The International Barley Sequencing Consortium - At the threshold of efficient access to the barley genome

Plant Physiology

Volumn 149, Issue 1, 2009, Pages 142-147

  Schulte, Daniela ^a   Close, Timothy J ^b   Graner, Andreas ^a   Langridge, Peter ^c   Matsumoto, Takashi ^d   Muehlbauer, Gary ^e   Sato, Kazuhiro ^f   Schulman, Alan H ^g   Waugh, Robbie ^h   Wise, Roger P ⁱ   Stein, Nils ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF ADELAIDE   (Australia)

^d NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^e UNIVERSITY OF MINNESOTA   (United States)

^f OKAYAMA UNIVERSITY   (Japan)

^g UNIVERSITY OF HELSINKI   (Finland)

^h SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

ⁱ IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HORDEUM;

EID: 58449113638     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.108.128967     Document Type: Review

References (48)

1. Baik BK, Ullrich SE (2008) Barley for food: characteristics, improvement, and renewed interest. J Cereal Sci 48: 233-242
2. Beales J, Turner A, Griffiths S, Snape J, Laurie D (2007) A pseudoresponse regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115: 721-733
3. Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci 274: 227-274
4. Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R (2004) A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.). Plant J 40: 143-150
5. Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134: 960-968
6. Cockram J, Jones H, Leigh FJ, O'Sullivan D, Powell W, Laurie DA, Greenland AJ (2007) Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity. J Exp Bot 58: 1231-1244
7. Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H, et al (2002) Access to the maize genome: an integrated physical and genetic map. Plant Physiol 128: 9-12
8. Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, Routledge APM (2001) Brachypodium distachyon: a new model system for functional genomics in grasses. Plant Physiol 127: 1539-1555
9. Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, et al (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics 6: 202-211
10. Fu D, Szucombining double acute accentcs P, Yan L, Helguera M, Skinner JS, von Zitzewitz J, Hayes PM, Dubcovsky J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Genet Genomics 273: 54-65
11. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154: 15-28
12. Grando S, Macpherson HG, editors (2005) Food Barley: Importance, Uses and Local Knowledge. ICARDA, Aleppo, Syria
13. Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83: 250-256
14. Gubatz S, Dercksen VJ, Brüß C, Weschke W, Wobus U (2007) Analysis of barley (Hordeum vulgare) grain development using three-dimensional digital models. Plant J 52: 779-790
15. Jones JDG, Dangl JL (2006) The plant immune system. Nature 444: 323-329
16. Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, et al (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104: 1424-1429
17. Lander ES, Waterman MS (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2: 231-239
18. Liu SC, Kowalski SP, Lan TH, Feldmann IA, Paterson AH (1996) Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics 142: 247-258
19. Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389
20. Madishetty K, Condamine P, Svensson JT, Rodriguez E, Close TJ (2007) An improved method to identify BAC clones using pooled overgos. Nucleic Acids Res 35: e5
21. Müller K, Romano N, Gerstner O, Garcia-Maroto F, Pozzi C, Salamini F, Rohde W (1995) The barley Hooded mutation caused by a duplication in a homeobox gene intron. Nature 374: 727-730
22. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, et al (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103: 18656-18661
23. Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C (2008) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20: 11-24
24. Sasaki T, Burr B (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3: 138-141
25. Schulze-Lefert P, Panstruga R (2003) Establishment of biotrophy by parasitic fungi and reprogramming of host cells for disease resistance. Annu Rev Phytopathol 41: 641-667
26. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145
27. Smith LG, Greene B, Veit B, Hake S (1992) A dominant mutation in the maize homeobox gene, Knotted-1, causes its ectopic expression in leaf cells with altered fates. Development 116: 21-30
28. Sreenivasulu N, Graner A, Wobus U (2008a) Barley genomics: an overview. Int J Plant Genomics 2008: 486258
29. Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, et al (2008b) Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol 146: 1738-1758
30. Stein N (2007) Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res 15: 21-31
31. Stein N, Graner A (2004) Map-based gene isolation in cereal genomes. In P Gupta, RVarshney, eds, Cereal Genomics. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 331-360
32. Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Graner A (2007) A 1000 loci transcript map of the barley genome - new anchoring points for integrative grass genomics. Theor Appl Genet 114: 823-839
33. Taketa S, Amano S, Tsujino Y, Sato T, Saisho D, Kakeda K, Nomura M, Suzuki T, Matsumoto T, Sato K, et al (2008) Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proc Natl Acad Sci USA 105: 4062-4067
34. Talame V, Bovina R, Sanguineti MC, Tuberosa R, Lundqvist U, Salvi S (2008) TILLMore, a resource for the discovery of chemically induced mutants in barley. Plant Biotechnol J 6: 477-485
35. Thangavelu M, James AB, Bankier A, Bryan GJ, Dear PH, Waugh R (2003) HAPPY mapping in a plant genome: reconstruction and analysis of a high-resolution physical map of a 1.9 Mbp region of Arabidopsis thaliana chromosome 4. Plant Biotechnol J 1: 23-31
36. The French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
37. Turner A, Beales J, Faure S, Dunford R, Laurie D (2005) The pseudoresponse regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310: 1031-1034
38. van Hintum T, Menting F (2003) Diversity in ex situ genebank collections of barley. In R von Bothmer, T van Hintum, H Knüpffer, K Sato, eds, Diversity in Barley (Hordeum vulgare). Elsevier Science B.V., Amsterdam, pp 247-257
39. Wendl MC, Waterston RH (2002) Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing. Genome Res 12: 1943-1949
40. Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, et al (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7: 206
41. Wicker T, Narechania A, Sabot F, Stein J, Vu GTH, Graner A, Ware D, Stein N (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9: 518
42. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982
43. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7: 275
44. Wise R, Caldo R, Hong L, Shen L, Cannon E, Dickerson J (2007) BarleyBase/PLEXdb: A unified expression profiling database for plants and plant pathogens. In D Edwards, ed, Methods in Molecular Biology, Plant Bioinformatics - Methods and Protocols, Vol 406. Humana Press, Totowa, NJ, pp 347-363
45. Yim YS, Moak P, Sanchez-Villeda H, Musket TA, Close P, Klein PE, Mullet JE, McMullen MD, Fang Z, Schaeffer ML, et al (2007) A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8: 47
46. Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101: 1093-1099
47. Zhang H, Sreenivasulu N, Weschke W, Stein N, Rudd S, Radchuk V, Potokina E, Scholz U, Schweizer P, Zierold U, et al (2004) Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J 40: 276-290
48. Zohary D, Hopf M (2001) Domestication of Plants in the Old World, Ed 3. Oxford University Press, Oxford, UK, pp 1-12