Skip to main content
SpringerLink
Log in

Sequence Diversity and Structural Variation

  • Chapter
  • First Online:
The Barley Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Barley is a phenotypically and genetically diverse crop that has adapted successfully to many agricultural environments. Moreover, its wild progenitor species is still abundant in Western Asia and provides a large untapped reservoir of allelic variation. Deriving a complete inventory of sequence variants of the barley genome for targeted utilization of natural diversity in crop improvement has long been a key goal of barley research. While the assessment of genetic diversity has traditionally focused on a few selected—mostly genic—loci, recent technology advances have made it possible to simultaneously obtain genome-wide sequence information for genes and noncoding regions alike. In addition to small-scale sequence changes, larger scale structural variation such as presence–absence or copy number variants are widespread throughout the barley genome. These types of variation can affect large genomic regions, possibly containing multiple genes or adjacent regulatory regions. Here, we review the recent progress on assaying genetic variants, large and small, in barley, understanding the mutational processes underlying them, and their relationship to phenotype and ultimately crop performance.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Agmon N, Pur S, Liefshitz B, Kupiec M (2009) Analysis of repair mechanism choice during homologous recombination. Nucleic Acids Res 37:5081–5092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aliyeva-Schnorr L, Beier S, Karafiatova M, Schmutzer T, Scholz U, Dolezel J, Stein N, Houben A (2015) Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant J 84:385–394

    Article  CAS  PubMed  Google Scholar 

  • Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363–376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ames N, Dreiseitl A, Steffenson BJ, Muehlbauer GJ (2015) Mining wild barley for powdery mildew resistance. Plant Pathol 64:1396–1406

    Article  CAS  Google Scholar 

  • Badr A, Sch R, El Rabey H, Effgen S, Ibrahim H, Pozzi C, Rohde W, Salamini F (2000) On the origin and domestication history of barley (Hordeum vulgare). Mol Biol Evol 17:499–510

    Article  CAS  PubMed  Google Scholar 

  • Begun DJ, Aquadro CF (1992) Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356:519–520

    Article  CAS  PubMed  Google Scholar 

  • Beier S, Himmelbach A, Colmsee C, Zhang X-Q, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 4

    Google Scholar 

  • Bennetzen JL, Wang H (2014) The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu Rev Plant Biol 65:505–530

    Article  CAS  PubMed  Google Scholar 

  • Berger GL, Liu S, Hall MD, Brooks WS, Chao S, Muehlbauer GJ, Baik B-K, Steffenson B, Griffey CA (2013) Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping. Theor Appl Genet 126:693–710

    Article  CAS  PubMed  Google Scholar 

  • Bernardo R (2017) Prospective targeted recombination and genetic gains for quantitative traits in maize. Plant Genome 10

    Google Scholar 

  • Bockelman HE, Valkoun J (2010) Barley germplasm conservation and resources. Barley: improvement, production, and uses. Wiley-Blackwell, Oxford, UK, pp 144–159

    Google Scholar 

  • Cantalapiedra CP, Contreras-Moreira B, Silvar C, Perovic D, Ordon F, Gracia MP, Igartua E, Casas AM (2016) A cluster of nucleotide-binding site–leucine-rich repeat genes resides in a barley powdery mildew resistance quantitative trait loci on 7HL. Plant Genome 9

    Google Scholar 

  • Carvalho CM, Lupski JR (2016) Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 17:224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature 517:608–611

    Article  CAS  PubMed  Google Scholar 

  • Charlesworth B, Morgan MT, Charlesworth D (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289–1303

    PubMed  PubMed Central  CAS  Google Scholar 

  • Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, Deyoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cockram J, Jones H, Leigh FJ, O’Sullivan D, Powell W, Laurie DA, Greenland AJ (2007) Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity. J Exp Bot 58:1231–1244

    Article  CAS  PubMed  Google Scholar 

  • Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44:1388–1392

    Article  CAS  PubMed  Google Scholar 

  • Dahleen LS, Bregitzer P, Mornhinweg D, Klos KE (2015) Genetic diversity for Russian wheat aphid resistance as determined by genome-wide association mapping and inheritance in progeny. Crop Sci 55:1925–1933

    Article  CAS  Google Scholar 

  • Dempewolf H, Baute G, Anderson J, Kilian B, Smith C, Guarino L (2017) Past and future of wild relatives in crop breeding. Crop Sci 57:1070–1082

    Article  Google Scholar 

  • Fang Z, Gonzales AM, Clegg MT, Smith KP, Muehlbauer GJ, Steffenson BJ, Morrell PL (2014) Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3-Genes Genom Genet 4:1193–1203

    CAS  Google Scholar 

  • Filler Hayut S, Melamed Bessudo C, Levy AA (2017) Targeted recombination between homologous chromosomes for precise breeding in tomato. Nat Commun 8:15605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Francia E, Rizza F, Cattivelli L, Stanca A, Galiba G, Toth B, Hayes P, Skinner J, Pecchioni N (2004) Two loci on chromosome 5H determine low-temperature tolerance in a ‘Nure’ (winter) × ‘Tremois’ (spring) barley map. Theor Appl Genet 108:670–680

    Article  CAS  PubMed  Google Scholar 

  • Francia E, Morcia C, Pasquariello M, Mazzamurro V, Milc JA, Rizza F, Terzi V, Pecchioni N (2016) Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley. Plant Mol Biol 92:161–175

    Article  CAS  PubMed  Google Scholar 

  • Fu D, Szűcs P, Yan L, Helguera M, Skinner JS, von Zitzewitz J, Hayes PM, Dubcovsky J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Genet Genomics 273:54–65

    Article  CAS  PubMed  Google Scholar 

  • Fujii M, Yokosho K, Yamaji N, Saisho D, Yamane M, Takahashi H, Sato K, Nakazono M, Ma JF (2012) Acquisition of aluminium tolerance by modification of a single gene in barley. Nat Commun 3:713

    Article  CAS  PubMed  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Taylor T (1996) Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144:1883–1891

    PubMed  PubMed Central  CAS  Google Scholar 

  • Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH (2009) A first-generation haplotype map of maize. Science 326:1115–1117

    Article  CAS  PubMed  Google Scholar 

  • Graebner RC, Wise M, Cuesta-Marcos A, Geniza M, Blake T, Blake VC, Butler J, Chao S, Hole DJ, Horsley R (2015) Quantitative trait loci associated with the tocochromanol (vitamin E) pathway in barley. PLoS One 10:e0133767

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gutiérrez 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 4:256–272

    Article  Google Scholar 

  • Hastings PJ, Lupski JR, Rosenberg SM, Ira G (2009) Mechanisms of change in gene copy number. Nat Rev Genet 10:551

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hodgkinson A, Eyre-Walker A (2011) Variation in the mutation rate across mammalian genomes. Nat Rev Genet 12:756

    Article  CAS  PubMed  Google Scholar 

  • Hudson RR, Kaplan NL (1995) Deleterious background selection with recombination. Genetics 141:1605–1617

    PubMed  PubMed Central  CAS  Google Scholar 

  • International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716

    Article  CAS  Google Scholar 

  • Jakob SS, Rodder D, Engler JO, Shaaf S, Ozkan H, Blattner FR, Kilian B (2014) Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling. Genome Biol Evol 6:685–702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94:7704–7711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knox AK, Dhillon T, Cheng H, Tondelli A, Pecchioni N, Stockinger EJ (2010) CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet 121:21–35

    Article  PubMed  Google Scholar 

  • Konishi T, Linde-Laursen I (1988) Spontaneous chromosomal rearrangements in cultivated and wild barleys. Theor Appl Genet 75:237–243

    Article  Google Scholar 

  • Künzel G (1982) Differences between genetic and physical centromere distances in the case of two genes for male sterility in barley. Theor Appl Genet 64:25–29

    Article  PubMed  Google Scholar 

  • Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412

    PubMed  PubMed Central  Google Scholar 

  • Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M (2012) Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol 30:771–776

    Article  CAS  PubMed  Google Scholar 

  • Lee S-I, Kim N-S (2014) Transposable elements and genome size gariations in plants. Genomics Inform 12:87–97

    Article  PubMed  PubMed Central  Google Scholar 

  • Looseley ME, Bayer M, Bull H, Ramsay L, Thomas W, Booth A, De La Fuente Canto C, Morris J, Hedley PE, Russell J (2017) Association mapping of diastatic power in UK winter and spring barley by exome sequencing of phenotypically contrasting variety sets. Front Plant Sci 8

    Google Scholar 

  • Loscos J, Igartua E, Contreras-Moreira B, Gracia MP, Casas AM (2014) HvFT1 polymorphism and effect—survey of barley germplasm and expression analysis. Front Plant Sci 5:251

    Article  PubMed  PubMed Central  Google Scholar 

  • Marroni F, Pinosio S, Morgante M (2014) Structural variation and genome complexity: is dispensable really dispensable? Curr Opin Plant Biol 18:31–36

    Article  CAS  PubMed  Google Scholar 

  • Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R (2013a) Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 76:718–727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 KF, 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 76:494–505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Simkova H, Stankova H, Vrana J, Chan S, Munoz-Amatriain M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Dolezel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427–433

    Article  CAS  PubMed  Google Scholar 

  • Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R, Chao S, Dong Y, Schwarz P, Muehlbauer G, Smith K (2011) Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breed 27:439–454

    Article  Google Scholar 

  • Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23:23–35

    Article  Google Scholar 

  • McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM (2012) Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol 159:1295–1308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morgante M, De Paoli M, Slobodanka R (2007) Transposable elements and the plant pan-genomes. Curr Opin Plant Biol 10:149–155

    Article  CAS  PubMed  Google Scholar 

  • Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KFX, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N (2013) Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol 14:R58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, Chao S, Russell J, Waugh R, Hayes PM (2014a) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 9:e94688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muñoz-Amatriaín M, Cuesta-Marcos A, Hayes PM, Muehlbauer GJ (2014b) Barley genetic variation: implications for crop improvement. Brief Funct Genomics 13:341–350

    Article  PubMed  Google Scholar 

  • Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Šimková H, Doležel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ (2015) Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J 84:216–227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Neumann K, Zhao Y, Chu J, Keilwagen J, Reif JC, Kilian B, Graner A (2017) Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis. BMC Plant Biol 17:137

    Article  PubMed  PubMed Central  Google Scholar 

  • Neupane A, Tamang P, Brueggeman R, Friesen T (2015) Evaluation of a barley core collection for spot form net blotch reaction reveals distinct genotype-specific pathogen virulence and host susceptibility. Phytopathology 105:509–517

    Article  CAS  PubMed  Google Scholar 

  • Nice LM, Steffenson BJ, Blake TK, Horsley RD, Smith KP, Muehlbauer GJ (2017) Mapping agronomic traits in a wild barley advanced backcross–nested association mapping population. Crop Sci

    Google Scholar 

  • Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443–451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nitcher R, Distelfeld A, Tan C, Yan L, Dubcovsky J (2013) Increased copy number at the HvFT1 locus is associated with accelerated flowering time in barley. Mol Genet Genomics 288:261–275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16

    Article  PubMed  PubMed Central  Google Scholar 

  • Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E (2014) The barley Frost resistance-H2 locus. Funct Integr Genomics 14:85–100

    Article  CAS  PubMed  Google Scholar 

  • Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, le Paslier MC, Zaina G, Bastien C, Cattonaro F, Marroni F, Morgante M (2016) Characterization of the poplar pan-genome by genome-wide identification of structural variation. Mol Biol Evol 33:2706–2719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R, Mascher M, Himmelbach A, Gottwald S, Nair SK, Tagiri A, Yukuhiro F, Nagamura Y, Kanamori H, Matsumoto T, Willcox G, Middleton CP, Wicker T, Walther A, Waugh R, Fincher GB, Stein N, Kumlehn J, Sato K, Komatsuda T (2015) Evolution of the grain dispersal system in barley. Cell 162:527–539

    Article  CAS  PubMed  Google Scholar 

  • Ramage R, Burnham C, Hagberg A (1961) A summary of translocation studies in barley. Crop Sci 1:277–279

    Article  Google Scholar 

  • Rey M-D, Calderón MC, Prieto P (2015) The use of the ph1b mutant to induce recombination between the chromosomes of wheat and barley. Front Plant Sci 6:160

    Article  PubMed  PubMed Central  Google Scholar 

  • Richards JK, Friesen TL, Brueggeman RS (2017) Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci. Theor Appl Genet 130:915–927

    Article  CAS  PubMed  Google Scholar 

  • Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243–256

    Article  PubMed  PubMed Central  Google Scholar 

  • Russell J, Dawson IK, Flavell AJ, Steffenson B, Weltzien E, Booth A, Ceccarelli S, Grando S, Waugh R (2011) Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes. New Phytol 191:564–578

    Article  PubMed  Google Scholar 

  • Russell J, Mascher M, Dawson IK, Kyriakidis S, Calixto C, Freund F, Bayer M, Milne I, Marshall-Griffiths T, Heinen S (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 48:1024–1030

    Article  CAS  PubMed  Google Scholar 

  • Sadhu MJ, Bloom JS, Day L, Kruglyak L (2016) CRISPR-directed mitotic recombination enables genetic mapping without crosses. Science 352:1113–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scherrer B, Isidore E, Klein P, Kim JS, Bellec A, Chalhoub B, Keller B, Feuillet C (2005) Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell 17:361–374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5:e1000734

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steffenson BJ, Olivera P, Roy JK, Jin Y, Smith KP, Muehlbauer GJ (2007) A walk on the wild side: mining wild wheat and barley collections for rust resistance genes. Crop Pasture Sci 58:532–544

    Article  Google Scholar 

  • Stein N, Steuernagel B (2014) Advances in sequencing the barley genome. In: Genomics of plant genetic resources. Springer

    Google Scholar 

  • Stockinger EJ, Skinner JS, Gardner KG, Francia E, Pecchioni N (2007) Expression levels of barley Cbf genes at the Frost resistance-H2 locus are dependent upon alleles at Fr-H1 and Fr-H2. Plant J 51:308–321

    Article  CAS  PubMed  Google Scholar 

  • Sutton T, Baumann U, Hayes J, Collins NC, Shi B-J, Schnurbusch T, Hay A, Mayo G, Pallotta M, Tester M (2007) Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318:1446–1449

    Article  CAS  PubMed  Google Scholar 

  • Szűcs P, Skinner JS, Karsai I, Cuesta-Marcos A, Haggard KG, Corey AE, Chen TH, Hayes PM (2007) Validation of the VRN-H2/VRN-H1 epistatic model in barley reveals that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity. Mol Genet Genomics 277:249–261

    Article  CAS  PubMed  Google Scholar 

  • Taketa S, Amano S, Tsujino Y, Sato T, Saisho D, Kakeda K, Nomura M, Suzuki T, Matsumoto T, Sato K, Kanamori H, Kawasaki S, Takeda K (2008) Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proc Natl Acad Sci USA 105:4062–4067

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 105:500–508

    Article  CAS  PubMed  Google Scholar 

  • Tang H, Lyons E, Town CD (2015) Optical mapping in plant comparative genomics. GigaScience 4:3

    Article  PubMed  PubMed Central  Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    Article  CAS  PubMed  Google Scholar 

  • Tondelli A, Xu X, Moragues M, Sharma R, Schnaithmann F, Ingvardsen C, Manninen O, Comadran J, Russell J, Waugh R, Schulman AH, Pillen K, Rasmussen SK, Kilian B, Cattivelli L, Thomas WTB, Flavell AJ (2013) Structural and temporal variation in genetic diversity of European spring two-row barley cultivars and association mapping of quantitative traits. Plant Genome 6

    Google Scholar 

  • Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J, Thomas W, Waugh R, Pecchioni N, Romagosa I, Comadran J (2013) Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics 14:424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • von Zitzewitz J, Szűcs P, Dubcovsky J, Yan L, Francia E, Pecchioni N, Casas A, Chen TH, Hayes PM, Skinner JS (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59:449–467

    Article  CAS  Google Scholar 

  • von Zitzewitz J, Cuesta-Marcos A, Condon F, Castro AJ, Chao S, Corey A, Filichkin T, Fisk SP, Gutierrez L, Haggard K (2011) The genetics of winterhardiness in barley: perspectives from genome-wide association mapping. Plant Genome 4:76–91

    Article  Google Scholar 

  • Wang Q, Dooner HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 103:17644–17649

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang C, Hu S, Gardner C, Lubberstedt T (2017a) Emerging avenues for utilization of exotic germplasm. Trends Plant Sci 22:624–637

    Article  CAS  PubMed  Google Scholar 

  • Wang R, Leng Y, Ali S, Wang M, Zhong S (2017b) Genome-wide association mapping of spot blotch resistance to three different pathotypes of Cochliobolus sativus in the USDA barley core collection. Mol Breed 37:44

    Article  CAS  Google Scholar 

  • Weischenfeldt J, Symmons O, Spitz F, Korbel JO (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet 14:125–138

    Article  CAS  PubMed  Google Scholar 

  • Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biol 8:e1000409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamasaki M, Tenaillon MI, Bi IV, Schroeder SG, Sanchez-Villeda H, Doebley JF, Gaut BS, McMullen MD (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17:2859–2872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu P, Wang C, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Tang S (2011) Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genomics 12:372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA

    María Muñoz-Amatriaín

  2. Leibniz Institute of Plant Genetic and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany

    Martin Mascher

  3. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany

    Martin Mascher

Authors
  1. María Muñoz-Amatriaín
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin Mascher
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to María Muñoz-Amatriaín .

Editor information

Editors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Sachsen-Anhalt, Germany

    Nils Stein

  2. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA

    Gary J. Muehlbauer

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Muñoz-Amatriaín, M., Mascher, M. (2018). Sequence Diversity and Structural Variation. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_8

Download citation

Publish with us

Policies and ethics

Search

Navigation