Application of Genomics to Molecular Breeding of Wheat and Barley

Advances in Genetics

Volumn 58, Issue , 2007, Pages 121-155

  Varshney, Rajeev K ^a   Langridge, Peter ^b   Graner, Andreas ^c  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c Institute of Plant Genetics and Crop Plant Research (IPK)   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; BARLEY; CHROMOSOME MAP; CROSS BREEDING; DNA SHUFFLING; GENE EXPRESSION PROFILING; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; GENOME; GENOMICS; METHODOLOGY; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; REVIEW; WHEAT;

ALLELES; CHROMOSOME MAPPING; CROSSES, GENETIC; DNA SHUFFLING; GENE EXPRESSION PROFILING; GENETIC MARKERS; GENOME, PLANT; GENOMICS; HORDEUM; LINKAGE DISEQUILIBRIUM; QUANTITATIVE TRAIT LOCI; TRITICUM; VARIATION (GENETICS);

EID: 34247332723     PISSN: 00652660     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2660(06)58005-8     Document Type: Review

References (195)

1. Aharoni A., and Vorst O. DNA microarrays for functional plant genomics. Plant Mol. Biol. 48 (2002) 99-118
2. Ahn S., Anderson J.A., Sorrells M.E., and Tanksley S.D. Homeologous relationships of rice, wheat and maize chromosomes. Mol. Gen. Genet. 241 (1993) 483-490
3. Andersen J.R., and Lubberstedt T. Functional markers in plants. Trends Plant Sci. 8 (2003) 554-560
4. Angerer N., Lengauer D., Steiner B., Lafferty J., Loeschenberger F., and Buerstmayr H. Validation of molecular markers linked to two Fusarium head blight resistance QTLs in wheat. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 1096-1098
5. Ayala L., Henry M., Gonzalez-de-Leon D., Van Ginkel M., Mujeeb-Kazi A., Keller B., and Khairallah M. A diagnostic molecular marker allowing the study of Th intermedium-derived resistance to BYDV in bread wheat segregating populations. Theor. Appl. Genet. 102 (2001) 942-949
6. Ayoub M., Armstrong E., Bridger G., Fortin M.G., and Mather D.E. Marker-based selection in barley for a QTL region affecting alpha-amylase activity of malt. Crop Sci. 43 (2003) 556-561
7. Blazkova V., Bartos P., Park R.F., and Goyeau H. Verifying the presence of leaf rust resistance gene Lr10 in sixteen wheat cultivars by use of a PCR-based STS marker. Cereal Res. Commun. 30 (2002) 9-16
8. Bonierbale M.W., Plaisted R.L., and Tanksley S.D. RFLP maps based on a common set of clones reveal modes of chromosomal evolution of potato and tomato. Genetics 120 (1988) 1095-1103
9. Borevitz J.O., Liang D., Plouffe D., Chang H.S., Zhu T., Weige D., Berry C.C., Winzeler E., and Chory J. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res. 13 (2003) 513-523
10. Börner A., Korzun V., and Worland A.J. Comparative genetic mapping of loci affecting plant height and development in cereals. Euphytica 100 (1998) 245-248
11. Botha A.M., Lacock L., Van Niekerk C., Matsioloko M.T., du Preez F.B., Myburg A.A., Kunert K., and Cullis C.A. Gene expression profiling during Diuraphis noxia infestation of Triticum aestivum cv 'Tugela DN' using microarrays. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 334-338
12. Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D.H., Johnson D., Luo S., McCurdy S., Foy M., Ewan M., Roth R., George D., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18 (2000) 630-634
13. Breseghello F., and Sorrells M.E. Association mapping of kernel size and milling quality in wheat. Genetics 172 (2005) 1165-1177
14. Brett D., Pospisil H., Valcarcel J., Reich J., and Bork P. Alternative splicing and genome complexity. Nat. Genet. 30 (2002) 29-30
15. Buckler E.S., and Thornsberry J.M. Plant molecular diversity and applications to genomics. Curr. Opin. Plant Biol. 5 (2002) 107-111
16. Cakir M., Appels R., Carter M., Loughman R., Francki M., Li C., Johnson J., Bhave M., Wilson R., McLean R., and Barclay Y. Accelerated wheat breeding using molecular marker. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 117-120
17. Carter M., Drake B.F., Cakir M., Jones M., and Appels R. Conversion of RFLP markers into PCR based markers in wheat. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 81-683
18. Close T., Wanamaker S.I., Caldo R.A., Turner S.M., Ashlock D.A., Dickerson J.A., Wing R.A., Muehlbauer G.J., Kleinhofs A., and Wise R.P. A new resource for cereal genomics: 22k barley genechip comes of age. Plant Physiol. 134 (2004) 960-968
19. Cui X., Xu J., Asghar R., Condamine P., Svensson J.T., Wanamaker S., Stein N., Roose M., and Close T.J. Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. Bioinformatics 21 (2005) 3852-3858
20. Czechowski T., Bari R.P., Stitt M., Scheible W.R., and Udvardi M.K. Real-time RT PCR profiling of over 1400 Arabidopsis transcription factor genes: Unprecedented sensitivity reveal novel root- and shoot-specific genes. Plant J. 38 (2004) 366-379
21. Desprez T., Amselem J., Caboche M., and Hofte H. Differential gene expression in Arabidopsis monitored using cDNA arrays. Plant J. 14 (1998) 643-652
22. Devos K.M. Updating the 'crop circle.'. Curr. Opin. Plant Biol. 8 (2005) 155-162
23. Devos K.M., and Gale M.D. Extended genetic maps of the homoeologous group-3 chromosomes of wheat, rye and barley. Theor. Appl. Genet. 85 (1993) 649-652
24. Devos K.M., and Gale M.D. Comparative genetics in the grasses. Plant Mol. Biol. 35 (1997) 3-15
25. Devos K.M., and Gale M.D. Genome relationships: The grass model in current research. Plant Cell 12 (2000) 637-646
26. Devos K.M., Atkinson M.D., Chinoy C.N., Liu C.J., and Gale M.D. RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye. Theor. Appl. Genet. 83 (1992) 931-939
27. Devos K.M., Atkinson M.D., Chinoy C.N., Francis H.A., Harcourt R.L., Koebner R.M.D., Liu C.J., Masojć P., Xie D.X., and Gale M.D. Chromosomal rearrangement in the rye genome relative to that of wheat. Theor. Appl. Genet. 85 (1993) 673-680
28. Devos K.M., Millan T., and Gale M.D. Comparative RFLP maps of the homoeologous group-2 chromosomes of wheat, rye and barley. Theor. Appl. Genet. 85 (1993) 784-792
29. Devos K.M., Chao S., Li Y., Simonetti M.C., and Gale M.D. Relationship between chromosome 9 of maize and wheat homoeologous group 7 chromosomes. Genetics 138 (1994) 1287-1292
30. Distelfeld A., Uauy C., Olmos S., Schlatter A.R., Dubcovsky J., and Fahima T. Microcolinearity between a 2 cM region encompassing the grain protein content locus Gpc-6B1 on wheat chromosome 6B and a 350 kb region on rice chromosome 2. Funct. Integr. Genomics 4 (2004) 59-66
31. Dubcovsky J., Luo M.C., Zhong G.Y., Bransteitter R., Desai A., Kilian A., Kleinhofs A., and Dvorak J. Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 143 (1996) 983-999
32. Dunford R.P., Kurata N., Laurie D.A., Money T.A., Minobe Y., and Moore G. Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucleic Acids Res. 23 (1995) 2724-2728
33. Ellis M.H., Spielmeyer W., Gale K.R., Rebetzke G.J., and Richards R.A. "Perfect" markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor. Appl. Genet. 105 (2002) 1038-1042
34. Eujayl I., Sorrells M.E., Baum M., Wolters P., and Powell W. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor. Appl. Genet. 104 (2002) 399-407
35. Fischer G., Ibrahim S.M., Brockmann G.A., Pahnke J., Bartocci E., Thiesen H.J., Serrano-Fernandez P., and Möller S. Expression view: Visualization of quantitative trait loci and gene-expression data in Ensembl. Genome Biol. 4 (2003) R477
36. Flint-Garcia S.A., Thornsberry J.M., and Buckler IV E.S. Structure of linkage disequilbrium in plants. Annu. Rev. Plant Biol. 54 (2003) 357-374
37. Forster B.P., Ellis R.P., Thomas W.T., Newton A.C., Tuberosa R., This D., El-Enein R.A., Bahri M.H., and Ben Salem M. The development and application of molecular markers for abiotic stress tolerance in barley. J. Exp. Bot. 51 (2000) 19-27
38. Francki M.G., Appels R., Hunter A., and Bellgard M. Comparative organization of 3BS and 7AL using wheat-rice synteny. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 254-257
39. Friebe B., Gill K.S., Tuleen N.A., and Gill B.S. Transfer of wheat streak mosaic resistance from Agropyron intermedium into wheat. Crop Sci. 36 (1996) 857-861
40. Fulton T.M., van der Hoeven R., Eannetta N.T., and Tanksley S.D. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14 (2002) 1457-1467
41. Gallego F., Feuillet C., Messmer M., Penger A., Graner A., Yano M., Sasaki T., and Keller B. Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome 41 (1998) 328-336
42. Gao L.F., Jing R.L., Huo N.X., Li Y., Li X.P., Zhou R.H., Chang X.P., Tang J.F., Ma Z.W., and Jia J.Z. One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor. Appl. Genet. 108 (2004) 1392-1400
43. Grandillo S., and Tanksley S.D. Advanced backcross QTL analysis: Results and perspectives. In: Tuberosa R., Phillips R.L., and Gale M. (Eds). "In the Wake of Double Helix: From the Green Revolution to the Gene Revolution" (2005), Avenue Media, Bologna, Italy 115-132
44. Graner A., Thiel T., Zhang H., Potokina E., Prasad M., Perovic D., Kota R., Varshney R.K., Scholz U., Grosse I., and Stein N. Molecular mapping in barley: Shifting from the structural to the functional level. Czech J. Genet. Plant Breed. 41 (2005) 81-88
45. Gudu S., Laurie D.A., Kasha K.J., Xia J.J., and Snape J.W. RFLP mapping of a Hordeum bulbosum gene highly expressed in pistils and its relationship to homoeologous loci in other Gramineae species. Theor. Appl. Genet. 105 (2002) 271-276
46. Gupta P.K., and Varshney R.K. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113 (2000) 163-185
47. Gupta P.K., and Varshney R.K. Cereal genomics: An overview. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 1-18
48. Gupta P.K., Varshney R.K., Sharma P.C., and Ramesh B. Molecular markers and their applications in wheat breeding. Plant Breed. 118 (1999) 369-390
49. Gupta P.K., Balyan H.S., Edwards K.J., Isaac P., Korzun V., Röder M., Gautier M.F., Joudrier P., Schlatter A.R., Dubcovsky J., De la Pena R., Khairallah M., et al. Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor. Appl. Genet. 105 (2002) 413-422
50. Gupta P.K., Varshney R.K., and Prasad M. Molecular markers: Principles and methodology. In: Jain S.M., Brar D.S., and Ahloowalia B.S. (Eds). "Molecular Techniques in Crop Improvement" (2002), Kluwer Academic Publishers, Dordrecht, The Netherlands 9-54
51. Gupta P.K., Kulwal P., and Rustgi S. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Mol. Biol. 57 (2005) 461-485
52. Gur A., and Zamir D. Unused natural variation can lift yield barriers in plant breeding. PLoS Biol. 2 (2004) e245
53. Guyomarc'h H., Sourdille P., Edwards K.J., and Bernard M. Studies of the transferability of microsatellites derived from Triticum tauschii to hexaploid wheat and to diploid related species using amplification, hybridization and sequence comparisons. Theor. Appl. Genet. 105 (2002) 736-744
54. Guyot R., Yahiaoui N., Feuillet C., and Keller B. In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S. Funct. Integr. Genomics 4 (2004) 47-58
55. Han F., Romagosa I., Ullrich S.E., Jones B.L., Hayes P.M., and Wesenberg D.M. Molecular marker-assisted selection for malting quality traits in barley. Mol. Breed. 3 (1997) 427-437
56. Han F., Kleinhofs A., Ullrich S.E., Kilian A., Yano M., and Sasaki T. Synteny with rice: Analysis of barley malting quality QTLs and rpg4 chromosome regions. Genome 41 (1998) 373-380
57. Han F., Kilian A., Chen J.P., Kudrna D., Steffenson B., Yamamoto K., Matsumoto T., Sasaki T., and Kleinhofs A. Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region. Genome 42 (1999) 1071-1076
58. Hayes P.M., Corey A.E., Mundt C., Toojinda T., and Vivar H. Registration of 'Tango' barley. Crop Sci. 43 (2003) 729-731
59. Hayes P.M., Castro A., Marquez-Cedillo L., Corey A., Henson C., Jones B.L., Kling J., Mather D., Matus I., Rossi C., et al. Genetic diversity for quantitatively inherited agronomic and malting quality traits. In: von Bothmer R., Van Hintum Th., Knüpffer H., and Sato K. (Eds). "Diversity in Barley (Hordeum vulagre)" (2003), Elsevier Science B.V., Amsterdam, The Netherlands 201-226
60. Hernandez P., Dorado G., Prieto P., Gimenez M.J., Ramirez M.C., Laurie D.A., Snape J.W., and Martin A. A core genetic map of Hordeum chilense and comparisons with maps of barley (Hordeum vulgare) and wheat (Triticum aestivum). Theor. Appl. Genet. 102 (2001) 1259-1264
61. Hohmann U., Graner A., Endo T.R., Gill B.S., and Herrmann R.G. Comparison of wheat physical maps with barley linkage maps for group 7 chromosomes. Theor. Appl. Genet. 91 (1995) 618-626
62. Horak C.E., and Snyder M. Global analysis of gene expression in yeast. Funct. Integr. Genomics 2 (2002) 171-180
63. Huang X.Q., Cöster H., Ganal M.W., and Röder M.S. Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor. Appl. Genet. 106 (2003) 1379-1389
64. Huang X.Q., Cöster H., Kemp H., Ganal M.W., and Röder M.S. Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.). Theor. Appl. Genet. 109 (2004) 933-943
65. Jahoor A., Eriksen L., and Backes G. QTLs and genes for disease resistance in barley and wheat. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 199-252
66. Jansen R.C. Studying complex biological systems using multifactorial perturbation. Nat. Rev. Genet. 4 (2003) 145-151
67. Jansen R.C., and Nap J.P. Genetical genomics: The added value from segregation. Trends Genet. 17 (2001) 388-391
68. Jefferies S.P. Marker-assisted backcrossing for gene introgression in barley (Hordeum vulgare L.) (2000), University of Adelaide, Australia Ph.D. Thesis
69. Jefferies S.P., King B.J., Barr A.R., Warner P., Logue S.J., and Langridge P. Marker-assisted backcross introgression of the yd2 gene conferring resistance to barley yellow dwarf virus in barley. Plant Breed. 122 (2003) 52-56
70. Johnson J.M., Castle J., Garrett-Engele P., Kan Z., Loerch P.M., Armour C.D., Santos R., Schadt E.E., Stoughton R., and Shoemaker D.D. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302 (2003) 2141-2144
71. Kato K., Miura H., and Sawada S. Comparative mapping of the wheat Vrn-A1 region with the rice Hd-6 region. Genome 42 (1999) 204-209
72. Kato K., Nakamura W., Tabiki T., Miura H., and Sawada S. Detection of loci controlling seed dormancy on group 4 chromosomes of wheat and comparative mapping with rice and barley genomes. Theor. Appl. Genet. 102 (2001) 980-985
73. Khlestkina E.K., Than M.H.M., Pestsova E.G., Röder M.S., Malyshev S.V., Korzun V., and Börner A. Mapping of 99 microsatellite loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theor. Appl. Genet. 109 (2004) 725-732
74. Kilian A., Kudrna D.A., Kleinhofs A., Yano M., Kurata N., Steffenson B., and Sasaki T. Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region. Nucleic Acids Res. 23 (1995) 2729-2733
75. Kilian A., Chen J., Han F., Steffenson B., and Kleinhofs A. Towards map-based cloning of the barley stem rust resistance genes Rpgl and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol. Biol. 35 (1997) 187-195
76. Koebner R.M.D., Powell W., and Donini R.M.D. Contributions of DNA molecular marker technologies to the genetics and breeding of wheat and barley. Plant Breed. Rev. 21 (2001) 181-220
77. Kota R., Varshney R.K., Thiel T., Dehmer K.J., and Graner A. Generation and comparison of EST-derived SSR and SNP markers in barley (Hordeum vulgare L.). Hereditas 135 (2001) 141-151
78. Kota R., Rudd S., Facius A., Kolesov G., Thiel T., Zhang H., Stein N., Mayer K., and Graner A. Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol. Gen. Genomics 270 (2003) 24-33
79. Kraakman A.T.W., Niks R.E., van den Berg P.M.M.M., Stam P., and van Eeuwijk F.A. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168 (2004) 435-446
80. Kuchel H., Wraner P., Fox R.L., Chalmers K., Howes N., Langridge P., and Jefferies S.P. Whole genome based marker assisted selection strategies in wheat breeding. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 144-147
81. Kuchel H., Fox G., Ye R., and Jefferies S. Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy. Mol. Breed. 16 (2005) 67-78
82. Kurata N., Moore G., Nagamura Y., Foote T., Yano M., Minobe Y., and Gale M. Conservation of genomic structure between rice and wheat. Bio/Technology 12 (1994) 276-278
83. La Rota C.M., and Sorrells M.E. Comparative DNA sequence analysis of mapped wheat ESTs reveals complexity of genome relationships between rice and wheat. Funct. Integr. Genomics 4 (2004) 34-46
84. Lagercrantz U. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150 (1998) 1217-1228
85. Lamoureux D., Boeuf C., Regad F., Garsmeur O., Charmet G., Sourdille P., Lagoda P., and Bernard M. Comparative mapping of the wheat 5B short chromosome arm distal region with rice, relative to a crossability locus. Theor. Appl. Genet. 105 (2002) 759-765
86. Langridge P. Molecular breeding of wheat and barley. In: Tuberosa R., Phillips R.L., and Gale M. (Eds). "In the Wake of Double Helix: From the Green Revolution to the Gene Revolution" (2005), Avenue Media, Bologna Italy 279-286
87. Langridge P., and Chalmers K. Techniques for marker development. In: Slinkard A.E. (Ed). "Proceedings of the Ninth International Wheat Genetics Symposium" Vol. 1 (1998), University Extension Press, University of Saskatchewan, Saskatoon, Canada 107-117
88. Langridge P., and Chalmers K. The principle: Identification and application of molecular markers. In: Lörz H., and Wenzel G. (Eds). "Biotechnology in Agriculture and Forestry, Vol 55, Molecular Markers Systems" (2004), Springer Verlag, Heidelberg, Germany 3-22
89. Langridge P., Lagudah E.S., Holton T.A., Appels R., Sharp P.J., and Chalmers K.J. Trends in genetic and genome analyses in wheat: A review. Aust. J. Agric. Res. 52 (2001) 1043-1077
90. Larkin J.E., Frank B.C., Gavras H., Sultana R., and Quackenbush J. Independence and reproducibility across microarray platforms. Nat. Methods 2 (2005) 337-343
91. Laubin B., Nicot N., Amiour N., Sourdille P., Branlard G., and Leroy P. In silico mapping and colinearity between the homoeologous group 5 of wheat and the rice genome. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 280-283
92. Lazo G.R., Chao S., Hummel D., Edwards H., Crosman C.C., Lui N., Matthews D.E., Carollo V.L., Hane D.L., You F.M., Butler G.E., Miller R.E., et al. Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000 locus bin-delineated map. Genetics 168 (2004) 585-593
93. Leader D.J., Cullup T., Ridley P., and van Dodeweerd A.M. Microarray analysis of wheat grain development: Applications to trait charcterization in the field. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 287-292
94. Li J.Z., Sjakste T.G., Röder M.S., and Ganal M.W. Development and genetic mapping of 127 new microsatellite markers in barley. Theor. Appl. Genet. 107 (2003) 1021-1027
95. Li J.Z., Huang X.Q., Heinrichs F., Ganal M.W., and Röder M.S. Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley. Theor. Appl. Genet. 110 (2005) 356-363
96. Li Z., Huang N., Rampling L., Wang J., Yu J., Morell M., and Rahman S. Detailed comparison between the wheat chromosome group 7 short arms and the rice chromosome arms 6S and 8L with special reference to genes involved in starch biosynthesis. Funct. Integr. Genomics 4 (2004) 231-240
97. Liu Z.W., Biyashev R.M., and Saghai-Maroof M.A. Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor. Appl. Genet. 93 (1996) 869-876
98. Liu J., Liu D., Tao W., Li W., Wang S., Chen P., Cheng S., and Gao D. Molecular marker-facilitated pyramiding of different genes for powdery mildew resistance in wheat. Plant Breed. 119 (2000) 21-24
99. Liu S.X., and Anderson J.A. Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. Genome 46 (2003) 817-823
100. Long A.D., and Langley C.H. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res. 9 (1999) 720-731
101. Maccaferri M., Sanguineti M., Noli E., and Tuberosa R. Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol. Breed. 15 (2005) 271-290
102. Mares D.J., and Mrva K. Mapping quantitative trait loci associated with variation in grain dormancy in Australian wheat. Aust. J. Agric. Res. 52 (2001) 1257-1265
103. Matsumura H., Reich S., Akiko I., Hiromasa S., Sophien K., Peter W., Günter K., Monika R., Detlev R., Krüger H., and Terauchi R. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc. Natl. Acad. Sci. USA 100 (2003) 15718-15723
104. Miklos G.L., and Maleszka R. Microarray reality checks in the context of a complex disease. Nat. Biotechnol. 22 (2004) 615-621
105. Milligan A.S., Lopato S., and Langridge P. Functional genomics studies of seed development in cereals. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 447-482
106. Moore G., Devos K.M., Wang Z., and Gale M.D. Cereal genome evolution-grasses, line up and form a circle. Curr. Biol. 5 (1995) 737-739
107. Moore G., Foote T., Helentjaris T., Devos K.M., Kurata N., and Gale M.D. Was there a single ancestral cereal chromosome?. Trends Genet. 11 (1995) 81-82
108. Morrell P.L., Toleno D.M., Lundy K.E., and Clegg M.T. Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. Spontaneum) despite high rates of self-fertilization. Proc. Natl. Acad. Sci. USA 102 (2005) 2442-2447
109. Namuth D.M., Lapitan N.L.V., Gill K.S., and Gill B.S. Comparative RFLP mapping of Hordeum vulgare and Triticum tauschii. Theor. Appl. Genet. 89 (1994) 865-872
110. Nicot N., Chiquet V., Gandon B., Amilhat L., Legeai F., Leroy P., Bernard M., and Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor. Appl. Genet. 109 (2004) 800-805
111. Nordborg M., Borevitz J.O., Bergelson J., Berry C.C., Chory J., Hagenblad J., Kreitman M., Maloof J.N., Noyes T., Oefner P.J., Stahl E.A., and Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30 (2002) 190-193
112. Ogihara Y., Mochida K., Nemoto Y., Murai K., Yamazaki Y., Shin-I T., and Kohara Y. Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses expressed sequence tags. Plant J. 33 (2003) 1001-1011
113. Palaisa K., Morgante M., Williams M., and Rafalski A. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15 (2003) 1795-1806
114. Pasquer F., Stein N., Isidore E., and Keller B. Microarray analysis of gene expression in wheat (Triticum aestivum) after fungicide application. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 1029-1031
115. Paterson A.H. Comparative genomics in cereals. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 119-134
116. Paull J.G., Pallotta M.A., and Langridge P. The RFLP markers associated with Sr22 and recombination between chromosome 7A of bread wheat and the diploid species Triticum boeoticum. Theor. Appl. Genet. 89 (1994) 1039-1045
117. Paull J.G., Chalmers K.J., Karakousis A., Kretschmer J.M., Manning S., and Langridge P. Genetic diversity in Australian wheat varieties and breeding material based on RFLP data. Theor. Appl. Genet. 96 (1998) 435-446
118. Pellio B., Streng S., Bauer E., Stein N., Perovic D., Schiemann A., Friedt W., Ordon F., and Graner A. High-resolution mapping of the Rym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2) in barley (Hordeum vulgare ssp. vulgare L.). Theor. Appl. Genet. 10 (2005) 283-293
119. Peng J.H., and Lapitan N.L.V. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct. Integr. Genomics 5 (2005) 80-96
120. Perovic D., Stein N., Zhang H., Drescher A., Prasad M., Kota R., Kopahnke D., and Graner A. An integrated approach for comparative mapping in rice and barley based on genomic resources reveals a large number of syntenic markers but no candidate gene for the Rph16 resistance locus. Funct. Integr. Genomics 4 (2004) 74-83
121. Pestsova E., Ganal M.W., and Röder M.S. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43 (2000) 689-697
122. Philips R.L., and Vasil I.K. "DNA-Based Markers in Plants." (2001), Kluwer Academic Publishers, The Netherlands
123. Pillen K., Binder A., Kreuzkam B., Ramsay L., Waugh R., Förster J., and Leon J. Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars. Theor. Appl. Genet. 101 (2000) 652-660
124. Pillen K., Zacharias A., and Léon J. Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor. Appl. Genet. 107 (2003) 340-352
125. Pillen K., Zacharias A., and Leon J. Comparative AB-QTL analysis in barley using a single exotic donor of Hordeum vulgare ssp spontaneum. Theor. Appl. Genet. 108 (2004) 1591-1601
126. Potokina E., Caspers M., Prasad M., Kota R., Zhang H., Sreenivasulu N., Wang M., and Graner A. Functional association between malting quality trait components and cDNA array based expression patterns in barley (Hordeum vulgare L.). Mol. Breed. 14 (2004) 153-170
127. Potokina E., Prasad M., Malysheva L., Röder M.S., and Graner A. Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.). Funct. Integr. Genomics 6 (2006) 25-35
128. Powell W., and Langridge P. Unfashionable crop species flourish in the 21st century. Genome Biol. 5, (2004) Art 233
129. Pritchard J.K., Stephens M., Rosenberg N.A., and Donnelly P. Association mapping in structured populations. Am. J. Hum. Genet. 67 (2000) 170-181
130. Pumphrey M.O., and Anderson J.A. QTL validation via systematic development of near-isogenic wheat lines from existing breeding populations. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 1227-1229
131. Qi L.-L., Echalier B., Chao S., Lazo G.R., Butler G.E., Anderson O.D., Akhunov E.D., Dvorak J., Linkiewicz A.M., Ratnasiri A., Dubcovsky J., Bermudez-Kandianis C.E., et al. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168 (2004) 701-712
132. Rafalski J.A. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5 (2002) 94-100
133. Rafalski A., and Morgante M. Corn and humans: Recombination and linkage disequilibrium in two genomes of similar size. Trends Genet. 20 (2004) 103-111
134. Ramsay L., Macaulay M., Ivanissevich D.S., MacLean K., Cardle L., Fuller J., Edwards K.J., Tuvesson S., Morgante M., Massari A., Maestri E., Marmiroli N., et al. A simple sequence repeat-based linkage map of barley. Genetics 156 (2000) 1997-2005
135. Röder M.S., Korzun V., Wendehake K., Plaschke J., Tixier M., Leroy P., and Ganal M.W. A microsatellite map of wheat. Genetics 149 (1998) 2007-2023
136. Rostoks N., Borevitz J.O., Headley P.E., Russel J., Sharon M., Jenny M., Cardle L., Marshall D.F., and Robbie W. Single-feature polymorphism discovery in the barley transcriptome. Genome Biol. 6 (2005) R54
137. Rudd S., Schoof H., and Mayer K. Plant Markers-a database of predicted molecular markers from plants. Nucleic Acids Res. 33 (2005) 628-632
138. Saghai-Maroof M.A., Tang G.P., Biyashev R.M., Maughan P.J., and Zhang Q. Analysis of the barley and rice genomes by comparative RFLP linkage mapping. Theor. Appl. Genet. 92 (1996) 541-551
139. Salvi S., and Tuberosa R. To clone or not to clone plant QTLs: Present and future challenges. Trends Plant Sci. 10 (2005) 297-304
140. Salvo-Garrido H., Laurie D.A., Jaffe B., and Snape J.W. An RFLP map of diploid Hordeum bulbosum L. and comparison with maps of barley (H. vulgare L.) and wheat (Triticum aestivum L). Theor. Appl. Genet. 103 (2001) 869-880
141. Sarma R.N., Gill B.S., Sasaki T., Galiba G., Sutka J., Laurie D.A., and Snape J.W. Comparative mapping of the wheat chromosome 5A Vrn-A1 region with rice and its relationship to QTL for flowering time. Theor. Appl. Genet. 97 (1998) 103-109
142. Sarma R.N., Fish L., Gill B.S., and Snape J.W. Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes. Genome 43 (2000) 191-198
143. Schadt E.E., Monks S.A., Drake T.A., Lusis A.J., Che N., Colinayo V., Ruff T.G., Milligan S.B., Lamb J.R., Cavet G., Linsley P.S., Mao M., et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422 (2003) 297-301
144. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
145. Schulman A.H., Gupta P.K., and Varshney R.K. Organization of microsatellites and retrotransposons in cereal genomes. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 83-118
146. Septiningshi E.M., Prasetiyono J., Lubis E., Tai T.H., Tjubaryat T., Moeljopawiro S., and McCouch S.R. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor. Appl. Genet. 107 (2003) 1419-1432
147. Shan X., Blake T.K., and Talbert L.E. Conversion of AFLP markers to sequence-specific PCR markers in barley and wheat. Theor. Appl. Genet. 98 (1999) 1072-1078
148. Shariflou M.R., Ghannadha M.R., and Sharp P.J. Multiplex PCR of microsatellite markers in wheat. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 1050-1052
149. Shinbata T., Vrinten P., Iida J., Sato M., Yonemaru J., Saito M., Mitsuse S., and Nakamura T. Microarray analysis of gene expression in developing endosperm from different wheat varities. In: Pogna N.E., Romano M., Pogna E.A., and Galterio G. (Eds). "Proceedings of the Tenth International Wheat Genetics Symposium" (2003), Paestum, Italy 1053-1055
150. Singh H., Prasad M., Varshney R.K., Roy J.K., Balyan H.S., Dhaliwal H.S., and Gupta P.K. STMS markers for grain protein content and their validation using near isogenic lines in bread wheat. Plant Breed. 120 (2001) 273-278
151. Singh N.K., Raghuvanshi S., Srivastava S.K., Gaur A., Pal K., Dalal V., Singh A., Ghazil I.A., Bhargav A., Yadav M., Dixit A., Batra K., et al. Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct. Integr. Genomics 4 (2004) 102-117
152. Smilde D.W., Haluskova J., Sasaki T., and Graner A. New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice
153. Somers D., Edwards K.J., and Issac P. A high density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 109 (2004) 1105-1114
154. Somers D.J., Kirkpatrick R., Moniwa M., and Walsh A. Mining single nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49 (2003) 431-437
155. Song Q.J., Fickus E.W., and Cregan P.B. Characterization of trinucleotide SSR motifs in wheat. Theor. Appl. Genet. 104 (2002) 286-293
156. Sorrells M.E., La Rota M., Bermudez-Kandianis C.E., Greene R.A., Kantety R., Munkvold J.D., Miftahudin Mahmoud A., Ma X., Gustafson P.J., Qi L.L., Echalier B., et al. Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13 (2003) 1818-1827
157. Sreenivasulu N., Kavikishor P.B., Varshney R.K., and Altschmied L. Mining functional information from cereal genomes--the utility of expressed sequence tags (ESTs). Curr. Sci. 83 (2002) 965-973
158. Sreenivasulu N., Varshney R.K., Kavikishore P.V., and Weschke W. Tolerance to abioitic stress--a functional genomics approach. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, The Netherlands 483-514
159. Stein N., and Graner A. Map-based gene isolation in cereal genomes. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 331-360
160. Stein N., Feuillet C., Wicker T., Schlagenhauf E., and Keller B. Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L). Proc. Natl. Acad. Sci. USA 97 (2000) 13436-13441
161. Stephenson P., Bryan G., Kirby J., Collins A., Devos K.M., Busso C., and Gale M.D. Fifty new microsatellite loci for the wheat genetic map. Theor. Appl. Genet. 97 (1998) 946-949
162. Talamè V., Sanguineti M.C., Chiapparino E., Bahri H., Salem B.M., Forster B.P., Ellis R.P., Rhouma S., Zoumarou W., Waugh R., and Tuberosa R. Identification of Hordeum spontaneum QTL alleles improving field performance of barley grown under rainfed conditions. Ann. Appl. Biol. 144 (2004) 309-319
163. Tan P.K., Downey T.J., Spitznagel Jr. E.L., Xu P., Fu D., Dimitrov D.S., Lempicki R.A., Raaka B.M., and Cam M.C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31 (2003) 5676-5684
164. Tanksley S.D., and McCouch S. Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277 (1997) 1063-1066
165. Tanksley S.D., and Nelson J.C. Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92 (1996) 191-203
166. Tanksley S.D., Ganal M.W., Prince J.P., de Vicente M.C., Bonierbale M.W., Broun P., Fulton T.M., Giovannoni J.J., Grandillo S., Martin G.B., Messeguer R., Miller J.C., et al. High density molecular linkage maps of the tomato and potato genomes. Genetics 132 (1992) 1141-1160
167. Thiel T., Michalek W., Varshney R.K., and Graner A. Exploiting EST databases for the developement and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106 (2003) 411-422
168. Thornsberry J.M., Goodman M.M., Doebley J., Kresovich S., Nielsen D., and Buckler E.S. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28 (2001) 286-289
169. Toojinda T., Baird E., Booth A., Broers L., Hayes P., Powell W., Thomas W., Vivar H., and Young G. Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: An example of marker-assisted line development. Theor. Appl. Genet. 96 (1998) 123-131
170. Tuberosa R., and Salvi S. QTLs and genes for tolerance to abiotic stress in cereals. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 253-315
171. Van Deynze A.E., Dubcovsky J., Gill K.S., Nelson J.C., Sorrells M.E., Dvorak J., Gill B.S., Lagudah E.S., McCouch S.R., and Appels R. Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38 (1995) 45-59
172. Van Deynze A.E., Nelson J.C., Yglesias E.S., Harrington S.E., Braga D.P., McCouch S.R., and Sorrells M.E. Comparative mapping in gasses-wheat relationships. Mol. Gen. Genet. 248 (1995) 744-754
173. Varshney R.K., Thiel T., Stein N., Langridge P., and Graner A. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell. Mol. Biol. Lett. 7 (2002) 537-546
174. Varshney R.K., Korzun V., and Börner A. Molecular maps in cereals: Methodology and progress. In: Gupta P.K., and Varshney R.K. (Eds). "Cereal Genomics" (2004), Kluwer Academic Publishers, Dordrecht, The Netherlands 35-82
175. Varshney R.K., Prasad M., and Graner A. A Molecular marker maps of barley: A resource for intra- and interspecific genomics. In: Lörz H., and Wenzel G. (Eds). "Biotechnology in Agriculture and Forestry, Vol. 55, Molecular Markers Systems" (2004), Springer Verlag, Heidelberg, Germany 229-245
176. Varshney R.K., Zhang H., Potokina E., Stein N., Langridge P., and Graner A. A simple hybridisation-based strategy for the generation of non-redundant EST collections. Plant Sci. 167 (2004) 629-634
177. Varshney R.K., Graner A., and Sorrells M.E. Genic microsatellite markers in plants: Features and applications. Trends Biotechnol. 23 (2005) 48-55
178. Varshney R.K., Graner A., and Sorrells M.E. Genomics-assisted breeding for crop improvement. Trends Plant Sci. 10 (2005) 621-630
179. Varshney R.K., Prasad M., Kota R., Sigmund R., Börner A., Valkoun J., Scholz U., Stein N., and Graner A. Functional molecular markers in barley: Development and applications. Czech. J. Genet. Plant Breed. 41 (2005) 128-133
180. Varshney R.K., Sigmund R., Korzun V., Boerner A., Stein N., Sorrells M., Langridge P., and Graner A. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci. 168 (2005) 195-202
181. Varshney R.K., Balyan H.S., and Langridge P. Wheat. In: Kole C. (Ed). "The Genomes: A Series on Genome Mapping, Molecular Breeding and Genomics of Economic Species, Vol. 1, Cereals & Millets" (2006), Springer, Dordrecht, The Netherlands 79-134
182. Varshney R.K., Grosse I., Haehnel U., Siefken R., Prasad M., Stein N., Langridge P., Altschmied L., and Graner A. Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor. Appl. Genet. 113 (2006) 239-250
183. Vassos E.J., Barr A.R., and Elington J.K. Genetic conversion of feed barley varieties to malting types. "Proceedings of Barley Technical/Cereal Chemistry Conference." (2003), Tasmania, Australia. www.cdesign.com.au/bts2005/pages/Papers_2003/papers/087VassosE.pdf
184. Velculescu V.E., Zhang L., Vogelstein B., and Kinzler K.W. Serial analysis of gene expression. Science 270 (1995) 484-487
185. Wall J.D., and Pritchard J.K. Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73 (2003) 502-516
186. Wang M.L., Atkinson M.D., Chinoy C.N., Devos K.M., and Gale M.D. Comparative RFLP-based genetic maps of barley chromosome-5 (1H) and rye chromosome-1 R. Theor. Appl. Genet. 84 (1992) 339-344
187. Weng Y., and Lazar M.D. Comparison of homoeologous group-6 short arm physical maps of wheat and barley reveals a similar distribution of recombinogenic and gene-rich regions. Theor. Appl. Genet. 104 (2002) 1078-1085
188. Yu G.X., Bush A.L., and Wise R.P. Comparative mapping of homoeologous group 1 regions and genes for resistance to obligate biotrophs in Avena, Hordeum, and Zea mays. Genome 39 (1996) 155-164
189. Yu J.K., Dake T.M., Singh S., Benscher D., Li W., Gill B.S., and Sorrells M.E. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47 (2004) 805-818
190. Yu J.K., La Rota M., Kantety R.V., and Sorrells M.E. EST derived SSR markers for comparative mapping in wheat and rice. Mol. Genet. Genomics 271 (2004) 742-751
191. Zamir D. Improving plant breeding with exotic genetic libraries. Nat. Rev. Genet. 2 (2001) 983-989
192. Zhang D., Choi D.W., Wanamaker S., Fenton R.D., Chin A., Malatrasi M., Turuspekov Y., Walia H., Akhunov E.D., Kianain P., Otto C., Simons K., et al. Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.). Genetics 168 (2004) 595-608
193. Zhang H., Sreenivasulu N., Weschke W., Stein N., Rudd S., Radchuk V., Potokina E., Scholz U., Schweizer P., Zierold U., Langridge P., Varshney R.K., et al. Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant J. 40 (2004) 276-290
194. Zhou W.C., Kolb F.L., Bai G.H., Domier L.L., Boze L.K., and Smith N.J. Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat. Plant Breed. 122 (2003) 40-46
195. Zhu X., Zhang S., Zhao H., and Cooper R.S. Association mapping using a mixture model for complex traits. Genet. Epidemiol. 23 (2002) 181-196