance to rusts and mildew in barley. PLoS One. 2010: 5 (8):e10495.

Hassan, M., K. Oldach, U. Baumann, P. Langridge, and T. Sutton. 2010. Genes mapping to

boron tolerance QTL in barley identified by suppression subtractive hybridization. Plant Cell Environ. 33:188-198.

March, T.J., J.A. Able, K. Willsmore, C.J. Schultz, and A.J. Able. 2008. Comparative

mapping of a QTL controlling black point formation in barley. Funct. Plant Biol. 35:427-437.

Mittal, S., L.S. Dahleen, and D. Mornhinweg, 2008. Locations of quantitative trait loci

conferring Russian wheat aphid resistance in barley germplasm STARS-9301B. Crop Sci. 48:1452-1458.

Roy, J.K., K.P. Smith, G.J. Muehlbauer, S. Chao, T.J. Close, and B.J. Steffenson. 2010.

Association mapping of spot blotch resistance in wild barley. Mol. Breeding 26:243-256. Sadeghzadeh, B., Z. Rengel, C. Li, and H. Yang. 2010. Molecular marker linked to a

chromosome region regulating seed Zn accumulation in barley. Mol. Breeding 25:167-177.

Saisho, D., M. Pourkheirandish, H. Kanamori, T. Matsumoto, and T. Komatsuda. 2009.

Allelic variation of row type gene Vrs1 in barley and implication of the functional divergence. Breed. Sci. 59:621-628.

Takeda, K. and C.L. Chang. 1996. Inheritance and geographical distribution of a phenol

reaction-less varieties of barley mutant of barley. Euphytica 90:217-221.


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Taketa, S., K. Matsuki, S. Amano, Satoko; D. Saisho, Daisuke; E. Himi, N. Shitsukawa, T.

Yuo, K. Noda, and K. Takeda. 2010. Duplicate polyphenol oxidase genes on barley chromosome 2H and their functional differentiation in the phenol reaction of spikes and grains. J. Exp. Bot. 61:3983-3993.

Vu, G.T.H., T. Wicker, J.P. Buchmann, P.M. Chandler, T. Matsumoto, A. Graner, and N.

Stein. 2010. Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Funct. Integr. Genomics 10:509-521.

Yu, G.T., J.D. Franckowiak, S.H. Lee, R.D. Horsley, and S.M. Neate. 2010a. A novel QTL

for Septoria speckled leaf blotch resistance in barley (Hordeum vulgare L.) accession PI 643302 by whole-genome QTL mapping. Genome 53:630-636.

Yu, G.T., J.D. Franckowiak, S.M. Neate, B. Zhang, and R.D. Horsley. 2010b. A native QTL

for Fusarium head blight resistance in North American barley (Hordeum vulgare L.) independent of height, maturity, and spike type loci. Genome 53:111-116.

Yu, G.T., R.D. Horsley, B. Zhang, and J.D. Franckowiak. 2010c. A new semi-dwarfing gene

identified by molecular mapping of quantitative trait loci in barley. Theor. Appl. Genet. 120:853-861.

http://www.ingentaconnect.com/content/oup/exbotj;jsessionid=70474c6jpcm2f.alexandra�


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Coordinator’s Report: Barley Chromosome 3H

Luke. Ramsay

Genetics Programme

Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK.

e-mail:

[email protected]

Over the last year there have been a number of publications reporting the mapping of genes and QTL on barley chromosome 3H. These included a number of publications (e.g. Chen et al,, 2009b, Joy et al., 2010 and Tyagi et al., 2010), that took advantage of the detailed knowledge now available on the syntenic relationship between 3H and rice chromosome 1 and the marker data now in the public domain (Close et al., 2009, Druka et al., 2008). The syntenic relationship with the Triticeae of a region on 3HS has also been explored in a recent publication (Fleury et al., 2010). This showed good co-linearity of gene-based markers between the physical map of Aegilops tauschii 3DS with the genetic map of barley 3HS with the exception of two lineage specific inversions within Bin 2. Other reports have concentrated on the mapping of members of gene families of particular interest in barley. Thus Kouzaki et al. (2009) mapped duplicated members of a gene family encoding the germinating scutellum specific gene P23k that encodes a 23 kDa protein involved in sugar translocation. Using an RFLP approach they mapped three copies to the terminal bin on 3HL (Bin 16) as well as other members to 1HS and 2HL. Li et al. (2010) mapped a number of putative universal stress proteins (USPs) including one, BUG4, to 3HL (Bin 10) that the authors postulate could be a candidate gene for the seedling spot blotch resistance QTL in the mapping population used (Steptoe x Morex). Gupta et al. (2010) mapped two QTL for resistance to net blotch in a doubled haploid population derived from a Pompadour x Sterling cross. One of these QTL was detected on 3H (Bin 6) with two of the five isolates used and the authors postulate that this could possibly be the same locus as found in previous QTL studies (e.g. Steffenson et al., 1996). Tah et al. (2010) used an F2 population derived from a Valier x Binalong cross to map regions associated with resistance to black point including one QTL on 3H (Bin 13-14). In a study using the Oregon Wolfe Barley doubled haploid mapping population Navakode et al. (2009) found three QTL for aluminum tolerance including one on 3H (Bin 10) that was evident at higher concentrations (20 μM Al, pH 4.7). Other QTL published in the last year include a number on quality characteristics for forage and feed as well as for malting. Abdel-Haleem et al. (2010) found a number of QTL for multiple traits associated with feed quality in F5 derived families derived from a cross between the hulled barley cultivar Valier and a hull-less Swiss landrace line, PI370970 but on 3H only found a QTL for protein content mapping to Bin 6. In contrast Siahsar et al. (2009) reported several QTL for


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forage quality traits on 3H using a subset of the Steptoe x Morex double haploid mapping population. These QTL included several that mapped to Bin 3 for six separate forage quality characteristics (including acid detergent fiber) and two other QTL elsewhere on 3H, one for acid detergent lignin (Bin 11-12) and one for ash (Bin 14) (Siahsar et al., 2009). Elia et al. (2010) presented results from malting quality studies using a doubled haploid population derived from a Triumph x Morex cross. QTL were found for malt extract and fermentability in the region of Bin 6-7 and for predicted spirit yield, protein content and malt extract in Bin 11 possibly associated with sdw1 which segregates in this population (Elia et al., 2010. Ullrich et al.2009) reported work on pre-harvest sprouting and dormancy also using the Triumph x Morex doubled population as well as that derived from Harrington x TR306. The QTL found include one on 3HL in Bin 16 interestingly the same region found by Kouzaki et al., (2009) for the P23k genes. Wang et al. (2010) reported on additional studies using the Bc2DH population and derived introgression lines from a cross between ISR 42-8 (H. v. ssp spontaneum) and Scarlett on the involvement of putative candidate genes on flowering time. The candidate genes included two on 3H, HvFT2 and HvGi in Bin 5 to 6, a region that was associated with an effect on flowering time on the Bc2DH population but which could not be validated in the introgression lines (Wang et al., 2010). As mentioned above several reports made particular use of the genetic resources and information now available for genes on 3H. Tyagi et al. (2010) reanalyzed data tissue culture regeneration on the Steptoe x Morex DH population using mapping data on the population published by Druka et al. (2008). The authors found a significant QTL for green plant regeneration in Bin 12 and suggestive evidence of another QTL in Bin 3 and were able to relate the peaks to potential candidate genes through the relationship with transcriptomic studies (Tyagi et al., 2010). Chen et al. (2009b) used information available on the syntenic relationship with rice chromosome 1 to continue earlier work (Chen et al., 2009a) and to fine map a drought hyper sensitive cuticle mutant eibi1 to a region containing sixteen genes within Bin 6. Roy et al. (2010) mapped spot blotch resistance in a collection of wild barleys using a whole genome association genetics approach that is now possible given the density of genetic markers available. They reported significant association with a number of loci across the genome including a DArT marker on 3HS in Bin 5 that they postulate could be the same position as the QTL previously reported in the region of Bin 4-6 in the bi-parental Dicktoo x Morex mapping population (Bilgic et al., 2005). References: Abdel-Haleem, H., J. Bowman, M. Giroux, V. Kanazin, H. Talbert, L. Surber, and T.

Blake. 2010. Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled x hull-less barley population. Euphytica 172: 405-418.

Bilgic H., B.J. Steffenson, and P. Hayes. 2005. Differential expression of seedling and adult

plant resistance to spot blotch in different genetic backgrounds of barley. Theor Appl Genet 111:1238–1250.


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Chen, G.X., T. Komatsudu, M. Pourkheirandish, M. Sameri, K. Sato, T. Krugman, T. Fahima, A.B. Korol, and E. Nevo. 2009a. Mapping of the eibi1 gene responsible for the drought hypersensitive cuticle in wild barley (Hordeum spontaneum). Breeding Science 59: 21-26.

Chen, G.X., M. Pourkheirandish, M. Sameri, N. Wang, S. Nair, Y.L. Shi, C. Li, E. Nevo,

and T. Komatsuda. 2009b. Genetic targeting of candidate genes for drought sensitive gene eibi1 of wild barley (Hordeum spontaneum). (6th International Triticeae Symposium May 31-June 5, 2009, Kyoto, Japan) Breeding Science 59: 637-644.

Close, T.J., P.R. Bhat, S. Lonardi, Y. Wu, N. Rostoks, L. Ramsay, A. Druka, N. Stein, J.T.

Svensson, S. Wanamaker, S. Bozdag, M.L. Roose, M.J. Moscou, S.Chao, R.K. Varshney, P. Szűcs, K. Sato, P.M. Hayes, D.E. Matthews, A. Kleinhofs, G.J. Muehlbauer, J. DeYoung, D.F. Marshall, K. Madishetty, R.D. Fenton, P. Condamine, A. Graner, and R. Waugh, 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10: 582.

Druka, A., I. Druka, A.G. Centeno, H.Q. Li, Z.H. Sun, W.T.B. Thomas, N. Bonar, B,

Steffenson, S.E. Ullrich, A. Kleinhofs, R.P. Wise, T.J. Close, E. Potokina, Z.W. Luo, C. Wagner, G.F. Schweizer, D.F. Marshall, M.J. Kearsey, R.W. Williams, and R. Waugh. 2008. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genetics 9: 73.

Elía M., J.S. Swanston , M. Moralejo, A. Casas, A-M. Pérez-Vendrell, F.J. Ciudad, W.T.B.

Thomas, P.L. Smith, S.E. Ullrich, and J.-L. Molina-Cano. 2010. A model of the genetic differences in malting quality between European and North American barley cultivars based on a QTL study of the cross Triumph x Morex. Plant Breeding 129, 280-290.

Fleury, D., M.C. Luo, J. Dvorak, L. Ramsay, B.S. Gill, O.D. Anderson, F.M. You, Z.

Shoaei, K.R. Deal, and P. Langridge. 2010. Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS. BMC Genomics 11.

Gupta, S., C.D. Li, R. Loughman, M. Cakir, G. Platz, S. Westcott, J. Bradley, S.

Broughton, and R. Lance. 2010. Quantitative trait loci and epistatic interactions in barley conferring resistance to net type net blotch (Pyrenophora teres f. teres) isolates. Plant Breeding 129: 362-368.

Kouzaki, H., S.-I. Kidou, H. Miura, and K. Kato. 2009. Genomic diversity of germinating

scutellum specific gene P23k in barley and wheat. Genetica 137: 233-242. Li, W.-T., Y.-M. Wei, J.-R. Wang, C.-J. Liu, X.-J. Lan, Q.-T. Jiang, Z.-E. Pu, and Y.-L.

Zheng. 2010. Identification, localization, and characterization of putative USP genes in barley. Theor Appl Genet 121: 907-917.


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Navakode, S., A. Weidner, R.K. Varshney, U. Lohwasser, U. Scholz, and A. Börner, 2009. A QTL analysis of Aluminium tolerance in barley, using gene-based markers. Cereal Research Communications 37: 531-540.

Roy, J.K., K.P. Smith, G.J. Muehlbauer, S.M. Chao, T.J. Close, and B.J. Steffenson. 2010.

Association mapping of spot blotch resistance in wild barley. Molecular Breeding 26: 243-256.

Siahsar, B.A., S.A. Peighambari, A.R. Taleii, M.R. Naghavi, A. Nabipour, and A. Sarrafi.

2009. QTL analysis of forage quality traits in barley (Hordeum vulgare L.). Cereal Research Communications 37: 479-488.

Steffenson, B.J., P.M. Hayes, and A. Kleinhofs. 1996. Genetics of seedling and adult plant

resistance to net blotch (Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) in barley. Theor Appl Genet 92: 552-558.

Tah, P.R., A. Lehmensiek, G.P. Fox, E. Mace, M. Sulman, G. Bloustein, and G.E. Daggard.

2010. Identification of genetic regions associated with black point in barley. Field Crops Research 115: 61–66.

Tyagi, N., L.S. Dahleen, and P. Bregitzer. 2010. Candidate genes within tissue culture

regeneration QTL revisited with a linkage map based on transcript-derived markers. Crop Science 50: 1697-1707.

Ullrich, S.E., H. Lee, J.A. Clancy, I.A. del Blanco, V.A. Jitkov, A. Kleinhofs, F. Han, D.

Prada, I. Romagosa, and J.-L. Molina-Cano. 2009. Genetic relationships between preharvest sprouting and dormancy in barley. (11th International Symposium on Pre-Harvest Sprouting in Cereals, Nov. 2007 Mendoza, Argentina). Euphytica 168: 331-345.

Wang, G., I. Schmalenbach, M. von Korff, J. Léon, B. Kilian, J. Rode, and K. Pillen. 2010.

Association of barley photoperiod and vernalization genes with QTLs for flowering time and agronomic traits in a BC2DH population and a set of wild barley introgression lines. Theor Appl Genet 120:1559–1574.


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Coordinator’s Report: Chromosome 4H

Arnis Druka

Genetics Programme

Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK.


Several papers that mention genetic stocks, genes and QTLs specifically related to chromosome 4H have been published in 2009 - 2010. Sakata M., Nasuda S. and Endo T.R. (2010) describe using two gametocidal (Gc) chromosomes 2C and 3C (SAT) to dissect barley chromosome 4H added to common wheat. The Gc chromosome induced chromosomal structural rearrangements in the progeny of the 4H addition line of common wheat carrying the monosomic Gc chromosome. They conducted in situ hybridization to select plants carrying rearranged 4H chromosomes and characterized the rearranged chromosomes by sequential C-banding and in situ hybridization. This resulted in establishment of 60 dissection lines of common wheat carrying single rearranged 4H chromosomes. The rearranged 4H chromosomes had either a deletion or a translocation or a complicated structural change. The breakpoints were distributed in the short arm, centromere and the long arm at a rough ratio of 2:2:1. PCR analysis was conducted using the dissection lines and 93 EST markers specific to chromosome 4H. Based on the PCR results, a cytological map of chromosome 4H with 18 regions separated by the breakpoints of the rearranged chromosomes was constructed. Thirty-seven markers were present in the short arm and 56 in the long arm, and about 70% of the markers were present in no more than the distal 25.6% and 43.1% regions of the short and long arms, respectively. It is noteworthy that nine of the short-arm markers and 13 of the long-arm markers existed in the small subtelomeric regions at both ends characterized by the HvT01 sequences. A reconstructed genetic map using 38 of the 93 markers that was used to construct the cytological map of chromosome 4H was generated. The order of the markers on the genetic map was almost the same as that on the cytological map. On the genetic map, no markers were available in the pericentromeric region, but on the cytological map, 14 markers were present in the proximal region, and one of the markers was in the centromeric region of the short arm. Kapazoglou A. et al. (2010) report characterization of the genes encoding barley PcG proteins HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b. They were mapped on barley chromosomes 7H, 4H, 2H and 5H, respectively. Expression analysis of the PcG genes revealed significant differences in gene expression among tissues and seed developmental stages and between barley cultivars with varying seed size. Furthermore, HvFIE and HvE(Z) gene expression was responsive to the abiotic stress-related hormone abscisic acid (ABA) known to be involved in seed maturation, dormancy and germination.



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Szakács, E. and Molnár-Láng, M. (2010) describe the isolation of two new disomic addition lines, the 7H disomic and 6HS ditelosomic additions, using fluorescence in situ hybridization with the repetitive DNA probes Afa-family and HvT01 in addition to their existing set of 2H, 3H, 4H, and 1HS isochromosomic lines from hybrids between the winter wheat 'Martonvásári 9 kr1' and the two-rowed winter barley cultivar 'Igri'. Wei K. et al. (2009) mapped beta-amylase and limit dextrinase activities and beta-glucan and protein fraction content QTLs using a doubled haploid (DH) population from a cross of CM72 (six-rowed) by Gairdner (two-rowed) barley cultivars. A total of nine QTLs for these traits were mapped to chromosomes 3H, 4H, 5H, and 7H. Five of them mapped to chromosome 3H. The loci of QTLs for beta-glucan and limit dextrinase were identified on chromosomes 4H and 5H, respectively. Comadran J. et al. (2009) investigated the population structure and genome-wide linkage disequilibrium (LD) in 192 Hordeum vulgare accessions from the past and present barley cultivars in the Mediterranean basin. They used 50 nuclear microsatellite and 1,130 DArT((R)) markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centered on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r (2) of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT((R)) markers, it was demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. By identifying associations with powdery mildew that map in genomic regions known to have resistance loci, it was shown that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. Schober M.S. et al. (2009) describe the transcription patterns of members of the callose synthase gene family from barley. Fragments of six barley (1,3)-beta-D-glucan synthase-like (GSL) cDNAs were obtained by PCR amplification using primers designed to barley expressed sequence tag (EST) sequences. The HvGSL genes, designated HvGSL2 to HvGSL7, were mapped to individual loci that were distributed across the barley genome on chromosomes 3H, 4H, 6H and 7H. The HvGSL1 gene has been isolated and characterized previously. Transcript levels for all the genes were analysed by quantitative real-time PCR in a range of barley tissues and organs, at various developmental stages. High levels of transcript for many of the HvGSL genes were detected in endosperm during the early stages of grain development, when cellularisation of the endosperm was occurring and it is likely that many of the genes participate in this process. Schmalenbach, I. and Pillen, K. (2009) describe a malting quality quantitative trait locus (QTL) study that was conducted using a set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs). Each S42IL harbors a single marker-defined chromosomal segment from the wild barley accession 'ISR 42-8' (Hordeum vulgare ssp. spontaneum) within the genetic background of the elite spring barley cultivar 'Scarlett' (Hordeum vulgare ssp. vulgare). The aim of the study was (1) to verify genetic effects previously identified in the advanced backcross population S42,


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(2) to detect new QTLs, and (3) to identify S42ILs exhibiting multiple QTL effects. For this, grain samples from field tests in three different environments were subjected to micro malting. Subsequently, a line x phenotype association study was performed with the S42ILs in order to localize putative QTL effects. A QTL was accepted if the trait value of a particular S42IL was significantly (P < 0.05) different from the recurrent parent as a control, either across all tested environments or in a particular environment. For eight malting quality traits, altogether 40 QTLs were localized, among which 35 QTLs (87.5%) were stable across all environments. Six QTLs (15.0%) revealed a trait improving wild barley effect. Out of 36 QTLs detected in a previous advanced backcross QTL study with the parent BC(2)DH population S42, 18 QTLs (50.0%) could be verified with the S42IL set. For the quality parameters alpha-amylase activity and Hartong 45 degrees C, all QTLs assessed in population S42 were verified by S42ILs. In addition, eight new QTL effects and 17 QTLs affecting two newly investigated traits were localized. Two QTL clusters harboring simultaneous effects on eight and six traits, respectively, were mapped to chromosomes 1H and 4H. References: Comadran, J., W.T.Thomas, F.A. van Eeuwijk, S. Ceccarelli, S. Grando, A.M. Stanca, N.

Pecchioni, T. Akar, A. Al-Yassin, A. Benbelkacem, H. Ouabbou, J. Bort, I. Romagosa, C.A. Hackett, and J.R. Russell. 2009. Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet. 2009 Jun; 119(1):175-187. Epub 2009 May 5.

Kapazoglou, A., A. Tondelli, D. Papaefthimiou, H. Ampatzidou, E. Francia, M.A. Stanca,

K. Bladenopoulos, and A.S. Tsaftaris. 2010. Epigenetic chromatin modifiers in barley: IV. The study of barley Polycomb group (PcG) genes during seed development and in response to external ABA. BMC Plant Biol. Apr 21; 10:73.

Sakata, M., S. Nasuda, and T.R.Endo. 2010. Dissection of barley chromosome 4H in common

wheat by the gametocidal system and cytological mapping of chromosome 4H with EST markers. Genes Genet Syst. Feb; 85(1):19-29.

Schmalenbach, I. and K. Pillen K. 2009. Detection and verification of malting quality QTLs

using wild barley introgression lines. Theor Appl Genet. May: 118(8):1411-1427. (Epub 2009 May 4th.

Schober, M.S., R.A. Burton, N.J. Shirley, A.K. Jacobs, and G.J. Fincher. 2009. Analysis of

the (1,3)-beta-D-glucan synthase gene family of barley. Phytochemistry. Apr; 70(6):713-720. Epub 2009 May 4.

Szakács, E. and M. Molnár-Láng. 2010. Identification of new winter wheat - winter barley

addition lines (6HS and 7H) using fluorescence in situ hybridization and the stability of the whole 'Martonvásári 9 kr1' - 'Igri' addition set. Genome. Jan; 53(1):35-44.


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Wei, K., D.W. Xue, Y.Z. Huang, X.L. Jin, F.B. Wu, and G.P. Zhang. 2009. Genetic mapping of quantitative trait loci associated with beta-amylase and limit dextrinase activities and beta-glucan and protein fraction contents in barley. J Zhejiang Univ Sci B. Nov;10(11):839-846.


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Coordinator’s Report: Chromosome 6H (6)

Victoria Carollo Blake

Montana State University Bozeman, MT 59717 USA


Intervarietal diversity of α-amylase (amy1) and the association analysis of the haplotype with malting quality was done on 326 cultivars (Matthies et al., 2009). Sequencing revealed six SNPs in the gene, four in the last exon (two silent and two causing an amino acid substitutions) and two in the 3’UTR, resulting in four haplotypes, amy1_H1 through amy1_H4. Interestingly, SNP3 which is an A>G substitution with no effect on amino acid structure was highly significant with the presence of Guanine accounting for ca. 45% average increase in the malt quality index. The first fine-mapping of a male sterility gene (msg6) was reported by Emebiri (2010). Although over 50 male sterile genes have been reported and msg6 was described nearly 70 years ago, this was the first to link the gene to molecular markers. Multi-point linkage mapping placed the EST-SSR GBM1267 at 4.9 cM from the msg6 gene. Since this is not a public domain marker, another EST-SSR marker, called VBMS103 was developed for MAS with a marker with a known sequence (AL501881). Another study found microsatellite markers HVM65, HVM74 and Bmgttttt1 which on the ‘Hordeum-Consensus2006-SNP-6H’ map on GrainGenes are mapped within a 2cM span, are tightly linked to the msg6-rob1-sex1 linkage block. (Gill, 2009). A 6H region near the centromere containing two closely-linked genes for net form net blotch (NB) previously described as rpt.t and rpt.k had 15 more EST-derived markers placed in the 27.0 cm Interval by Lui et al., (2010). Mapping was done on a set of 23 barley lines routinely used to evaluate NB resistance. This region is collinear with Rice chromosome 2 and colinearity with Brachypodium in this region was observed. A mapping population developed by St. Pierre et al., (2010) identified two major NB QTL on 6H, one on bin 2 explaining 25-44% of the phenotypic variation and one in bin 6 explaining 19-48% of the variation. References: Emebiri, L.C. 2010. An EST-SSR marker tightly linked to the barley male sterility gene (msg6)

located on chromosome 6H. J. Heredity 101:769-774. Gill, R. 2009. Characterization of phenotypic and genotypic selection for simple and complex

traits of barley (Hordeum vulgare L.). Ph.D. Dissertation. Murdoch University, Australia.



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Liu, Z., J.D. Faris, M.C. Edwards, and T.L. Friesen. 2010. Development of expressed sequence ta (EST)-based markers for genomic analysis of a barley 6H region harboring multiple net form net blotch resistance genes.

Matthies, I.E., S. Weise, and M.S. Röder. 2009. Association of haplytype diversity in the α-

amylase gene amy1 with malting quality parameters in barley. Mol. Breeding. 23:139-152.

St. Pierre, S., C. Gustus, B. Steffenson, R. Dill-Macky, and K.P. Smith. 2010. Mapping net

form net blotch and Septoria specked leaf blotch resistance loci in barley. Phytopath. 100:80-84.


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Coordinator’s Report: Chromosome 7H (1)

Lynn S. Dahleen

USDA-Agricultural Research Service

Fargo, ND 58105, USA

e-mail:

[email protected]

This was another active year in barley genetics. New markers were developed by a number of research groups, mostly gene/EST-based such as single nucleotide polymorphism (SNP) and SSR markers, and assembled into high resolution maps. Close et al., (2009) describe the development of a large number of SNP markers in barley and a high density linkage map to aid in high resolution and comparative mapping. Their consensus map contained 417 SNP markers on chromosome 7H, in 133 bins covering 167.2 cM. These markers showed synteny with rice chromosome 6, with a small section of rice chromosome 8 syntenous with the barley 7H centromere region. Drader et al., (2009) developed a high resolution map of the chromosome 7H bin 2-5 region that has very high recombination rates. QTL mapping has identified numerous traits in this region, including the Rcs5 gene for spot blotch resistance. Comparative mapping with rice was used to identify putative ESTs in the region and design markers for barley. A total of 850 BAC clones were assembled into 56 contigs spanning bins 2-5. The saturation of markers will aid in isolating Rcs5 and other genes controlling important traits. Markers to assess SNPs by temperature switch PCR (TSP) were developed by Hayden., (2009). Out of the 87 TSP markers developed, nine were located on chromosome 7H. These markers and the methods used to develop them provide for rapid, low-tech SNP genotyping, without specialized equipment. The markers were robust for both cultivated and wild barley. Pietsch et al., (2009) developed marker assays for 76 transcription factors and kinases that are potential regulators of barley grain development in four mapping populations. Nine of the markers mapped to chromosome 7H and another five markers were placed on 7H using wheat-barley addition lines. Putative rice orthologs were identified for many of the markers. Emibiri 2009 developed new EST-based SSR markers targeting genes expressed during grain development. Five of the markers were located on chromosome 7H. Three closely linked new markers flanked QTL for wort beta-glucan content, and the positions of two QTL for wort beta-glucan content and beta-glucanase activity previously located on chromosome 7H were confirmed. A cellulose synthase-like gene was located in the interval associated with beta-glucanase activity. Hanemann et al., (2009) examined the chromosome 7HS region that contains the Rrs2 gene for scald resistance in an ‘Atlas’ x ‘Steffi’ mapping population. They developed a fine map of the region, including the identification of co-segregating markers and flanking BAC contigs for Rrs2. Several candidate gene sequences have been identified containing domains typically found in resistance genes. A survey of 58 genotypes showed that those in the Rrs2 subgroup by cluster analysis all shared a haplotype in the analyzed regions suggesting that this several hundred kb chromosome region is recombinationally inactive. Sato et al., (2009) developed a high density transcript map in ‘Haruna Nijo’ x H602 consisting of 2890 SNP, INDEL, and CAPS markers.


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Chromosome 7H contained 423 markers. Their linkage map is estimated to contain 9% of the genes in barley. Sato and Takeda (2009) then combined markers from this map with BOPA1 SNP markers (Close et al., 2009) to develop an integrated linkage map. They used the map to identify regions of integration from the wild barley H602 into Haruna Nijo. Segments of most of chromosome 7H were present in recombinant chromosome substitution lines, but part of 7HL from H602 was not represented in any of the lines. Bauer et al., (2009) compared QTL detection methods in an advanced backcross between the wild barley ISR42-8 and Scarlett. The restricted maximum likelihood (REML) single locus method detected four QTL on chromosome 7H, one each for heading date, height, yield and thousand kernel weight (tkw). REML with forward selection also detected the QTL for heading date and tkw, while the Bayesian multi-locus single environment method only detected the QTL for tkw on chromosome 7H. The height QTL has not been previously identified in QTL studies. Wild barley introgression lines, each containing a single region from ‘ISR 42-8’ in ‘Scarlett’ background, were evaluated for agronomic trait (Schmalenbach et al., 2009) and malting quality (Schmalenbach and Pillen, 2009) QTL. Seven of the lines contained introgressions in chromosome 7H, which were associated with grains/ear, heading date, height, lodging, yield, alpha-amylase activity, fine-grind extract, grain protein content, grain sieving fraction, and Kolbach index. Candidate genes in these regions include Amy2, HvCO1(photoperiod response), Vrn.H3 (vernalization, aka HvFT1), and eps7L (earliness per se). These lines will be valuable for fine mapping and eventual map-based cloning of these genes. A set of H. bulbosum introgression lines were evaluated by Johnston et al., 2009. For chromosome 7H, three lines had a small introgression of the end of the long arm, one line had a small introgression of the end of the short arm and one line had a longer introgression of the short arm. These introgression lines provide a valuable resource for barley improvement. A number of QTL studies were conducted to locate regions associated with a variety of traits. Bovill et al., 2009 located two QTL that increased recombination frequency on chromosome 7H. These QTL were located on the short arm and only identified in one of the five barley populations tested, WI2875-1/Alexis. The QTL with the largest effect explained 9.4% of the variation in recombination frequency. Yield and heading date QTL were located in a ‘Beka’ x ‘Mogador’ DH population by Cuesta-Marcos et al., 2009. One of the yield QTL was on chromosome 7H near the centromere and explained 4% of the variation. This region has been previously detected as containing QTL for yield and heading date. Finnie et al., (2009) used 2-D protein electrophoresis and AFLP and SSR markers to examine differences between 18 barley cultivars and correlate differences with malting quality. Mapping 15 protein groups in a DH population from Scarlett x Meltan identified three groups on chromosome 7H, including a grain peroxidase that had previously reported to be affected by stress. Lamb et al., (2009) examined QTL for FHB severity, DON accumulation, heading date, physiological maturity, and height in a cross between C93-3230-24 and Foster. The resistance from C93-3230-24 is derived from Heitpas 5. Only one QTL, for FHB severity, was found on the long arm of chromosome 7H, which was only detected in two of the eight environments tested, indicating this region does not have consistent effects on the disease. Dormancy and preharvest sprouting can influence both barley grain and malt quality. Lin et al., (2009) located QTL for dormancy in two populations, Harrington x Morex and Chevron x


26

Stander. Two QTL were identified in each population, including one on the short arm of chromosome 7H in the Chevron/Stander population. This QTL explained 3-9% of the phenotypic variation for dormancy. Preharvest sprouting and dormancy QTL also were examined by Ullrich et al., (2009) in three crosses. Several loci for each trait were located on chromosome 7H, explaining 3-7% of the variation for these traits. Xue et al., (2009) located QTLs for salinity tolerance at the stem elongation stage in a population derived from CM72 (salt tolerant) x Gairdner (salt sensitive). Loci for spikes/plant and grain yield were located on chromosome 7H in the control environment, but only one QTL for spikes/line was found on 7H under saline conditions, which may prove useful to increase salinity tolerance in breeding programs. Sameri et al., (2009) located QTL for individual components of height, including stem and spike internode length and spike length, and measured the effects on lodging over two years. The previously identified locus qCUL.ak on the end of the long arm of chromosome 7H was associated with length of the upper four internodes and culm length in at least one of the environments and influenced lodging. Spike internode and spike length were associated with the dsp1 locus near the centromere on chromosome 7HL. Unlike other dwarfing genes, qCUL does not appear to have pleiotropic effects on yield components, so it may have application in breeding semidwarf barley cultivars. Marker-assisted backcrossing was used by Emibiri et al., (2009) to examine malting quality QTL, including a region from Morex on chromosome 7H and from Harrington on chromosome 5H. Bin 4 and 6 from 7H were selected using flanking SSR markers. BC6F1-derived DH lines were found with similar quality profiles to Morex and Harrington that will be useful in developing an elite germplasm pool for breeding, but none exceeded their quality. Association mapping continued with a study by Inostroza et al., (2009). They tested a set of 80 recombinant chromosome substitution lines (BC2F6) derived from a cross between the donor H. spontaneum accession Caeserea 26-24 and the recurrent parent Harrington for height and yield over six environments with different moisture profiles. Even with only a total of 47 markers tested, three markers on chromosome 7H were associated with height and yield, but no loci associated with yield adaptability were found on this chromosome. The 7H alleles from the wild parent reduced yield and increased height. These appear to reside in the same locations previously identified by QTL analyses. Comadran et al., (2009) studied linkage disequilibrium and association mapping in 192 Mediterranean accessions. Their linkage map consisted of 1130 DArT and 50 SSR markers with a marker every 1.5 cM. When they scanned the map for markers associated with powdery mildew resistance, they found seven significant markers on chromosome 7H, one associated with mlt, three associated with Mlf, and three unassociated markers. The study showed that this population of diverse accessions can be used for association mapping provided that the analysis incorporates the structure of the population in the models. Strake et al., (2009) used association mapping of flowering time to evaluate gene action and interactions, and examined sequence diversity at three flowering loci in 220 spring barley lines (two on chromosome 7H). The CONSTANS locus (HvCO1) showed 14 SNPs and two indels, while HvFT1 (Vrn-H3) showed 21 SNPs and four indels, mostly in the non-coding regions. The haplotypes at these loci did not group the lines into specific early or late flowering times, but both loci explained a small amount of the variation for flowering time. HvCO1 showed significant epistasis with Ppd-H1 photoperiod sensitivity gene on chromosome 2H.


27

Other genes also were examined for position and expression patterns. Kikuchi et al., (2009) examined five PEBP (phosphatidylethanolamine-binding protein) genes for their role in flowering. One PEBP, HvFT1, was mapped to the short arm of chromosome 7H, syntenous to the rice orthologous gene Hd3a on chromosome 6. When overexpressed in rice, HvFT1 induced early heading under both long- and short-day conditions. In long day conditions, HvFT1 had higher expression in Steptoe than in Morex, and was expressed at the first leaf stage. Under short days, Morex showed higher expression of HvFT1 at the same early stage. Tightly bound to DNA proteins (TBPs) were examined in two genes, including Amy32b on chromosome 7H, by Sjakste et al., (2009). Changes in genes expression during development corresponded to changes in TBP distribution. They propose that the TBPs may help stabilize enhancers or that their absence may inactivate gene promoters. Tonooka et al., (2009) investigated bgl, a mutant gene that eliminates beta-glucan in the grain. The gene showed linkage to nud and several molecular markers in the centromeric region of chromosome 7H and cosegregated with HvCslF6, a member of the cellulose synthase-like gene family. The bgl mutant is proposed to be a loss of function mutant of HvCslF6 and should aid in developing low beta-glucan cultivars for malting and brewing. Orabi et al., (2009) examined genetic diversity in 185 wild and cultivated barley accessions from five countries in the West Asia and North Africa region using SSR markers. Six of the markers, on chromosome 7H, detected between 8-28 alleles, providing good estimates of the high levels of diversity within this germplasm. A review by Kleinhofs et al., (2009) describes current knowledge of barley stem rust resistance genes, including Rpg1 on chromosome 7H. The review compares the structure and function of different Rpg loci, including induced mutants that have helped better understand the genetic components making up Rpg1. References: Bauer, A. M, F. Hoti, M. von Korff, K. Pillen, J. Léon, and M. Sillanpää. 2009. Advanced

backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials. Theor Appl Genet 119:105-123.

Bovill, W.D., P. Devashwar, S. Kapoor, and J.A. Able. 2009. Whole genome approaches to

identify early meiotic gene candidates in cereals. Funct Integr Genomics 9:219-229. Close, T.J, P.R Bhat, S. Lonardi, Y. Wu, N. Rostoks, L. Ramsay, A. Druka, N. Stein, J.T.

Svensson, S. Wanamaker, S. Bozdag, M.L. Roose, M.J. Moscou, S. Chao, R.K. Varshney, P. Szűcs, K. Sato, P.M. Hayes, D.E. Matthews, A. Kleinhofs, G.J. Muehlbauer, J. DeYoung, D.F. Marshall, K. Madishetty, R.D. Fenton, P. Condamine, A. Graner, and R. Waugh. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582.

Comadran J., W.T.P. Thomas, F.Á. van Eeuwijk, S. Ceccarelli, S. Grando, A.M. Stanca, N.

Pecchioni, T. Akar, A. Al-Yassin, A. Benbelkacem, H. Ouabbou, J. Bort, I. Romagsa, C.A. Hackett, and J.R. Russell. 2009. Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119:175-187.


28

Cuesta-Marcos, A., A.M. Casas, P.M. Hayes, M.P. Gracia, J.M. Lasa, F. Ciudad, P.

Codesal, J.L. Molina-Cano, and E. Igartua. 2009. Yield QTL affected by heading date in Mediterranean grown barley. Plant Breeding 128:46-53.

Drader, T., K. Johnson, R. Brueggeman, D. Kudrna, and A. Kleinhofs. 2009. Genetic and

physical mapping of a high recombination region on chromosome 7H(1) in barley. Theor Appl Genet 118:811-820.

Emebiri, L.C. 2009. EST-SSR markers derived from an elite barley cultivar (Hordeum vulgare

L. ‘Morex’): polymorphism and genetic marker potential. Genome 52:665-676. Emebiri, L, P. Michael, D.B. Moody, F.C. Ogbonnaya, and C. Black. 2009. Pyramiding

QTLs to improve malting quality in barley: gains in phenotype and genetic diversity. Mol Breeding 23:219-228.

Finnie, C., M. Bagge, T. Steenholdt, O. Østergaard, K.S. Bak-Jensen, G. Backes, A. Jensen,

H. Giese, J. Larsen, P. Roepstorff, and B. Svensson. 2009. Integration of the barley genetic and seed proteome maps for chromosome 1H, 2H, 3H, 5H and 7H. Funct Integr Genomics 9:135-143.

Hanemann, A., G.F. Schweizer, R. Cossu, T. Wicker, and M.S. Röder. 2009. Fine mapping,

physical mapping and development of diagnostic markers for the Rrs2 scald resistance gene in barley. Theor Appl Genet 119:1507-1522.

Hayden, M.J., T. Tabone, and D.E. Mather. 2009. Development and assessment of simple

PCR markers for SNP genotyping in barley. Theor Appl Genet 119:939-951. Inostroza, L, A. del Pozo, I. Matus, D. Castillo, P. Hayes, S. Machado, and A. Corey. 2009.

Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol Breeding 23:365-376.

Johnston. P.A., G.M. Timmerman-Vaughan, K.J.F. Farnden, and R. Pickering. 2009.

Marker development and characterization of Hordeum bulbosum introgression lines: a resource for barley improvement. Theor Appl Genet 118:1429-1437.

Kikuchi, R., H. Kawahigashi, T. Ando, T. Tonooka, and H. Handa. 2009. Molecular and

functional characterization of PEBP genes in barley reveal the diversification of their roles in flowering. Plant Physiol 149:1341-1353.

Kleinhofs, A., R. Brueggeman, J.Nirmala, L. Zhang, A. Mirlohi, A. Druka, N. Rostoks, and

B.J. Steffenson. 2009. Barley stem rust resistance genes: structure and function. Plant Genome 2:109-120.


29

Lamb, K.E., J.L. Gonzalez-Hernandez, B. Zhang, M. Green, S.M. Neate, P.B. Schwarz, and R.D. Horsley. 2009. Identification of QTL conferring resistance to Fusarium head blight resistance in the breeding line C93-3230-24. Crop Sci 49:1675-1680.

Lin, R., R.D. Horsley, N.L.V. Lapitan, Z. Ma, and P.B. Schwarz. 2009. QTL mapping of

dormancy in barley using the Harrington/Morex and Chevron/Stander mapping populations. Crop Sci 49:841-849.

Orabi, J., A. Jahoor, and G. Backes. 2009. Genetic diversity and population structure of wild

and cultivated barley from West Asia and North Africa. Plant Breed 128:606-614. Pietsch, C., N. Sreenivasulu, U. Wobus, and M.S. Röder. 2009. Linkage mapping of putative

regulator genes of barley grain development characterized by expression profiling. BMC Plant Biology 9:4.

Sameri, M., S. Nakamura, S.K. Nair, K. Takeda, and T. Komatsuda. 2009. A quantitative

trait locus for reduced culm internode length in barley segregates as a Mendelian gene. Theor Appl Genet 118:643-652.

Sato, K. and K. Takeda. 2009. An application of high-throughput SNP genotyping for barley

genome mapping and characterization of recombinant chromosome substitution lines. Theor Appl Genet 119:613-619.

Sato, K., N. Nankaku, and K. Takeda. 2009. A high-density transcript linkage map of barley

derived from a single population. Heredity 103:110-117. Schmalenbach, I., J. Léon, and K. Pillen. 2009. Identification and verification of QTLs for

agronomic traits using wild barley introgression lines. Theor Appl Genet 118:483-497. Schmalenbach, I. and K. Pillen. 2009. Detection and verification of malting quality QTLs

using wild barley introgression lines. Theor Appl Genet 118:1411-1427. Sjakste, T., K. Bielskiene, M. Röder, O. Sugoka, D. Labeikyte, L. Bagdoniene, B. Juodka,

Y. Vassetzky, and N. Sjakste. 2009. Development-dependent changes in the tight DNA-protein complexes of barley on chromosome and gene level. BMC Plant Biology 9:56.

Stracke, S., G. Haseneyer, J-B. Veyrieras, H.H. Geiger, S. Sauer, A. Graner, and H-P.

Piepho. 2009. Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118:259-273.

Tonooka, R., E. Aoki, T. Yoshioka, and S. Taketa. 2009. A novel mutant gene for (1-3, 1-4)-

β-D-glucanless grain on barley (Hordeum vulgare L.) chromosome 7H. Breeding Sci 59:47-54.


30

Ullrich, S.E., H. Lee, J.A. Clancy, I.A. del Blanco, V.A. Jitkov, A. Kleinhofs, F. Han, D. Prada, I. Romagosa, and J.L. Molina-Cano. 2009. Genetic relationships between preharvest sprouting and dormancy in barley. Euphytica 168:331-345.

Xue, D., Y. Huang, X. Zhang, K. Wei, S. Wescott, C. Li, M. Chen, G. Zhang, and R. Lance.

2009. Identification of QTLs associated with salinity tolerance at later growth stage in barley. Euphytica 169:187-196.


31

Barley Genetic Stock Collection (GSHO)

USDA-ARS National Small Grains Collection

1691 S. 2700 W. Aberdeen, Idaho 83210, USA

Curator: Harold E. Bockelman


In the past year there have no additions to the GSHO. There are currently 2,103 active accessions with 1,998 available for distribution. All GSHO accessions are described on the Germplasm Resources Information Network (GRIN) online at http://www.ars-grin.gov/npgs. A total of 101 samples of seed were distributed in 24 separate requests placed on GRIN in the past year.


http://www.ars-grin.gov/npgs�


32

Coordinator’s report: Translocations and balanced tertiary trisomics

Andreas Houben

Leibniz-Institute of Plant Genetics and Crop Plant Research

D-06466 Gatersleben, Germany

email:

[email protected]

Dimitrova and colleagues studied the chromatin structure of ribosomal RNA (rRNA) genes in barley lines with modulated activity of nucleolus organizers (NORs) caused by three different types of chromosomal rearrangements were studied. It was found that when the whole rDNA long unit was used as DNA hybridization probe, DNase I digestion led to a gradual decrease in rDNA-generated fragments in control (T-1586), translocation (T-30) and deletion (T-35) lines. In duplication line (D-2946) rDNA was relatively more resistant to nuclease digestion as compared to other lines. In addition, this study revealed defined regions of DNase I hypersensitivity within intergenic spacer (IGS), which possibly coincide with the cis-regulatory elements (transcription initiation site - TIS and termination site - TTS). No appreciable differences in DNase I hypersensitivity of IGS were found in control and tested lines. Therefore, the alterations in barley NOR expression observed earlier in lines T-35 and E-2946 most probably were not accompanied with significant changes in DNase I susceptibility of the rRNA genes (Dimitrova et al., 2009). Colleagues form Martonvasar (Hungary) characterised a wheat/barley translocation line from the Mv9kr1 x Igri hybrid which was identified as a 5HS.7D translocation using FISH and 5H-specific barley SSR markers. The elimination of the 7DS terminal region was proved by three of the twenty-four tested markers. The breakpoint of the 5HS. 7DS translocation was considered to be closer to the telomere than the breakpoint of known deletion lines, which provides a new physical landmark for future deletion mapping studies. The fine mapping of 7D makes it possible to localize agronomically useful genes to the precise chromosomal region of the eliminated 7DS segment, opening up the possibility of marker-assisted breeding and map-based cloning (Sepsi and Bucsi, 2009). Cseh and colleagues identified a spontaneous wheat-barley translocation chromosomes in the progenies of wheat/barley addition lines produced from the wheat cultivar Asakaze komugi and the Ukrainan six-rowed barley cultivar Manas. The wheat chromosome arm involved in the translocation was identified by FISH as 4BS. The barley chromosome segment could not be unequivocally determined. The microsatellite marker analysis revealed the presence of an almost complete 7HL chromosome arm, but the centromeric region of 7HL was missing from this translocation line. The rearranged chromosome, identified as 4BS. 7HL with a centromeric deletion of 7HL, represents a unique genetic material which can be used for the physical mapping of genes or genetic markers within 7HL. As the barley chromosome 7H is considered to be the most important chromosome for drought tolerance, the translocation line will make it possible to reveal the effect of the abiotic stress-related genes situated on the incorporated 7HL segment in the genetic background of wheat (Cseh et al., 2009).



33

The collection is being maintained in cold storage. To the best knowledge of the coordinator, there are no new publications dealing with balanced tertiary trisomics in barley. Limited seed samples are available any time, and requests can be made to the coordinator. References: Cseh, A., K. Kruppa, and I. Molnar. 2009. Incorporation of a Winter Barley Chromosome

Segment into Cultivated Wheat and Its Characterization with Gish, Fish and Ssr Markers. Cereal Res Commun 37, 321-324.

Dimitrova, A.D., E.D. Ananiev, and K.I. Gecheff. 2009. Dnase I Hypersensitive Sites within

the Intergenic Spacer of Ribosomal Rna Genes in Reconstructed Barley Karyotypes. Biotechnol Biotec Eq 23, 1039-1043.

Sepsi, A. and J. Bucsi. 2009. Physical Mapping of the 7d Chromosome Using a Wheat/Barley

Translocation Line (5hs.7dl) Produced in a Martonvasari Wheat Background Using Microsatellite Markers. Cereal Res Commun 37, 297-300.


34

Coordinator´s Report: Disease and Pest resistance genes

Tina Lange and Frank Ordon

Julius Kühn-Institute (JKI)

Institute for Resistance Research and Stress Tolerance Erwin-Baur-Strasse 27

DE-06484 Quedlinburg, Germany

e-mail:

[email protected]

In the table below you will find papers published in 2010 extending last year´s list of information available on molecular markers for major resistance genes in barley published in Barley. Genet. Newsl. 39. List of papers on mapped major resistance genes in barley in 2010. Resistance gene

Chromsomal location

Reference(s)

Powdery mildew (Blumeria graminis) Mlo 4HL Reinstaedler et al. 2010

Mla 1HS Repkova & Dreiseitl 2010, Teturova et al. 2010, Sedlacek & Stemberkova 2010

N.N. 2HS Repkova & Dreiseitl 2010

Puccinia graminis

Rpg1 7HS Drader & Kleinhofs 2010

rpg4 5HL Drader & Kleinhofs 2010

Rpg5 5HL Drader & Kleinhofs 2010

Puccinia hordei

Rph7 3HS Sedlacek & Stemberkova 2010

Cochliobolus sativus

Rcs5 7HS Drader & Kleinhofs 2010, Bovill et al. 2010

Septoria passerinii

Rsp4 6H Pierre et al. 2010

Pyrenophora graminea

Rdg1 2HL Biselli et al. 2010


35

Rdg2 7HS Bulgarelli et al. 2010

References: Biselli, C., S. Urso, L. Bernardo, A. Tondelli, G. Tacconi, V. Martino, S. Grando, and G.

Vale. 2010. Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum. Theor Appl Genet 120: 1207-1218.

Bovill, J., A. Lehmensiek, M.W. Sutherland, G.J. Platz, T. Usher, J. Franckowiak, and E.

Mace. 2010. Mapping spot blotch resistance genes in four barley populations. Mol Breeding 26:653-666.

Bulgarelli, D., C. Biselli, N.C. Collins, G. Consonni, A.M. Stanca, P. Schulze-Lefert, and G.

Vale. 2010. The CC-NB-LRR-type Rdg2a resistance gene confers immunity to the seed borne leaf stripe pathogen in the absence of hypersensitive cell death. PLOS ONE 5: DOI: 10.1371/journal.pone.0012599.

Drader, T. and A. Kleinhofs. 2010. A synteny map and disease resistance gene comparison

between barley and the model monocot Brachypodium distachyon. Genome 53: 406-417. Pierre, S.S., C. Gustus, B. Steffenson, R. Dill-Macky, and K.P. Smith. 2010. Mapping net

form of net blotch and septoria speckled leaf blotch resistance loci in barley. Phytopathology 100: 80-84.

Reinstaedler, A. J. Mueller, J.H. Czembor, P. Piffanelli, and R. Panstruga.R. 2010. Novel

induced mlo mutant alleles in combination with site-directed mutagenesis reveal functionally important domains in the heptahelical barley Mlo protein. BMC Plant Biology 10: 31.

Repkova, J. and A. Dreiseitl. 2010. Candidate markers for powdery mildew resistance genes

from wild barley PI284752. Euphytica 175:283-292. Sedlacek, T. and L. Stemberkova. 2010. Development of a molecular marker for simultaneous

selection of Rph7 gene and effective Mla alleles in barley. Cereal Research Comm 38: 75-183. Teturova, K., J. Repkova, P. Lizal, and A. Dreiseitl. 2010. Mapping of powdery mildew

resistance genes in a newly determined accession of Hordeum vulgare ssp. spontaneum. Annals of Applied Biology 156: 157-165.


36

Coordinator’s report: Eceriferum genes

Udda Lundqvist

Nordic Genetic Resource Center (Nordgen)

P.O. Box 41, SE-230 53 Alnarp, Sweden


No research work on gene localization has been reported on Eceriferum and Glossy genes. All descriptions in Barley Genetics Newsletter (BGN) Volume 26 and later issues are valid and up-to-date. They are also available in the International Database for Barley Genes and Barley Genetic Stocks, the Untamo database www.untamo.net/bgs.They can also be searched through the Triticeaea database GrainGenes. Several BGS descriptions are on the way to be revised and updated and will be published in this issue of Barley Genet. Newsletter. All the genes have been backcrossed to a common genetic background, the cultivar Bowman, by J.D. Franckowiak, Australia, and are available as Near Isogenic Lines (NIL). Many of them are increased during summer 2010 for incorporation into the Nordic Genetic Resource Center (Nordgen), Sweden. These lines are extraordinary valuable for gene mapping, valuable molecular genetical analyses of cloned mutant genes, Single Nucleotide Polymorphism (SNP) genotyping and provides a detailed understanding of the genetic composition of the barley genome (Druka et al., 2010). All Near Isogenic Lines will be incorporated in early 2011 into the Nordic Genetic Resource Center (Nordgen) and are available for every research in barley. Every research of interest in this field and literature references are very useful to report to the coordinator as well. Seed requests of the original Swedish material can be forwarded to the coordinator [email protected] or to the Nordic Genetic Resource Center (Nordgen) www.nordgen.org . All original Glossy genes can be requested to the Small Grain Germplasm Research Facility (USDA)–ARS), Aberdeen, ID 83210, USA, [email protected] or to the coordinator at any time. Reference: Druka, A., J. Franckowiak, U. Lundqvist, N. Bonar, J. Alexander, K. Houston, S. Radovic,

F. Shahinnia, V. Vendramin, M. Morgante, N. Stein, and R. Waugh. 2010. Genetic Dissection of barley morphology and development. Plant Physiology. Epubl. 2010 November 18, 2010 as DOI:10.1104/pp110.166249.


http://www.untamo.net/bgs.They�


http://www.nordgen.org/�



37

Coordinator’s report: Nuclear genes affecting the chloroplast

Mats Hansson

Carlsberg Laboratory,

Gamle Carlsberg Vej 10, DK-2500 Valby,

Copenhagen, Denmark

e-mail:

[email protected]

Barley mutants deficient in chlorophyll biosynthesis and chloroplast development display a wide palette of white, yellow and green colours, which are easily observed at an early stage of plant development. Most often the seedling leaves are homogenously coloured, such in the case of albina, chlorina, viridis and xantha mutants. However, in the tigrina mutants the leaves are transversely striped, while striata mutants are stripped along the leaves. Most of the mutants were induced by irradiation or chemical treatment fifty years ago (Lundqvist 1992). Still they are regularly used in various investigations. Campoli et al. (2009) explored the white mutants albina-e.16 and albina-f.17, and the yellow mutants xantha-b.12 and xantha-s.46 in order to provide an overall transcriptional picture of genes which expression is interconnected with chloroplast activities. The analyses provide additional evidences on a chloroplast-dependent co-variation of large sets of nuclear genes. The barley tigrina-d.12 mutant accumulates the chlorophyll biosynthetic intermediate protochlorophyllide in the dark due to a relaxed synthesis of the precursor 5-aminolevulinic acid. Upon illumination, protochlorophyllide operates as photosensitizer and triggers singlet oxygen production and cell death. It was shown that both protochlorophyllide and singlet oxygen operate as signals that control gene expression and metabolite accumulation in tigrina-d.12 plants (Khandal et al. 2009). Together, the results identify translation as a major target of singlet oxygen-dependent growth control and cell death in higher plants. The light green viable chlorina seedling-fch2 mutant of barley specifically exhibits reduced levels of the major light-harvesting polypeptides associated with photosystem II. Therefore, the chlorina seedling-fch2 mutant has been used extensively to investigate this photosystem. Krol et al. (2009) showed that the absence of the major light-harvesting polypeptides affects the redox properties of photosystem II reaction centers, and that the chlorina-fch2 mutation has a significant pleiotropic affect on the structure and function of photosystem II. The stock list of barley mutants defective in chlorophyll biosynthesis and chloroplast development is to be found in Barley Genet. Newsl.37:37-43. Soon it can also be found at

bhttp://www.carlsberglab.dk/scientists/ Hansson/ Lundqvist, U. 1992. Mutation research in barley. PhD Thesis. The Swedish University of Agricultural Sciences. Svalöv. Available from


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http://www.mps.lu.se/fileadmin/mps/People/Hansson/Uddas_thesis.pdf http://www.nordgen,org/ngdoc/plants/uddas_ New references: Campoli, C., S. Caffarri, J. T. Svensson, R. Bassi, A. M. Stanca, L. Cattivelli, and C.

Crosatti. 2009. Parallel pigment and transcriptomic analysis of four barley albina and xantha mutants reveals the complex network of the chloroplast-dependent metabolism. Plant Mol. Biol. 71: 173-191.

Khandal, D., I. Samol, F. Buhr, S. Pollmann, H. Schmidt, S. Clemens, S. Reinbothe, and C.

Reinbothe. 2009. Singlet oxygen-dependent translational control in the tigrina-d.12 mutant of barley. Proc. Natl. Acad. Sci. USA 106: 13112-13117.

Krol, M., A. G. Ivanov, I. Booij-James, A. K. Mattoo, P. V. Sane, and N. P. Hüner. 2009.

Absence of the major light-harvesting antenna proteins alters the redox properties of photosystem II reaction centres in the chlorine F2 mutants of barley. Biochem. Cell Biol. 87: 557-566.

http://www.mps.lu.se/fileadmin/mps/People/Hansson/Uddas_thesis.pdf�

http://www.nordgen,org/ngdoc/plants/uddas�


39

Coordinator’s report: ear morphology genes.

Michele Stanca

Faculty of Agricultural Science, UNIMORE-Reggio Emilia, Italy


and

Valeria Terzi

CRA-GPG, Genomics Research Centre, Via Protaso 302,

IT-29017 Fiorenzuola d’Arda, Italy

e-mail:

[email protected]

The six rowed spike is a recessive character, conditionated by a major gene at the vrs1 locus on the long arm of chromosome 2H, that has been isolated by means of positional cloning by Komatsuda et al. (2007) and identified as a homeobox gene. The wild type Vrs1 gene, present in two-rowed barley, encodes a transcription factor that includes a homeodomain-leucine zipper I (HD-ZipI) sequence (HvHoxI). VRS1 protein suppresses lateral rows and gives two-rowed spike, whereas a mutation in the homeodomain-leucine zipper of Vrs1 resulted into loss of function and development of six-rowed phenotype, in which all three lateral spikelets are fertile. The full development of lateral spikelets needs the additional action of the intermedium (I) gene, that is responsible for the increase of the size of lateral spikelets. In the work of Shahinnia et al. (2009) the genotyping of near-isogenic lines for I placed the locus on chromosome 4H, proximal to CB873567 marker. However, the morphology of the barley spike can be quite diverse and, in addition to the two-rowed or six-rowed spikes, more subtle variants have been described. In the work of Saisho et al. (2009) these variants have been correlated with sequence polymorphisms at the DNA and peptide levels. To find association between Vrs1-related spike traits and VRS1 variants, the following phenotypes have been evaluated:

• 13 six rowed barley accessions with both “awnletted” and “awnless” spikelets; • 14 accessions characterized by labile or irregular spike, with a variable number of fertile

spikelets at each rachis node; • 10 accessions of deficiens type, in which all lateral spikelets are rudimentary; • wild barley accessions with proskowetzii spike, pointed-awn or short-awned lateral

spikelets Moreover, the correspondence between peptide sequence and spike variants was studied by re-sequencing the HvHox1 sequence in a large sample of wild and domesticated accessions. The sequence diversification discovered might imply the functional diversification of this locus, whose alleles may have a number of pleiotropic effects in domesticated barley and may have a role in ecological adaptation of wild barley.



40

Micro-colinearity between rice and barley is disrupted in the Vrs1 region and this gene is unique to the barley tribe (Sakuma et al., 2010). As demonstrated by phylogenetic analysis, Vrs1 arose following the duplication of HvHox2 after the separation of Brachypodium distachyon from the Poideae and acquired its new function during the evolution of barley tribe (Sakuma et al., 2010). The extent of co-linearity between rice chromosome 4 and barley chromosome 2H in the region surrounding cly1 gene has been studied by Turuspekov et al. (2009). Cleistogamy in barley is in fact controlled either by the single, multiallelic gene cly1 or by the two closely linked and epistatic genes cly1 and Cly2. Cly1 locus was located in a high resolution map, however the results obtained cannot still confirm or refute the one gene hypothesis. References: Pourkheirandish, M. and T. Komatsuda. 2007. The importance of barley genetics and

domestication in a global perspective. Annals of Botany, 104: 1424-1429. Sakuma, S., M. Pourkheirandish, T. Matsumoto, T. Koba, and T. Komatsuda. 2010.

Uplication of a well-conserved homeodomain-leucine zipper transcription factor gene in barley generates a copy with more specific functions. Func. Integr. Genomics, 10:123-133.

Saisho, D., M. Pourkheirandish, H. Kanamori, T. Matsumoto, and T. Komatsuda. 2009.

Allelic variation of row type gene Vrs1 in barley and implication of the functional divergence. Breeding Science 59: 621-628.

Shahinnia, F., B.E. Sayed-Tabatabaei, K. Sato, M. Pourkheirandish, and T. Komatsuda.

2009. Mapping of QTL for intermedium spike on barley chromosome 4H using EST-based markers. Breeding Science 59: 383-390.

Turuspekov, Y., I. Honda, Y. Watanabe, N. Stein, and T. Komatsuda. 2009. An inverted and

micro-colinear genomic regions of rice and barley carrying the cly1 gene for cleistogamy. Breeding Science, 59: 657-663.


41

Coordinator’s report: Semidwarf genes

J. D, Franckowiak

Hermitage Research Station

Agri-Science Queensland Department of Employment, Economic Development and Innovation

Warwick, Queensland 4370, Australia

e-mail: [email protected] Fine mapping of the gene controlling a gibberellin-insensitive, semidwarf mutant, sdw3, was attempted by Vu et al. (2010). The sdw3 gene was mapped to a 0.04 cM region of 2HS near the centromere, likely in 2H bin 07. Orthologous regions in rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium sylvaticum were examined and four candidate genes for sdw3 were identified based on analysis of barley BAC sequences. Ren et al. (2010) identified and mapped a new dwarfing gene in chromosome 7H. The spontaneous mutant was isolated from the Chinese landrace Daofu Bai Qing Ke in Daofu county, Sichuan and identified as Huaai 11. The mutant was reported to be about 40 cm tall while Daofu Bai Qing Ke was about 119 cm. Huaai 11 headed 7 days earlier than Zaoshu 3, an early maturing Chinese cultivar. For inheritance studies, plants shorter than 60 cm were classified as mutants. Segregation ratios confirmed a simple recessive inheritance pattern. Allelism tests were conducted using Chinese cultivars having semi-dwarfing genes (sdw1, sdw4, and uzu1) and the results were negative. A doubled haploid population and SSR markers were used to construct a map for the dwarfing gene in Huaai 11. The mutant gene, named btwd1, was mapped in the long arm of chromosome 7H near the centromere, 2.2 cM distal from SSR marker Bmac167 (Ren et al., 2010), likely in 7H bin 07. No other genes with strong dwarfing effects or short-day photoperiod responses have been mapped to this region of 7HL. Yu et al. (2010) studied a single seed descent population in both long- and short-day environments and found seven QTL for plant height. In this cross between a Chinese cultivar, Zhenogda 7, and a North Dakota cultivar, a QTL on 7HL was observed in all environments. Other plant height QTL were associated with photoperiod responses, Eam1 (PpdH1) and Eam5, or not consistently expressed over environments. This is a second paper on identification of a new semidwarf (sdw) gene located in 7HL. The origin of the sdw gene studied by Yu et al. (2010) was a Chinese cultivar, which has the semidwarf cultivar Zhepi 1 in its parentage. The other 7HL semidwarf gene studied by Sameri et al. (2009) is from the Japanese cultivar, Kanto Nakate Gold (OUJ518). Both mutant genes mapped same region of 7H, nearly DArT marker bPb-2328 in bin 11 and had similar phenotypic effects on plant height (Yu et al., 2010). Since a common or independent origins of the mutants could not be determined, only one locus symbol, sdw4, and only one allele symbol sdw4.ba are suggested.



42

References: Ren, X., D. Sun W. Guan, G. Sun, and C. Li. 2010. Inheritance and identification of molecular

markers associated with a novel dwarfing gene in barley. BMC Genetics 2010 11:89. doi: 1186/1471-2156-11-89. http://www.biomedcentral.com/1471-2156/11/89.

Sameri, M., S. Nakamura, S. Nair, K. Takeda, and T. Komatsuda. 2009. A quantitative trait

locus for reduced culm internode length in barley segregates as a Mendelian gene. Theor. Appl. Genet. 118:643-652.

Vu, G.T.H., T. Wicker, J.P. Buchmann, P.M. Chandler, T. Matsumoto, A. Graner, and N.

Stein. 2010. Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Funct. Integr. Genomics 10:509-521.

Yu, G.T., R.D. Horsley, B. Zhang, and J.D. Franckowiak. 2010. A new semi-dwarfing gene

identified by molecular mapping of quantitative trait loci in barley. Theor. Appl. Genet. 120:853-861.

http://www.biomedcentral.com/1471-2156/11/89�


43

Coordinator’s report: Early maturity and

Praematurum genes

Udda Lundqvist

Nordic Genetic Resource Center (Nordgen) P-O. Box 41

SE-23 053 Alnarp, Sweden

e-mail:

[email protected]

Not much research work on gene localization has been reported on the Early maturity or Praematurum genes. All descriptions in Barley Genetics Newsletter (BGN) Volume 26 and later issues are valid and still up-to-date. They are also available in the International Database for Barley Genes and Barley Genetic Stocks, the Untamo database www.untamo.net/bgs . They can also be searched through the Triticeae database GrainGenes. All Early maturity and Praematurum genes have been backcrossed to a common genetic background, the cultivar Bowman, by J.D. Franckowiak, Australia and are available as Near Isogenic Lines (NIL). All of them have been increased during summer 2009 for incorporation into the Nordic Genetic Resource Center (Nordgen), Sweden. These lines are extraordinary valuable for gene mapping, valuable molecular genetical analyses of cloned mutant genes, Single Nucleotide Polymorphism (SNP) genotyping and provides a detailed understanding of the genetic composition of the barley genome (Druka et al., 2010). There is made a decision to incorporate all Near Isogenic Lines into the Nordic Genetic Resource Center (Nordgen), Sweden. It is also planned to get the Nordic Genetic Resource Center as an International Barley Center for barley stocks for distribution world-wide. Every research of interest in this field and literature references are very useful to report to the coordinator as well. Seed requests regarding the Swedish mutant alleles and the Near Isogenic lines in Bowman can be forwarded to the coordinator [email protected] or directly to the Nordic Genetic Resource Center (Nordgen), www.nordgen.org/ngb, all other original stocks can be requested to the Small Grain Germplasm Research Facility (USDA-ARS), Aberdeen, ID 83210, USA, [email protected] or to the coordinator at any time. Reference: Druka, A., J. Franckowiak, U. Lundqvist, N. Bonar, J. Alexander, K. Houston, S. Radovic,

F. Shahinnia, V. Vendramin, M. Morgante, N. Stein, and R. Waugh. 2010, Genetic Dissection of barley morphology and development. Plant Physiology. Epubl. 2010 November 18, 2010 as DOI:10.1104/pp110.166249.

http://www.untamo.net/bgs�




44

Coordinator’s report: Wheat-barley genetic stocks

A.K.M.R. Islam

Faculty of Agriculture, Food & Wine,

The University of Adelaide, Waite Campus,

Glen Osmond, SA 5064, Australia

e-mail:

[email protected]

The production of six different disomic addition lines (IHm, 2Hm, 4Hm, 5Hm, 6Hm and 7Hm) of Hordeum marinum chromosomes to Chinese Spring wheat has been reported earlier. It has now been possible to isolate the remaining 3Hm disomic addition line in a commercial wheat background (Westonia). Since the H. marinum-wheat amphiploids are all in H. marinum cytoplasm, they suffer some loss in fertility due to the interaction of H. marinum cytoplasm with the wheat genome. Attempts are now being made to improve fertility of some selected amphiploids by transferring their cytoplasm back to wheat. (Islam and Colmer, unpublished). Reference: Malik, AI Imran, AKMR. Islam, and T.D. Colmer. 2010. Transfer of the barrier to radial

oxygen loss in roots of Hordeum marinum to wheat (Triticum aestivum): evaluation of four H. marinum-wheat amphiploids. New Phytologist (in press).

overall coordinator’s reportwheat.pw.usda.gov/ggpages/bgn/40/coordinators.pdfbarley genetics...

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