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Genomics-Based Barley Breeding

  • Kevin P. Smith
  • William Thomas
  • Lucia Gutierrez
  • Hazel Bull
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

The creation of the first barley reference genome opens up new and improved avenues for the translation of genetics and genomics to application in plant breeding. Despite steady progress in barley breeding, there is still a great need for improved barley cultivars that provide raw materials for a wide array of products, are adapted to diverse growing conditions, and provide sustainable and profitable income for farmers. In this chapter, we investigate some of the major challenges in barley breeding and describe how our ever-increasing understanding of the barley genome has led to new methods and approaches to meet those challenges. There are several excellent reviews of barley breeding that detail progress in breeding over time (e.g., Friedt et al. 2010). Here, we will focus on how genetic tools and resources have affected progress so far and the prospects to utilize current and emerging genomic tools to sustain barley improvement. In particular, we explore the evolution of marker development for mapping, genomic approaches to selecting parent combinations and from within segregating breeding populations, exploiting diverse germplasm, tapping into genomic regions of limited recombination, and utilizing bioinformatic characterization of genetic load. Access to a complete reference genome is already providing breeders and geneticists information about candidate genes for QTL that are targets for marker-assisted selection, the physical order of genetically linked markers in regions explored by fine mapping, and the ultimate consensus map with which to compare mapping studies. Additional full genome sequences leading to a pan-genome for barley, refinement of the reference genome, and new tools to access, analyze, and utilize genomic information will foster further integration of genomics into barley improvement.

References

  1. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248–249PubMedPubMedCentralCrossRefGoogle Scholar
  2. Ahmad Naz A, Ehl A, Pillen K, Léon J (2012) Validation for root-related quantitative trait locus effects of wild origin in the cultivated background of barley (Hordeum vulgare L.). Plant Breed 3:392–398CrossRefGoogle Scholar
  3. Akdemir D, Sanchez JI, Jannink JL (2015) Optimization of genomic selection training populations with a genetic algorithm. Genet Sel Evol 47:38PubMedPubMedCentralCrossRefGoogle Scholar
  4. Albrecht T, Auinger HJ, Wimmer V, Ogutu JO, Knaak C, Ouzunova M, Piepho H-P, Schön CC (2014) Genome-based prediction of maize hybrid performance across genetic groups, testers, locations, and years. Theor Appl Genet 127(6):1375–1386PubMedCrossRefGoogle Scholar
  5. Asoro FG, Newell MA, Beavis WD, Scott MP, Jannink JL (2011) Accuracy and training population design for genomic selection on quantitative traits in elite North American oats. Plant Genome 4:132CrossRefGoogle Scholar
  6. Asoro FG, Newell MA, Beavis WD, Scott MP, Tinker NA, Jannink JL (2013) Genomic, marker-assisted, and pedigree-BLUP selection methods for β-glucan concentration in elite oat. Crop Sci 53(5):1894–1906CrossRefGoogle Scholar
  7. Barr AR, Jefferies SP, Warner P, Moody DB, Chalmers KJ, Langridge P (2000) Marker assisted selection in theory and practice. In: The 8th international barley genetics symposium Australia, 2000Google Scholar
  8. Barua UM, Chalmers KJ, Hackett CA, Thomas WTB, Powell W, Waugh R (1993) Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis. Heredity 71(2):177–184PubMedCrossRefGoogle Scholar
  9. Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, Ramsay L, Russell J, Shaw PD, Thomas WTB, Waugh R (2017) Development and evaluation of a barley 50k iSelect SNP array. Front Plant Sci 8:1792PubMedPubMedCentralCrossRefGoogle Scholar
  10. Beattie AD, Edney MJ, Scoles G, Rossnagel B (2010) Association mapping of malting quality data from Western Canadian two-row barley cooperative trials. Crop Sci 50:1649–1662.  https://doi.org/10.2135/cropsci2009.06.0334
  11. Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, New York, pp p145–p162Google Scholar
  12. Bernardo R (2010) Breeding for quantitative traits in plants, 2nd edn. Stemma Press, MinnesotaGoogle Scholar
  13. Bernardo R (2017) Prospective targeted recombination and genetic gains for quantitative traits in maize. Plant Genome 10.  https://doi.org/10.3835/plantgenome2016.11.0118
  14. Beyene Y, Semagn K, Mugo S, Tarekegne A, Babu R, Meisel B, Sehabiague P et al (2015) Genetic gains in grain yield through genomic selection in eight bi-parental maize populations under drought stress. Crop Sci 55(1):154–163CrossRefGoogle Scholar
  15. Biffen R (1907) Studies in the inheritance of disease-resistance. J Agric Sci 2:109–128CrossRefGoogle Scholar
  16. Bradbury P, Parker T, Hamblin MT, Jannink JL (2011) Assessment of power and false discovery rate in genome-wide association studies using the BarleyCAP germplasm. Crop Sci 51:52–59CrossRefGoogle Scholar
  17. Bringhurst TA (2015) 125th anniversary review: barley research in relation to Scotch whisky production: a journey to new frontiers. J Inst Brew 121:1–18.  https://doi.org/10.1002/jib.192CrossRefGoogle Scholar
  18. Brøndum RF, Su G, Janss L, Sahana G, Guldbrandtsen B, Boichard D, Lund MS (2015) Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction. J Dairy Sci 98:4107–4116PubMedCrossRefGoogle Scholar
  19. Burgueño J, de los Campos G, Weigel K, Crossa J (2012) Genomic prediction of breeding values when modeling genotype × environment interaction using pedigree and dense molecular markers. Crop Sci 52:707–719Google Scholar
  20. Cahill DJ, Schmidt DH (2004) Use of marker-assisted selection in a product development breeding program. In: Fischer T (ed) New directions for a diverse planet. Proceedings of the 4th international crop science congress, Brisbane, QLD, Australia 26 Sept–1 Oct 2004Google Scholar
  21. Cakir M, Gupta S, Platz GJ, Ablett GA, Loughman R, Emebiri LC, Poulsen D, Li CD, Lance RCM, Galwey NW, Jones MGK (2003) Mapping and validation of the genes for resistance to Pyrenophora teres f. teres in barley (Hordeum vulgare L.). Crop Pasture Sci 54:1369–1377CrossRefGoogle Scholar
  22. Canci PC, Nduulu LM, Dill-Macky R, Muehlbauer GJ, Rasmusson DC, Smith KP (2003) Genetic relationship between kernel discoloration and grain protein concentration in barley. Crop Sci 43(5):1671–1679CrossRefGoogle Scholar
  23. Canci PC, Nduulu LM, Muehlbauer GJ, Dill-Macky R, Rasmusson DC, Smith KP (2004) Validation of quantitative trait loci for Fusarium head blight and kernel discoloration in barley. Mol Breed 14:91–104.  https://doi.org/10.1023/B:MOLB.0000037998.27661.58CrossRefGoogle Scholar
  24. Castro AJ, Capettini F, Corey AE, Filichkina T, Hayes PM, Kleinhofs A, Kudrna D, Richardson K, Sandoval-Islas S, Rossi C, Vivar H (2003) Mapping and pyramiding of qualitative and quantitative resistance to stripe rust in barley. Theor Appl Genet 107:922–930PubMedCrossRefGoogle Scholar
  25. Charcosset A, Moreau L (2004) Use of molecular markers for the development of new cultivars and the evaluation of genetic diversity. Euphytica 137(1):81–94CrossRefGoogle Scholar
  26. Christopher J, Richard C, Chenu K, Christopher M, Borrell A, Hickey L (2015) Integrating rapid phenotyping and speed breeding to improve stay green and root adaptation of wheat in changing, water-limited, Australian environments. In: Edwards D, Oldroyd G (eds) Agriculture and climate change - adapting crops to increased uncertainty (vol 29). Procedia Environmental Sciences, pp 175–176.  https://doi.org/10.1016/j.proenv.2015.07.246
  27. Chun S, Fay JC (2009) Identification of deleterious mutations within three human genomes. Genome Res 19:1553–1561PubMedPubMedCentralCrossRefGoogle Scholar
  28. Chutimanitsakun Y, Cuesta-Marcos A, Chao S, Corey A, Filichkin T, Fisk S, Kolding M, Meints B, Ong YL, Rey JI, Ross AS (2013) Application of marker-assisted selection and genome-wide association scanning to the development of winter food barley germplasm resources. Plant Breed 132(6):563–570CrossRefGoogle Scholar
  29. Close TJ, Bhat P, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson J, Wanamaker S, Bozdag S, Roose M, Moscou M, Chao S, Varshney R, Szucs P, Sato K, Hayes P, Matthews D, Kleinhofs A, Muehlbauer G, DeYoung J, Marshall D, Madishetty K, Fenton R, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10(1):582.  https://doi.org/10.1186/1471-2164-10-582CrossRefPubMedPubMedCentralGoogle Scholar
  30. Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Mackay IJ, Powell W, O’Sullivan DM (2008) Association mapping of partitioning loci in barley. BMC Genet 9(1):16PubMedPubMedCentralCrossRefGoogle Scholar
  31. Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay I, Balding DJ, Consortium TA, Waugh R, O’Sullivan DM (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. PNAS 107:21611–21616Google Scholar
  32. Cockram J, Jones H, Norris C, O’Sullivan DM (2012) Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.). Theor Appl Genet 125 (8):1735–1749.  https://doi.org/10.1007/s00122-012-1950-3
  33. Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44(12):1388–1392.  https://doi.org/10.1038/ng.2447CrossRefPubMedPubMedCentralGoogle Scholar
  34. Combs E, Bernardo R (2013) Genomewide selection to introgress semidwarf maize germplasm into US corn belt inbreds. Crop Sci 53:1427–1436CrossRefGoogle Scholar
  35. Condon F, Gustus C, Rasmusson DC, Smith KP (2008) Effect of advanced cycle breeding on genetic diversity in barley breeding germplasm. Crop Sci 48(3):1027–1036.  https://doi.org/10.2135/cropsci2007.07.0415CrossRefGoogle Scholar
  36. Condon F, Rasmusson DC, Schiefelbein E, Velasquez G, Smith KP (2009) Effect of advanced cycle breeding on genetic gain and phenotypic diversity in barley breeding germplasm. Crop Sci 49:1751–1761.  https://doi.org/10.2135/cropsci2008.10.0585CrossRefGoogle Scholar
  37. Costa JM, Corey A, Hayes PM, Jobet C, Kleinhofs A, Kopisch-Obusch A, Kramer SF, Kudrna D, Li M, Riera-Lizarazu O, Sato K, Szucs P, Toojinda T, Vales MI, Wolfe RI (2001) Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population. Theor Appl Genet 103(2–3):415–424CrossRefGoogle Scholar
  38. Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1999) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811–818CrossRefGoogle Scholar
  39. Crosbie TM, Eathington SR, Johnson GR, Edwards M, Reiter R, Stark S, Mohanty RG, Oyervides M, Buehler RE, Walker AK, Dobert R, Delannay X, Pershing JC, Hall MA, Lamkey KR (2006) Plant breeding: past, present, and future. In: Lamkey KR, Lee M (eds) Plant breeding: the Arnel R. Hallauer international symposium. Blackwell, Ames, pp 3–50Google Scholar
  40. Crossa J, de los Campos G, Pérez P, Gianola D, Burgueño J, Araus JL, Makumbi D, Singh RP, Dreisigacker S, Yan J, Arief V, Banziger M, Braun H-J (2010) Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713–724  https://doi.org/10.1534/genetics.110.118521
  41. Crossa J, Pérez P, de los Campos G, Mahuku G, Dreisigacker S et al (2011) Genomic selection and prediction in plant breeding. J Crop Improv 25:239–261Google Scholar
  42. Crossa J, Beyene Y, Kassa S, Pérez P, Hickey JM, Chen C, de los Campos G, Burgueño J, Windhausen VS, Buckler E, Jannink JL, Lopez Cruz MA, Babu R (2013) Genomic prediction in maize breeding populations with genotyping-by-sequencing. G3 3:1903–1926Google Scholar
  43. Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de los Campos G, Burgueño J, Camacho-González JM, Pérez-Elizalde S, Beyene Y, Dreisigacker S (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci.  https://doi.org/10.1016/j.tplants.2017.08.011
  44. Cuesta-Marcos A, Igartua E, Codesal P, Russell JR, Molina-Cano JL, Moralejo M, Szűcs P, Gracia MP, Lasa JM, Casas AM (2008) Heading date QTL in a spring × winter barley cross evaluated in Mediterranean environments. Mol Breed 21(4):455–471CrossRefGoogle Scholar
  45. Cuesta-Marcos A, Casas AM, Hayes PM, Gracia MP, Lasa JM, Ciudad F, Codesal P, Molina-Cano JL, Igartua E (2009) Yield QTL affected by heading date in Mediterranean grown barley. Plant Breed 128(1):46–53CrossRefGoogle Scholar
  46. Cuesta-Marcos A, Szűcs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM (2010) Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genom 11(1):707CrossRefGoogle Scholar
  47. Dahleen LS, Agrama HA, Horsley RD, Steffenson BJ, Schwarz PB, Mesfin A, Franckowiak JD (2003) Identification of QTLs associated with Fusarium head blight resistance in Zhedar 2 barley. Theor Appl Genet 108(1):95–104PubMedCrossRefGoogle Scholar
  48. Dawson JC, Endelman JB, Heslot N, Crossa J, Poland J, Dreisigacker S, Manès Y, Sorrells ME, Jannink J-L (2013) The use of unbalanced historical data for genomic selection in an international wheat breeding program. Field Crop Res 154:12–22CrossRefGoogle Scholar
  49. de la Peña RC, Smith KP, Capettini F, Muehlbauer GJ, Gallo-Meagher M, Dill-Macky R, Somers DA, Rasmusson DC (1999) Quantitative trait loci associated with resistance to Fusarium head blight and kernel discoloration in barley. Theor Appl Genet 99:561–569PubMedCrossRefGoogle Scholar
  50. de los Campos G, Vazquez AI, Fernando R, Klimentidis YC, Sorensen D (2013) Prediction of complex human traits using the genomic best linear unbiased predictor. PLoS Genet 9:e1003608PubMedCentralCrossRefPubMedGoogle Scholar
  51. del Pozo A, Castillo D, Inostroza L, Matus I, Mendez AM, Morcuende R (2012) Physiological and yield responses of recombinant chromosome substitution lines of barley to terminal drought in a Mediterranean-type environment. Ann Appl Biol 160(2):157–167.  https://doi.org/10.1111/j.1744-7348.2011.00528CrossRefGoogle Scholar
  52. Distelfeld A, Avni R, Fischer AM (2014) Senescence, nutrient remobilization, and yield in wheat and barley. J Exp Bot 65(14):3783–3798.  https://doi.org/10.1093/jxb/ert477CrossRefPubMedGoogle Scholar
  53. Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Waugh R (2011) Genetic dissection of barley morphology and development. Plant Physiol 155(2):617–627.  https://doi.org/10.1104/pp.110.166249CrossRefPubMedGoogle Scholar
  54. Dubcovsky J (2004) Marker-assisted selection in public breeding programs: the wheat experience. Crop Sci 44:1895–1898CrossRefGoogle Scholar
  55. Dubcovsky J, Chen C, Yan L (2005) Molecular characterization of the allelic variation at the VRN-H2 vernalization locus in barley. Mol Breed 15(4):395–407CrossRefGoogle Scholar
  56. Eathington SR (2005) Practical applications of molecular technology in the development of commercial maize hybrids. In: Proceedings of the 60th annual corn and sorghum seed research conference, 7–9 Dec 2005. American Seed Trade Association, Washington, DCGoogle Scholar
  57. Fehr WR (1991) Principles of cultivar development. Vol. 1. Theory and technique. Macmillan Publishing Company, LondonGoogle Scholar
  58. Felsenstein J (1974) The evolutionary advantage of recombination. Genetics 78(2):737–756PubMedPubMedCentralGoogle Scholar
  59. Francia E, Rizza F, Cattivelli L, Stanca AM, Galiba G, Toth B, Hayes PM, Skinner JS, Pecchioni N (2004) Two loci on chromosome 5H determine low-temperature tolerance in a ‘Nure’ (winter) × ‘Tremois’ (spring) barley map. Theor Appl Genet 108(4):670–680PubMedCrossRefGoogle Scholar
  60. Friedt W, Horsley RD, Harvey BL, Poulsen DME, Lance RCM, Ceccarelli S, Grando S, Capettini F (2010) Barley breeding history, progress, objectives, and technology. In: Barley. Wiley-Blackwell, pp 160–220.  https://doi.org/10.1002/9780470958636.ch8
  61. Gao W, Clancy JA, Han F, Jones BL, Budde A, Wesenberg DM, Kleinhofs A, Ullrich SE (2004) Fine mapping of malting-quality QTL complex near the chromosome 4HS telomere in barley. Theor Appl Genet 109:750–760PubMedCrossRefGoogle Scholar
  62. Graner A, Bauer E (1993) RFLP mapping of the ym4 virus resistance gene in barley. Theor Appl Genet 86(6):689–693PubMedCrossRefGoogle Scholar
  63. 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(2):250–256PubMedCrossRefGoogle Scholar
  64. Graner A, Foroughi-Wehr B, Tekauz A (1996) RFLP mapping of a gene in barley conferring resistance to net blotch (Pyrenophora teres). Euphytica 91:229–234Google Scholar
  65. Graner A, Streng S, Kellermann A, Schiemann A, Bauer E, Waugh R, Pellio B, Ordon F (1999) Molecular mapping and genetic fine-structure of the rym5 locus encoding resistance to different strains of the Barley Yellow Mosaic Virus Complex. Theor Appl Genet 98(2):285–290.  https://doi.org/10.1007/s001220051070CrossRefGoogle Scholar
  66. Grewal TS, Rossnagel BG, Pozniak CJ, Scoles GJ (2008) Mapping quantitative trait loci associated with barley net blotch resistance. Theor Appl Genet 116(4):529–539.  https://doi.org/10.1007/s00122-007-0688-9CrossRefPubMedGoogle Scholar
  67. Gutierrez L, Cuesta-Marcos A, Castro AJ, von Zitzewitz J, Schmitt M, Hayes PM (2011) Association mapping of malting quality quantitative trait loci in winter barley: positive signals from small germplasm arrays. Plant Genome 4:256–272CrossRefGoogle Scholar
  68. Gutierrez L, German S, Pereyra S, Hayes PM, Perez CA, Capettini F, Locatelli A, Berberian NM, Falcioni E, Estrada R, Fros D, Gonza V, Altamirano H, Huerta-Espino J, Neyra E, Orjeda G, Sandoval-Islas S, Singh R, Turkington K, Castro AJ (2015) Multi-environment multi-QTL association mapping identifies disease resistance QTLs in barley germplasm from Latin America. Theor Appl Genet 128(3):501–516.  https://doi.org/10.1007/s00122-014-2448-yCrossRefPubMedGoogle Scholar
  69. Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324PubMedCrossRefGoogle Scholar
  70. Han F, Romagosa I, Ullrich SE, Jones BL, Hayes PM, Wesenberg DM (1997) Molecular marker-assisted selection for malting quality traits in barley. Mol Breed 3(6):427–437CrossRefGoogle Scholar
  71. Hartfield M, Otto SP (2011) Recombination and hitchhiking of deleterious alleles. Evolution 65:2421–2434.  https://doi.org/10.1111/j.1558-5646.2011.01311.x Epub 2011 Apr 26CrossRefPubMedGoogle Scholar
  72. Hayes P, Szűcs P (2006) Disequilibrium and association in barley: thinking outside the glass. Proc Natl Acad Sci 103(49):18385–18386PubMedCrossRefGoogle Scholar
  73. Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392–401PubMedCrossRefGoogle Scholar
  74. Hayes BJ, Cogan NOI, Pembleton LW, Goddard ME, Wang J, Spangenberg GC, Forster JW (2013) Prospects for genomic selection in forage plant species (OA Rognli, ed). Plant Breed 132:133–143Google Scholar
  75. He S, Schulthess AW, Mirdita V et al (2016) Theor Appl Genet 129:641.  https://doi.org/10.1007/s00122-015-2655-1
  76. Hedley PE, Russell JR, Hein I, Booth A, Williamson S, Morris J, Lacomme C, Powell W (2005) Epiheterodendrin in malting barley: molecular evidence for cytochrome P450-mediated production. In: 2nd UK small grain cereals workshop, SCRI, Dundee, UKGoogle Scholar
  77. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1–12CrossRefGoogle Scholar
  78. Heffner EL, Lorenz AJ, Jannink J-L, Sorrells ME (2010) Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50:1681CrossRefGoogle Scholar
  79. Heffner EL, Jannink J-L, Sorrells ME (2011) Genomic selection accuracy using multifamily prediction models in a wheat breeding program. Plant Genome 4:65–75CrossRefGoogle Scholar
  80. Heidlebaugh NM, Trethewey BR, Jukanti AK, Parrott DL, Martin JM, Fischer AM (2008) Effects of a barley (Hordeum vulgare) chromosome 6 grain protein content locus on whole-plant nitrogen reallocation under two different fertilisation regimes. Funct Plant Biol 35(7):619–632CrossRefGoogle Scholar
  81. Heslot N, Yang H-P, Sorrells ME, Jannink J-L (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52:146CrossRefGoogle Scholar
  82. Higgins JD, Perry RM, Barakate A, Ramsay L, Waugh R, Halpin C, Armstrong SJ, Franklin F (2012) Spatiotemporal asymmetry of the meiotic program underlies the predominantly distal distribution of meiotic crossovers in barley. Plant Cell 24:4096–4109PubMedPubMedCentralCrossRefGoogle Scholar
  83. Hirota N, Kaneko T, Kuroda H, Kaneda H, Takashio M, Ito K, Takeda K (2005) Characterization of lipoxygenase-1 null mutants in barley. Theor Appl Genet 111(8):1580–1584.  https://doi.org/10.1007/s00122-005-0088-yCrossRefPubMedGoogle Scholar
  84. Hirota N, Kaneko T, Ito K, Takeda K (2006a) Mapping a factor controlling the thermostability of seed lipoxygenase-1 in barley. Plant Breed 125(3):231–235CrossRefGoogle Scholar
  85. Hirota N, Kuroda H, Takoi K, Kaneko T, Kaneda H, Yoshida I, Takashio M, Ito K, Takeda K (2006b) Development of novel barley with improved beer foam and flavor stability-the impact of lipoxygenase-1-less barley in the brewing industry. Tech Quarterly-Master Brewers Assoc Am 43(2):131–135Google Scholar
  86. Hoffstetter A, Cabrera A, Huang M, Sneller C (2016) Optimizing training population data and validation of genomic selection for economic traits in soft winter wheat. G3 6:2919–2928.  https://doi.org/10.1534/g3.116.032532
  87. Hofheinz N, Borchardt D, Weissleder K, Frisch M (2012) Genome-based prediction of test cross performance in two subsequent breeding cycles. Theor Appl Genet 125:1639–1645.  https://doi.org/10.1007/s00122-012-1940-5CrossRefPubMedGoogle Scholar
  88. Hofinger BJ, Russell JR, Bass CG, Baldwin T, Dos Reis M, Hedley PE, Li Y, Macaulay M, Waugh R, Hammond-Kosack KE (2011) An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Mol Ecol 20(17):3653–3668PubMedGoogle Scholar
  89. Hoki T, Saito W, Hirota N, Shirai M, Kihara M, Rossnagel BG, Ichikawa S (2010) The outcomes of joint breeding program in Western Canada-the breeding of LOX-1-less malting barley variety ‘CDC-Polarstar’. In: 6th Canadian barley symposium proceedings, Saskatchewan, Canada, 2010Google Scholar
  90. Honsdorf N, March T, Hecht A, Eglinton J, Pillen K (2014) Evaluation of juvenile drought stress tolerance and genotyping by sequencing with wild barley introgression lines. Mol Breed 34:1475.  https://doi.org/10.1007/s11032-014-0131-2CrossRefGoogle Scholar
  91. Horsley RD, Schmierer D, Maier D, Kudrna D, Urrea CA, Steffenson BJ, Schwarz PB, Franckowiak JD, Green MJ, Zhang B, Kleinhofs A (2006) Identification of QTLs associated with Fusarium head blight resistance in barley accession CIho 4196. Crop Sci 46:145–156CrossRefGoogle Scholar
  92. Hospital F (2005) Selection in backcross programmes. Phil Trans R Soc B 360:1503–1511.  https://doi.org/10.1098/rstb.2005.1670CrossRefPubMedGoogle Scholar
  93. Hospital F, Charcosset A (1997) Marker-assisted introgression of quantitative trait loci. Genetics 147(3):1469–1485PubMedPubMedCentralGoogle Scholar
  94. Huang Y, Li L, Smith KP, Muehlbauer GJ (2016) Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance. BMC Genom 17(1):387CrossRefGoogle Scholar
  95. Hung H-Y, Browne C, Guill K, Coles N, Eller M, Garcia A, Lepak N, Melia-Hancock S, Oropeza-Rosas M, Salvo S, Upadyayula N, Buckler ES, Flint-Garcia S, McMullen MD, Rocheford TR, Holland JB (2012) The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population. Heredity 108:490.  https://doi.org/10.1038/hdy.2011.103CrossRefPubMedGoogle Scholar
  96. Isidro J, Jannink J-L, Akdemir D, Poland J, Heslot N, Sorrells ME (2014) Training set optimization under population structure in genomic selection. Theor Appl Genet 128:145–158PubMedPubMedCentralCrossRefGoogle Scholar
  97. Iwata H, Jannink JL (2011) Accuracy of genomic selection prediction in barley breeding programs: a simulation study based on the real single nucleotide polymorphism data of barley breeding lines. Crop Sci 51(5):1915–1927CrossRefGoogle Scholar
  98. Jannink J-L, Bink MCAM, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342PubMedCrossRefPubMedCentralGoogle Scholar
  99. Jarquín D, Crossa J, Lacaze X, Du Cheyron P, Daucourt J, Lorgeou J, Piraux F, Guerreiro L, Pérez P, Calus M, Burgueño J, de los Campos G (2014) A reaction norm model for genomic selection using high-dimensional genomic and environmental data. Theor Appl Genet 127:595–607PubMedCrossRefGoogle Scholar
  100. Jefferies SP, King BJ, Barr AR, Warner P, Logue SJ, Langridge P (2003) Marker-assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley. Plant Breed 122(1):52–56CrossRefGoogle Scholar
  101. Johnson GR (2004) Marker-assisted selection. Plant Breed Rev 24:293–301Google Scholar
  102. Johnson EB, Haggard JE, St. Clair DA (2012) Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum). G3 2(10):1145–1159.  https://doi.org/10.1534/g3.112.003459
  103. Jones H, Norris C, Smith D, Cockram J, Lee D, O’sullivan DM, Mackay Í (2013) Evaluation of the use of high-density SNP genotyping to implement UPOV Model 2 for DUS testing in barley. Theor Appl Genet 126(4):901PubMedCrossRefGoogle Scholar
  104. Jukanti AK, Fischer AM (2008) A high-grain protein content locus on barley (Hordeum vulgare) chromosome 6 is associated with increased flag leaf proteolysis and nitrogen remobilization. Physiol Plant 132(4):426–439PubMedCrossRefGoogle Scholar
  105. Jukanti AK, Heidlebaugh NM, Parrott DL, Fischer IA, McInnerney K, Fischer AM (2008) Comparative transcriptome profiling of near-isogenic barley (Hordeum vulgare) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation. New Phytol 177(2):333–349PubMedGoogle Scholar
  106. Karsai I, Meszaros K, Hayes PM, Bedő Z (1997) Effects of loci on chromosomes 2 (2H) and 7 (5H) on developmental patterns in barley (Hordeum vulgare L.) under different photoperiod regimes. Theor Appl Genet 94(5):612–618CrossRefGoogle Scholar
  107. Karsai I, Szűcs P, Mészáros K, Filichkina T, Hayes PM, Skinner JS, Láng L, Bedő Z (2005) The Vrn-H2 locus is a major determinant of flowering time in a facultative × winter growth habit barley (Hordeum vulgare L.) mapping population. Theor Appl Genet 110(8):1458–1466PubMedCrossRefGoogle Scholar
  108. Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants; where are we now? Heredity 80(2):137–142PubMedCrossRefPubMedCentralGoogle Scholar
  109. Kleinhofs A, Kilian A, Maroof MAS, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86(6):705–712PubMedCrossRefGoogle Scholar
  110. Komatsuda T, Pourkheirandish M, He CF, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, Lundqvist U, Fujimura T, Matsuoka M, Matsumoto T, Yano M (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104:1424–1429PubMedCrossRefPubMedCentralGoogle Scholar
  111. Konishi T, Kawada N, Yoshida H, Sohtome K (1989) Linkage relationship between two loci for the Barley Yellow Mosaic resistance of Mokusekko 3 and esterase isozymes in barley (Hordeum vulgare L.). Jpn J Breed 39(4):423–430.  https://doi.org/10.1270/jsbbs1951.39.423
  112. Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL (2016) The role of deleterious substitutions in crop genomes. Mol Biol Evol 33:2307–2317.  https://doi.org/10.1093/molbev/msw102CrossRefPubMedPubMedCentralGoogle Scholar
  113. Kraakman AT, Niks RE, Van den Berg PM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168(1):435–446PubMedPubMedCentralCrossRefGoogle Scholar
  114. Kraakman ATW, Martinez F, Mussiraliev B, van Eeuwijk FA, Niks RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed 17:41–58CrossRefGoogle Scholar
  115. Krchov L, Gordillo GA, Bernardo R (2015) Multienvironment validation of the effectiveness of phenotypic and genomewide selection within biparental maize populations. Crop Sci 55:1068–1075.  https://doi.org/10.2135/cropsci2014.09.0608CrossRefGoogle Scholar
  116. Kretschmer JM, Chalmers KJ, Manning S, Karakousis A, Barr AR, Islam AKMR, Logue SJ, Choe YW, Barker SJ, Lance RCM, Langridge P (1997) RFLP mapping of the Ha 2 cereal cyst nematode resistance gene in barley. Theor Appl Genet 94(8):1060–1064.  https://doi.org/10.1007/s001220050515CrossRefGoogle Scholar
  117. Kuczynska A, Surma M, Adamski T (2007) Methods to predict transgressive segregation in barley and other self-pollinated crops. J Appl Genet 48:321–328PubMedCrossRefPubMedCentralGoogle Scholar
  118. Künzel G, Waugh R (2002) Integration of microsatellite markers into the translocation-based physical RFLP map of barley chromosome 3H. Theor Appl Genet 105:660–665PubMedCrossRefPubMedCentralGoogle Scholar
  119. Lacerenza JA, Parrott DL, Fischer AM (2010) A major grain protein content locus on barley (Hordeum vulgare L.) chromosome 6 influences flowering time and sequential leaf senescence. J Exp Bot 61(11):3137–3149.  https://doi.org/10.1093/jxb/erq139CrossRefPubMedPubMedCentralGoogle Scholar
  120. Lado B, Gonzalez-Barrios P, Quincke M, Silva P, Gutierrez L (2016) Modelling genotype by environment interaction for genomic selection with unbalanced data from a wheat (Triticum aestivum L.) breeding program. Crop Sci 56:1–15.  https://doi.org/10.2135/cropsci2015.04.0207CrossRefGoogle Scholar
  121. Lado B, Battenfield S, Guzman C, Quincke M, Singh RP, Dreisigacker S, Peña J, Fritz A, Poland J, Gutiérrez L (2017a) Strategies to select crosses using genomic prediction in two wheat breeding programs. Plant Genome.  https://doi.org/10.3835/plantgenome2016.12.0128CrossRefPubMedGoogle Scholar
  122. Lado B, Battenfield S, Guzman C, Quincke M, Singh RP, Dreisigacker S, Peña J, Fritz A, Poland J, Gutiérrez L (2017b) Strategies to select crosses using genomic prediction in two wheat breeding programs. Plant Genome.  https://doi.org/10.3835/plantgenome2016.12.0128CrossRefPubMedGoogle Scholar
  123. Lamb KE, Gonzalez-Hernandez JL, Zhang B, Green M, Neate SM, Schwarz PB, Horsley RD (2009) Identification of QTL conferring resistance to Fusarium head blight resistance in the breeding line C93–3230–24. Crop Sci 49:1675–1680.  https://doi.org/10.2135/cropsci2008.11.0642CrossRefGoogle Scholar
  124. Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756PubMedPubMedCentralGoogle Scholar
  125. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199PubMedPubMedCentralGoogle Scholar
  126. Langridge P, Karakousis A, Collins N, Kretschmer J, Manning S (1995) A consensus linkage map of barley. Mol Breed 1(4):389–395CrossRefGoogle Scholar
  127. Langridge P, Lagudah ES, Holton TA, Appels R, Sharp PJ, Chalmers KJ (2001) Trends in genetic and genome analyses in wheat: a review. Crop Pasture Sci 52:1043–1077CrossRefGoogle Scholar
  128. Li JZ, Sjakste TG, Röder MS, Ganal MW (2003) Development and genetic mapping of 127 new microsatellite markers in barley. Theor Appl Genet 107(6):1021–1027.  https://doi.org/10.1007/s00122-003-1345-6CrossRefPubMedGoogle Scholar
  129. Lin H, Yamamoto T, Sasaki T et al (2000) Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021.  https://doi.org/10.1007/s001220051576CrossRefGoogle Scholar
  130. Locatelli A, Cuesta-Marcos A, Gutierrez L, Hayes PM, Smith KP, Castro AJ (2013) Genome-wide association mapping of agronomic traits in relevant barley germplasm in Uruguay. Mol Breed 31(3):631–654CrossRefGoogle Scholar
  131. Longin CF, Mi X, Würschum T (2015) Genomic selection in wheat: optimum allocation of test resources and comparison of breeding strategies for line and hybrid breeding. Theor Appl Genet 128:1297–1306PubMedCrossRefPubMedCentralGoogle Scholar
  132. Lorenz AJ (2013) Resource allocation for maximizing prediction accuracy and genetic gain of genomic selection in plant breeding: a simulation experiment. G3 3:481–491PubMedCrossRefPubMedCentralGoogle Scholar
  133. Lorenz AAJ, Smith KP (2015) Adding genetically distant individuals to training populations reduces genomic prediction accuracy in barley. Crop Sci.  https://doi.org/10.2135/cropsci2014.12.0827CrossRefGoogle Scholar
  134. Lorenz A, Smith KP, Jannink J-L (2012) Potential and optimization of genomic selection for Fusarium head blight resistance in six-row barley. Crop Sci 52:1609–1621CrossRefGoogle Scholar
  135. Lorenzana RE, Bernardo R (2009) Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120(1):151–161PubMedCrossRefPubMedCentralGoogle Scholar
  136. Lundqvist U, Lundqvist A (1987) An intermedium gene present in a commercial 6-row variety of barley. Hereditas 107(2):131–135CrossRefGoogle Scholar
  137. Ma Z, Steffenson BJ, Prom LK, Lapitan NL (2000) Mapping of quantitative trait Loci for Fusarium head blight resistance in barley. Phytopathology 90(10):1079–1088  https://doi.org/10.1094/PHYTO.2000.90.10.1079
  138. Mackay I, Horwell A, Garner J, White J, McKee J, Philpott H (2011) Reanalyses of the historical series of UK variety trials to quantify the contributions of genetic and environmental factors to trends and variability in yield over time. Theor Appl Genet 122:225–238.  https://doi.org/10.1007/s00122-010-1438-yCrossRefPubMedPubMedCentralGoogle Scholar
  139. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, Visscher PM et al (2009) Finding the missing heritability of complex diseases. Nature 461(7265):747–753PubMedPubMedCentralCrossRefGoogle Scholar
  140. Marulanda JJ, Mi X, Melchinger AE et al (2016) Theor Appl Genet 129:1901.  https://doi.org/10.1007/s00122-016-2748-5
  141. Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Waugh R (2013a) Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 76(4):718–727.  https://doi.org/10.1111/tpj.12319CrossRefPubMedPubMedCentralGoogle Scholar
  142. Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D’Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KFX, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N (2013b) Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J 76(3):494–505.  https://doi.org/10.1111/tpj.12294CrossRefPubMedPubMedCentralGoogle Scholar
  143. Mascher M, Wu S, Amand PS, Stein N, Poland J (2013c) Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS ONE 8(10):e76925.  https://doi.org/10.1371/journal.pone.0076925CrossRefPubMedPubMedCentralGoogle Scholar
  144. Mascher M et al (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427–433.  https://doi.org/10.1038/nature22043CrossRefPubMedPubMedCentralGoogle Scholar
  145. Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R, Chao S, Dong Y, Schwarz P, Muehlbauer GJ, Smith KP (2011) Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breed 27(4):439–454CrossRefGoogle Scholar
  146. Massman JM, Jung HJG, Bernardo R (2013) Genomewide selection versus marker-assisted recurrent selection to improve grain yield and stover-quality traits for cellulosic ethanol in maize. Crop Sci 53:58–66CrossRefGoogle Scholar
  147. Mathews KL, Malosetti M, Chapman S, McIntyre L, Reynolds M, Shorter R, van Eeuwijk F (2008) Multi-environment QTL mixed models for drought stress adaptation in wheat. Theor Appl Genet 117(7):1077–1091PubMedCrossRefPubMedCentralGoogle Scholar
  148. Matus I, Corey A, Filichkin T, Hayes PM, Vales MI, Kling J, Riera-Lizarazu O, Sato K, Powell W, Waugh R (2003) Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp spontaneum as a source of donor alleles in a Hordeum vulgare subsp vulgare background. Genome 46(6):1010–1023PubMedCrossRefPubMedCentralGoogle Scholar
  149. McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol 123(2):439–442PubMedPubMedCentralCrossRefGoogle Scholar
  150. Mejlhede N, Kyjovska Z, Backes G, Burhenne K, Rasmussen SK, Jahoor A (2006) EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley. Plant Breed 125(5):461–467CrossRefGoogle Scholar
  151. Melchinger AE, Utz HF, Schön CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149(1):383–403PubMedPubMedCentralGoogle Scholar
  152. Mesfin A, Smith KP, Dill-Macky R, Evans CK, Waugh R, Gustus CD, Muehlbauer GJ (2003) Quantitative trait loci for Fusarium head blight resistance in barley detected in a two-rowed by six-rowed population. Crop Sci 43:307–318CrossRefGoogle Scholar
  153. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedPubMedCentralGoogle Scholar
  154. Meuwissen T, Hayes B, Goddard M (2016) Genomic selection: a paradigm shift in animal breeding. Anim Front 6:6–14CrossRefGoogle Scholar
  155. Michel S, Ametz C, Gungor H, Epure D, Grausgruber H, Löschenberger F, Buerstmayr H (2016) Genomic selection across multiple breeding cycles in applied bread wheat breeding. Theor Appl Genet 129:1179–1189PubMedPubMedCentralCrossRefGoogle Scholar
  156. Mickelson S, See D, Meyer FD, Garner JP, Foster CR, Blake TK, Fischer AM (2003) Mapping of QTL associated with nitrogen storage and remobilization in barley (Hordeum vulgare L.) leaves. J Exp Bot 54(383):801–812.  https://doi.org/10.1093/jxb/erg084CrossRefPubMedGoogle Scholar
  157. Mohammadi M, Endelman JB, Nair S, Chao S, Jones SS, Muehlbauer GJ, Ullrich SE, Baik BK, Wise ML, Smith KP (2014) Association mapping of grain hardness, polyphenol oxidase, total phenolics, amylose content, and β-glucan in US barley breeding germplasm. Mol Breed 34(3):1229–1243CrossRefGoogle Scholar
  158. Mohammadi M, Tiede T, Smith KP (2015) PopVar: a genomewide procedure for predicting genetic variance and correlated response in bi-parental breeding populations. Crop Sci 55:2068–2077CrossRefGoogle Scholar
  159. Morell PL, Buckler ES, Ross-Ibarra J (2011) Crop genomics: advances and applications. Nat Rev Genet 13:85–96CrossRefGoogle Scholar
  160. Muller HJ (1964) The relation of recombination to mutational advance. Mutat Res-Fundam Mol Mech 1:2–9CrossRefGoogle Scholar
  161. Muñoz-Amatriaín M, Castillo AM, Chen XW, Cistué L, Vallés MP (2008) Identification and validation of QTLs for green plant percentage in barley (Hordeum vulgare L.) anther culture. Mol Breed 22:119–129CrossRefGoogle Scholar
  162. Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman J, Comadran J, Bonman J, Bockelman H, Chao S, Russell J, Waugh R, Hayes P, Muehlbauer G (2014) The USDA collection of barley landraces and cultivars: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 14 9(4):394688Google Scholar
  163. Navara S, Smith KP (2014) Using near-isogenic barley lines to validate deoxynivalenol (DON) QTL previously identified through association analysis. Theor Appl Genet 127(3):633–645PubMedCrossRefGoogle Scholar
  164. Nduulu LM, Mesfin A, Muehlbauer GJ, Smith KP (2007) Analysis of the chromosome 2(2H) region of barley associated with the correlated traits Fusarium head blight resistance and heading date. Theor Appl Genet 115:561–570PubMedCrossRefGoogle Scholar
  165. Neyhart JL, Tiede T, Lorenz AJ, Smith KP (2017) Evaluating methods of updating training data in long-term genomewide selection. G3 1499–1510.  https://doi.org/10.1534/g3.117.040550
  166. Ng PC (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812–3814PubMedPubMedCentralCrossRefGoogle Scholar
  167. Nice LM, Steffenson BJ, Brown-Guedira GL, Akhunov ED, Liu C, Kono TJY, Morrell PL, Blake TK, Horsley RD, Smith KP, Muehlbauer GJ (2016) Development and genetic characterization of an advanced backcross-nested association mapping (AB-NAM) population of wild × cultivated barley. Genetics 203(3):1453+.  https://doi.org/10.1534/genetics.116.190736
  168. Niebur WS, Rafalski JA, Smith OS, Cooper M (2004) Applications of genomics technologies to enhance rate of genetic progress for yield of maize within a commercial breeding program. In: Fischer T (ed) New directions for a diverse planet. Proceedings of 4th international crop science congress, Brisbane, QLD, Australia, 26 Sept–1 Oct 2004. The Regional Institute Ltd., Gosford, NSW, AustraliaGoogle Scholar
  169. Okada Y, Kanatani R, Arai S, Ito K (2004) Interaction between barley yellow mosaic disease-resistance genes rym1 and rym5, in the response to BaYMV strains. Breed Sci 54(4):319–325CrossRefGoogle Scholar
  170. Pan A, Hayes PM, Chen F, Chen THH, Blake T, Wright S, Karsai I, Bedö Z (1994) Genetic analysis of the components of winterhardiness in barley (Hordeum vulgare L.). Theor Appl Genet 89(7):900–910PubMedGoogle Scholar
  171. Paris M, Jones MGK, Eglinton JK (2002) Genotyping single nucleotide polymorphisms for selection of barley β-amylase alleles. Plant Mol Biol Report 20(2):149–159.  https://doi.org/10.1007/bf02799430CrossRefGoogle Scholar
  172. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln S, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335(721726):6170Google Scholar
  173. Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742PubMedPubMedCentralGoogle Scholar
  174. Pauli D, Muehlbauer GJ, Smith KP, Cooper B, Hole D, Obert DE, Ullrich SE, Blake TK (2014) Association mapping of agronomic QTLs in US spring barley breeding germplasm. Plant Genome 1 7(3)Google Scholar
  175. Paulitz TC, Steffenson BJ (2010) Biotic stress. In: Ullrich SE (ed). Barley: disease problems and solutions. Barley: production, improvement, and uses. Wiley-Blackwell, Oxford, UK.  https://doi.org/10.1002/9780470958636.ch11
  176. Piffanelli P, Ramsay L, Waugh R, Benabdelmouna A, D’Hont A, Hollricher K, Jorgensen JH, Schulze-Lefert P, Panstruga R (2004) A barley cultivation-associated polymorphism conveys resistance to powdery mildew. Nature 430(7002):887–891PubMedCrossRefGoogle Scholar
  177. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012a) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7(2):e32253PubMedPubMedCentralCrossRefGoogle Scholar
  178. Poland J, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, Dreisigacker S, Crossa J, Sánchez-Villeda H, Sorrells M, Jannink J-L (2012b) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113.  https://doi.org/10.3835/plantgenome2012.06.0006CrossRefGoogle Scholar
  179. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  180. Qi X, Lindhout P (1997) Development of AFLP markers in barley. MGG 254(3):330–336.  https://doi.org/10.1007/s004380050423CrossRefPubMedGoogle Scholar
  181. Ragot M, Lee M (2007) Marker-assisted selection in maize: current status, potential, limitations and perspectives from the private and public sectors. In: Guimaraes EP et al (eds) Marker-assisted selection, current status and future perspectives in crops, livestock, forestry, and fish. FAO, Rome, pp 117–150Google Scholar
  182. Rajala A, Peltonen-Sainio P, Jalli M, Jauhiainen L, Hannukkala A, Tenhola-Roininen T, Ramsay L, Manninen O (2017) One century of Nordic barley breeding: nitrogen use efficiency, agronomic traits and genetic diversity. J Agric Sci 155(4):582–598.  https://doi.org/10.1017/s002185961600068xCrossRefGoogle Scholar
  183. Ramsay L, Macaulay M, Ivanissevich Sd, MacLean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156(4):1997–2005PubMedPubMedCentralGoogle Scholar
  184. Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WTB, Macaulay M, MacKenzie K, Simpson C, Fuller J, Bonar N, Hayes PM, Lundqvist U, Franckowiak JD, Close TJ, Muehlbauer GJ, Waugh R (2011) INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nat Genet 43(2):169–172PubMedCrossRefGoogle Scholar
  185. Resende MFR, Muñoz P, Acosta JJ, Peter GF, Davis JM, Grattapaglia D, Resende MDV, Kirst M (2011) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol 193:617–624PubMedCrossRefGoogle Scholar
  186. Richter K, Schondelmaier J, Jung C (1998) Mapping of quantitative trait loci affecting Drechslera teres resistance in barley with molecular markers. TAG Theor Appl Genet 97(8):1225–1234.  https://doi.org/10.1007/s001220051014CrossRefGoogle Scholar
  187. Riedelsheimer C, Melchinger AE (2013) Optimizing the allocation of resources for genomic selection in one breeding cycle. Theor Appl Genet 126:2835–2848.  https://doi.org/10.1007/s00122-013-2175-9CrossRefPubMedGoogle Scholar
  188. Riggs T, Hayter A (1976) Practical aspects of the single seed descent method in barley breeding. In: Proceedings of the international barley genetics symposiumGoogle Scholar
  189. Riggs TJ, Hanson PR, Start ND, Miles DM, Morgan CL, Ford MA (1981) Comparison of spring barley varieties grown in England and Wales between 1880 and 1980. J Agric Sci 97(DEC):599–610Google Scholar
  190. Rincent R, Laloë D, Nicolas S, Altmann T, Brunel D, Revilla P, Rodriguez VM et al (2012) Maximizing the reliability of genomic selection by optimizing the calibration set of reference individuals: comparison of methods in two diverse groups of maize inbreds (Zea mays L.). Genetics 192(2):715–728PubMedPubMedCentralCrossRefGoogle Scholar
  191. Romagosa I, Han F, Ullrich SE, Hayes PM, Wesenberg DM (1999) Verification of yield QTL through realized molecular marker-assisted selection responses in a barley cross. Mol Breed 5:143–152CrossRefGoogle Scholar
  192. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genom 274(5):515–527.  https://doi.org/10.1007/s00438-005-0046-zCrossRefGoogle Scholar
  193. Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243–256PubMedPubMedCentralCrossRefGoogle Scholar
  194. Rutkoski JE, Heffner EL, Sorrells ME (2010) Genomic selection for durable stem rust resistance in wheat. Euphytica 179:161–173CrossRefGoogle Scholar
  195. Rutkoski J, Singh RP, Huerta-Espino J, Bhavani S, Poland J, Jannink J-L, Sorrells ME (2015) Efficient use of historical data for genomic selection: a case study of stem rust resistance in wheat. Plant Genome 8.  https://doi.org/10.3835/plantgenome2014.09.0046
  196. Saade S, Maurer A, Shahid M, Oakey H, Schmockel SM, Negrao S, Pillen K, Tester M (2016) Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Sci Rep 6.  https://doi.org/10.1038/srep32586
  197. Sallam AH, Smith KP (2016) Genomic selection performs similarly to phenotypic selection in barley. Crop Sci 56:2871–2881.  https://doi.org/10.2135/cropsci2015.09.0557CrossRefGoogle Scholar
  198. Sameri M, Komatsuda T (2004) Identification of quantitative trait loci (QTLs) controlling heading time in the population generated from a cross between oriental and occidental barley cultivars (Hordeum vulgare L.). Breed Sci 54(4):327–332CrossRefGoogle Scholar
  199. Sarker A, Singh M (2015) Improving breeding efficiency through application of appropriate experimental designs and analysis models: a case of lentil (Lens culinaris Medikus subsp. culinaris) yield trials. Field Crops Res 179:26–34.  https://doi.org/10.1016/j.fcr.2015.04.007CrossRefGoogle Scholar
  200. Sayed MA, Schumann H, Pillen K, Naz AA, Leon J (2012) AB-QTL analysis reveals new alleles associated to proline accumulation and leaf wilting under drought stress conditions in barley (Hordeum vulgare L.). BMC Genet 13.  https://doi.org/10.1186/1471-2156-13-61
  201. Schmidt M, Kollers S, Maasberg-Prelle A, Großer J, Schinkel B, Tomerius A, Graner A, Korzun V (2016) Prediction of malting quality traits in barley based on genome-wide marker data to assess the potential of genomic selection. Theor Appl Genet 129:203–213PubMedCrossRefGoogle Scholar
  202. Schnell FW, Utz HF (1975) F1-leistung und elternwahl euphyder züchtung von selbstbefruchtern. In: Bericht über die Arbeitstagung der Vereinigung Österreichischer Pflanzenzüchter. BAL Gumpenstein, Gumpenstein, AustriaGoogle Scholar
  203. Skadhauge B, Lok F, Breddam K, Olsen O, Bech LM, Knudsen S (2010) Barley with reduced lipoxygenase activity. Google PatentsGoogle Scholar
  204. Skov Kristensen P, Dockter C, Lundqvist U, Lu Q, Gregersen PL, Thordal-Christensen H, Hansson M (2016) Genetic mapping of the barley lodging resistance locus Erectoides-k. Plant Breed 135(4):420–428.  https://doi.org/10.1111/pbr.12377CrossRefGoogle Scholar
  205. Smith KP, Evans CK, Dill-Macky R, Gustus C, Xie W, Dong Y (2004) Host genetic effect on deoxynivalenol accumulation in Fusarium head blight of barley. Phytopathology 94(7):766–771.  https://doi.org/10.1094/PHYTO.2004.94.7.766CrossRefPubMedGoogle Scholar
  206. Solberg TR, Sonesson AK, Woolliams JA, Meuwissen THE (2009) Reducing dimensionality for prediction of genome-wide breeding values. Genet Sel Evol 41:29PubMedPubMedCentralCrossRefGoogle Scholar
  207. Souza E, Sorrells ME (1991) Prediction of progeny variation in oat from parental genetic relationships. Theor Appl Genet 82:233–241.  https://doi.org/10.1007/BF00226219CrossRefPubMedGoogle Scholar
  208. Spaner D, Rossnagel BG, Legge WG, Scoles GJ, Eckstein PE, Penner GA, Tinker NA, Briggs KG, Falk DE, Afele JC, Hayes PM, Mather DE (1999) Verification of a quantitative trait locus affecting agronomic traits in two-row barley. Crop Sci 39:248–252CrossRefGoogle Scholar
  209. Steffenson BJ (2003) Fusarium head blight of barley: impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. In: Leonard KJ, Bushnell WR (eds) Fusarium head blight of wheat and barley, pp 241–295Google Scholar
  210. Steffenson BJ, Hayes PM, Kleinhofs A (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(5):552–558.  https://doi.org/10.1007/s001220050162
  211. Storlie E, Charmet G (2013) Genomic selection accuracy using historical data generated in a wheat breeding program. Plant Genome 6.  https://doi.org/10.3835/plantgenome2013.01.0001
  212. Stracke S, Haseneyer G, Veyrieras J-B, Geiger HH, Sauer S, Graner A, Piepho H-P (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118:259–273PubMedCrossRefGoogle Scholar
  213. Stuber CW (1992) Biochemical and molecular markers in plant breeding. Plant Breed Rev 9:37–61Google Scholar
  214. Stuber CW, Polacco M, Senior ML (1999) Synergy of empirical breeding, marker-assisted selection, and genomics to increase crop yield potential. Crop Sci 39(6):1571–1583CrossRefGoogle Scholar
  215. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 20:1689–1699Google Scholar
  216. Swanston JS (1987) The consequences, for malting quality, of Hordeum laevigatum as a source of mildew resistance in barley breeding. Ann Appl Biol 110(2):351–355CrossRefGoogle Scholar
  217. Szűcs P, Blake VC, Bhat VR, Close TJ, Cuesta-Marcos A, Muehlbauer GJ, Ramsay LV, Waugh R, Hayes PM (2009) An integrated resource for barley linkage map and malting quality QTL alignment. Plant Genome 2:123–140CrossRefGoogle Scholar
  218. Szűcs P, Karsai I, von Zitzewitz J, Meszaros K, Cooper LLD, Gu YQ, Chen THH, Hayes PM, Skinner JS (2006) Positional relationships between photoperiod response QTL and photoreceptor and vernalization genes in barley. Theor Appl Genet 112:1277–1285PubMedCrossRefGoogle Scholar
  219. Talame V, Sanguineti MC, Chiapparino E, Bahri H, Ben Salem M, Forster BP, Ellis RP, Rhouma S, Zoumarou W, Waugh R, Tuberosa R (2004) Identification of Hordeum spontaneum QTL alleles improving field performance of barley grown under rainfed conditions. Ann Appl Biol 144(3):309–319CrossRefGoogle Scholar
  220. 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(5):477–485PubMedCrossRefPubMedCentralGoogle Scholar
  221. Tamang P, Neupane A, Mamidi S, Friesen T, Brueggeman R (2015) Association mapping of seedling resistance to spot form net blotch in a worldwide collection of barley. Phytopathology 26 105(4):500–508Google Scholar
  222. Tanksley D (1983) Molecular markers in plant breeding. Plant Mol Biol Rep 1:3–8CrossRefGoogle Scholar
  223. Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134(2):585–596PubMedPubMedCentralGoogle Scholar
  224. Tayeh N, Klein A, Le Paslier M-C, Jacquin F, Houtin H, Rond C, Chabert-Martinello M et al (2015) Genomic prediction in pea: effect of marker density and training population size and composition on prediction accuracy. Front Plant Sci 6:941.  https://doi.org/10.3389/fpls.2015.00941CrossRefPubMedPubMedCentralGoogle Scholar
  225. Thomas W, Comadran J, Ramsay L, Shaw P, Marshall D, Newton A, O’Sullivan D, Cockram J, Mackay I, Bayles R, White J, Kearsey M, Luo Z, Wang M, Tapsell C, Harrap D, Werner P, Klose S, Bury P, Wroth J, Argillier O, Habgood R, Glew M, Bochard A-M, Gymer P, Vequaud D, Christerson T, Allvin B, Davies N, Broadbent R, Brosnan J, Bringhurst T, Booer C, Waugh R (2014) Project report No. 528: association genetics of UK elite barley (AGOUEB). HGCA. http://cereals.ahdb.org.uk/media/337662/pr528-final-project-report.pdf
  226. Tiede T, Kumar L, Mohamadi M, Smith KP (2015) Predicting genetic variance in bi-parental breeding populations is more accurate when explicitly modeling the segregation of informative genomewide markers. Mol Breed.  https://doi.org/10.1007/s11032-015-0390-6CrossRefGoogle Scholar
  227. Toojinda T, Baird E, Booth A, Broers L, Hayes P, Powell W, Thomas W, Vivar H, Young G (1998) Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development. Theor Appl Genet 96(1):123–131CrossRefGoogle Scholar
  228. Torkamaneh D, Laroche J, Bastien M, Abed A, Belzile F (2017) Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. BMC Bioinform 18(1):5.  https://doi.org/10.1186/s12859-016-1431-9CrossRefGoogle Scholar
  229. Tyrka M, Perovic D, Wardyńska A, Ordon F (2008) A new diagnostic SSR marker for selection of theRym4/Rym5 locus in barley breeding. J Appl Genet 49(2):127–134.  https://doi.org/10.1007/bf03195605CrossRefPubMedPubMedCentralGoogle Scholar
  230. van Berloo R, Aalbers H, Werkman A, Niks RE (2001) Resistance QTL confirmed through development of QTL-NILs for barley leaf rust resistance. Mol Breed 8(3):187–195CrossRefGoogle Scholar
  231. Visscher PM, Haley CS, Knott SA (1996) Mapping QTLs for binary traits in backcross and F2 populations. Genet Res 68:55–63CrossRefGoogle Scholar
  232. von Zitzewitz J, Cuesta-Marcos A, Condon F, Castro AJ, Chao S, Corey A, Filichkin T, Fisk SP, Gutierrez L, Haggard K, Karsai I, Muehlbauer GJ, Smith KP, Veisz O, Hayes PM (2011) The genetics of winterhardiness in barley: perspectives from genome-wide association mapping. Plant Genome 4(1):76–91CrossRefGoogle Scholar
  233. Wang M, Jiang N, Jia T, Leach L, Cockram J, Waugh R, Ramsay L, Thomas B, Luo Z (2012) Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 124(2):233–246PubMedCrossRefPubMedCentralGoogle Scholar
  234. Waugh R, Jannink J-L, Muehlbauer GJ, Ramsay L (2009) The emergence of whole genome association scans in barley. Curr Opin Plant Biol 12:218–222PubMedCrossRefPubMedCentralGoogle Scholar
  235. Werner K, Friedt W, Ordon F (2005) Strategies for pyramiding resistance genes against the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2). Mol Breed 16(1):45–55CrossRefGoogle Scholar
  236. Wiberg A (1974) Genetical studies of spontaneous sources of resistance to powdery mildew in barley. Hereditas 77(1):89–148.  https://doi.org/10.1111/j.1601-5223.1974.tb01357.xCrossRefPubMedPubMedCentralGoogle Scholar
  237. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48(2):391–407CrossRefGoogle Scholar
  238. Yun SJ, Gyenis L, Bossolini E, Hayes PM, Matus I, Smith KP, Steffenson BJ, Tuberosa R, Muelbauer GJ (2006) Validation of quantitative trait loci for multiple disease resistance in barley using advanced backcross lines developed with a wild barley. Crop Sci 46:1179–1186CrossRefGoogle Scholar
  239. Zhao Y, Gowda M, Liu W, Wurschum T, Maurer HP, Longin FH, Ranc N, Reif JC (2012) Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124:769–776PubMedCrossRefPubMedCentralGoogle Scholar
  240. Zhong S, Dekkers JC, Fernando RL, Jannink J-L (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355–364PubMedPubMedCentralCrossRefGoogle Scholar
  241. Zhou H, Steffenson BJ, Muehlbauer G, Wanyera R, Njau P, Ndeda S (2014) Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm. Theor Appl Genet 127(6):1293–1304PubMedPubMedCentralCrossRefGoogle Scholar
  242. Zhu H, Gilchrist L, Hayes P, Kleinhofs A, Kudrna D, Liu Z, Prom L, Steffenson B, Toojinda T, Vivar H (1999) Does function follow form? Principal QTLs for Fusarium head blight (FHB) resistance are coincident with QTLs for inflorescence traits and plant height in a doubled-haploid population of barley. Theor Appl Genet 99(7):1221–1232CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Kevin P. Smith
    • 1
  • William Thomas
    • 2
  • Lucia Gutierrez
    • 3
  • Hazel Bull
    • 4
  1. 1.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulUSA
  2. 2.The James Hutton InstituteDundeeUK
  3. 3.Department of AgronomyUniversity of WisconsinMadisonUSA
  4. 4.James Hutton LimitedDundeeUK

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