Skip to main content
SpringerLink
Log in

Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.)

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

The deployment of genetic markers is of interest in crop assessment and breeding programmes, due to the potential savings in cost and time afforded. As part of the internationally recognised framework for the awarding of Plant Breeders’ Rights (PBR), new barley variety submissions are evaluated using a suite of morphological traits to ensure they are distinct, uniform and stable (DUS) in comparison to all previous submissions. Increasing knowledge of the genetic control of many of these traits provides the opportunity to assess the potential of deploying diagnostic/perfect genetic markers in place of phenotypic assessment. Here, we identify a suite of 25 genetic markers assaying for 14 DUS traits, and implement them using a single genotyping platform (KASPar). Using a panel of 169 UK barley varieties, we show that phenotypic state at three of these traits can be perfectly predicted by genotype. Predictive values for an additional nine traits ranged from 81 to 99 %. Finally, by comparison of varietal discrimination based on phenotype and genotype resulted in correlation of 0.72, indicating that deployment of molecular markers for varietal discrimination could be feasible in the near future. Due to the flexibility of the genotyping platform used, the genetic markers described here can be used in any number or combination, in-house or by outsourcing, allowing flexible deployment by users. These markers are likely to find application where tracking of specific alleles is required in breeding programmes, or for potential use within national assessment programmes for the awarding of PBRs.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Arens P, Mansilla C, Deinum D, Cavellini L, Moretti A, Rolland S, van der Schoot H, Calvache D, Ponz F, Collonnier C, Mathis R, Smilde D, Caranta C, Vosman B (2010) Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing. Theor Appl Genet 120:655–664. doi:10.1007/s00122-099-1183-2

    Article  PubMed  CAS  Google Scholar 

  • Boyd WJR, Li CD, Grime CE, Cakir CR, Potipibol S, Kaveeta L, Men S, Jalal Kamali MR, Barr AR, Moody DB, Lance RCM, Logue SJ, Raman H, Read BJ (2003) Conventional and molecular genetic analyses of factors contributing to the variation in the timing of heading among spring barley (H. vulgare L.) genotypes grown over a mild winter growing season. Aust J Agric Res 54:1277–1301. doi:10.1071/ar03014

    Article  CAS  Google Scholar 

  • Chono M, Honda I, Zeniya H, Yoneyama K, Saisho D, Takeda K, Takatsuto S, Hoshino T, Wantanabe Y (2003) A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor. Plant Physiol 133:1209–1219. doi:10.1104/pp103.026195

    Article  PubMed  CAS  Google Scholar 

  • Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S et al (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:e582. doi:10.1186/1471-2164-10-582

    Article  Google Scholar 

  • Cockram J, Jones H, Leigh FJ, O’Sullivan D, Powell W, Laurie DA, Greenland AJ (2007a) Control of flowering time in temperate cereals: genes, domestication and sustainable productivity. J Exp Bot 58:1231–1244. doi:10.1093/jxb/erm042

    Article  PubMed  CAS  Google Scholar 

  • Cockram J, Chiapparino E, Taylor SA, Stamati K, Donini P, Laurie DA, O’Sullivan DM (2007b) Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype. Theor Appl Genet 115:993–1001. doi:10.1007/s00122-007-0626-x

    Article  PubMed  CAS  Google Scholar 

  • Cockram J, Mackay IJ, O’Sullivan DM (2007c) The role of double-stranded break repair in the creation of phenotypic diversity at cereal VRN1 loci. Genetics 177:1–5. doi:10.1534/genetics.107.074765

    Article  Google Scholar 

  • 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 (Hordeum vulgare ssp. vulgare L.). BMC Genet 9:e16. doi:10.1186/1471-2156-9-16

    Article  Google Scholar 

  • Cockram J, Norris C, O’Sullivan DM (2009) PCR markers diagnostic for seasonal growth habit in barley. Crop Sci 49:403–410. doi:10.2135/cropsci2008.07.0398

    Article  CAS  Google Scholar 

  • Cockram J, Howells RM, O’Sullivan DM (2010a) Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals. Genome 53:231–240. doi:10.1139/g09-101

    Article  PubMed  CAS  Google Scholar 

  • Cockram J, White J, Zuluaga DL, Smith D, Comadran J et al (2010b) Genome-wide association mapping to candidate polymorphism resolution in the un-sequenced barley genome. Proc Natl Acad Sci USA 107:21611–21616. doi:10.1073/pnas.1010179107

    Article  PubMed  CAS  Google Scholar 

  • Devos KM (2005) Updating the ‘crop circle’. Curr Opin Plant Biol 8:155–162. doi:10.1016/j.pbi.2005.01.005

    Article  PubMed  CAS  Google Scholar 

  • Dubcovsky J, Chen C, Yan L (2005) Molecular characterization of allelic variation at the VRN-H2 vernalization locus in barley. Mol Breed 15:395–407. doi:10.1007/s11032-005-0084-6

    Article  CAS  Google Scholar 

  • Ellis RP, J Russell, L Ramsay, R Waugh (1999) Barley domestication–Hordeum spontaneum, a source of new genes for crop improvement. Scottish Crop Research Institute report. http://www.scri.ac.uk/scri/file/individualreports/1999/14BARLEY.PDF. Accessed 25 Jan 2012

  • Faure S, Higgins J, Turner A, Laurie DA (2007) The FLOWERING LOCUS-T-like family in barley (Hordeum vulgare). Genetics 176:599–609. doi:10.1534/genetics.106.069500

    Article  PubMed  CAS  Google Scholar 

  • Franckowiak JD (1995) Notes on linkage drag in Bowman backcross derived lines of spring barley. Barley Genet Newsl 24:63–70

    Google Scholar 

  • Gunjaca J, Buhinicek I, Jukic M, Sarcevic H, Vragolovic A, Kozic Z, Jambrovic A, Pejic I (2008) Discriminating maize inbred lines using molecular and DUS data. Euphytica 161:165–172. doi:10.1007/s10681-007-9518-z

    Article  CAS  Google Scholar 

  • Ibáñez J, Vargas AM, Palancar M, Borrego J, de Andrés MT (2009a) Genetic relationships among table-grape varieties. Am J Enol Vitic 60:35–42

    Google Scholar 

  • Ibáñez J, Vélez MD, de Andrés MT, Borrego J (2009b) Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine. Theor Appl Genet 119:1213–1222. doi:10.1007/s00122-009-1122-2

    Article  PubMed  Google Scholar 

  • Islam AKMR (1983) Ditelosomic additions of barley chromosomes to wheat. In: Sakamoto S (ed) Proceedings of the 6th international wheat symposium. Maruzen Co. Ltd, Koyota, pp 223–238

    Google Scholar 

  • Jia Q, Zhang J, Wescott S, Zhang XQ, Bellgard M, Lance R, Li C (2009) GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley. Funct Integr Genomics 9:255–262. doi:10.1007/s10142-009-0120-4

    Article  PubMed  CAS  Google Scholar 

  • Karsai I, Szűcs P, Mészáros K, Filichkina T, Hayes PM, Skinner JS, Láng L, Bedö Z (2005) The Vrn-H2 locus is a major determinant of flowering time in a facultative x winter growth habit barley (Hordeum vulgare L.) mapping population. Theor Appl Genet 110:1458–1466. doi:10.1007/s00122-005-1979-7

    Article  PubMed  CAS  Google Scholar 

  • Komatsuda T, Mano Y (2002) Molecular mapping of the intermedium spike-c (int-c) and non-brittle rachis 1 (btr1) loci in barley (Hordeum vulgare L.). Theor Appl Genet 105:85–90. doi:10.1007/s00122-001-0858-0

    Article  PubMed  CAS  Google Scholar 

  • Komatsuda T, Tanno K (2004) Comparative high resolution map of the six-rowed spike locus 1 (vrs1) in several populations of barley, Hordeum vulgare L. Hereditas 141:68–73. doi:0.1111/j.1601-5223.2004.01820.x

    Article  PubMed  CAS  Google Scholar 

  • Komatsuda T, Pourkheirandish M, He C, 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 104:1424–1429. doi:10.1073/pnas.0608580104

    Google Scholar 

  • Laurie DA, Pratchett N, Bezant JH, Snape JW (1995) RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. Genome 38:575–585. doi:10.1139/g95-074

    Article  PubMed  CAS  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi:10.1093/bioinformatics/bti282

    Article  PubMed  CAS  Google Scholar 

  • Lundqvist U, Franckowiak J, Konishi T (1996) New and revised descriptions of barley genes. Barley Genet Newsl 26:22–43

    Google Scholar 

  • Lundqvist U, Franckowiak JD, Konoshi T (1997) New and revised descriptions of barley genes. Barley Genet Newsl 26:22–516

    Google Scholar 

  • Matzumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hiri K, Itoh T, Sato K (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol 156:20–28. doi:10.1104/pp110.171579

    Article  Google Scholar 

  • Maughan PJ, Yourstone SM, Byers RL, Smith SM, Udall JA (2010) Single-nucleotide polymorphism genotyping in mapping populations via genomic reduction and next-generation sequencing: proof of concept. Plant Genome 3:166–178. doi:10.3835/plantgenome2010.07.0016

    Article  CAS  Google Scholar 

  • Mayer KFX, Martis M, Hedley PE, Šimokova H, Liu H, Morris JA, Steuernagel B, Taudien S et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263. doi:10.1105/tpc.110.082537

    Article  PubMed  CAS  Google Scholar 

  • Nair SK, Wang N, Turuspekov Y, Pourkheirandish M, Sinsuwongwat S et al (2010) Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proc Natl Acad Sci USA 107:490–495. doi:10.1073/pnas.0909097107

    Article  PubMed  CAS  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. doi:10.1038/nrg2986

    Article  PubMed  CAS  Google Scholar 

  • Noli E, Teriaca MS, Sanguineti MC, Conti S (2008) Utilization of SSR and AFLP markers for the assessment of distinctness in durum wheat. Mol Breed 22:301–313. doi:10.1007/s11032-008-9176-4

    Article  CAS  Google Scholar 

  • Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WT, 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 43:169–172. doi:10.1038/ng.745

  • Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang W, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360–1364. doi:10.1038/ng.197

    Article  PubMed  CAS  Google Scholar 

  • Turner A, Beales J, Faure S, Dunford RP, Laurie DA (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034. doi:10.1126/science.1117619

    Article  PubMed  CAS  Google Scholar 

  • Von Korff M, Grando S, Del Greco A, This D, Baum M, Ceccarelli S (2008) Quantitative trait loci associated with adaptation in Mediterranean dryland conditions in barley. Theor Appl Genet 117:653–669. doi:10.1007/s00122-008-0787-2

    Article  Google Scholar 

  • von Zitzewitz J, Szűcs P, Dubcovsky J, Yan L, Francia E, Pecchioni N, Casas A, Chen THH, Hayes P, Skinner J (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59:449–467. doi:10.1007/s11103-005-0351-2

    Article  CAS  Google Scholar 

  • Waugh R, Marshall D, Thomas B, Comadran J, Russell J, Close T, Stein N, Hayes P, Muehlbauer G, Cockram J, O’Sullivan D, Mackay I, Flavell A, Agoueb A, Barleycap RL (2010) Whole-genome association mapping in elite inbred crop varieties. Genome 53:967–972. doi:10.1139/G10-078

    Article  PubMed  CAS  Google Scholar 

  • Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Bruggeman RS, Meuhlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101:1093–1099. doi:10.1007/s001220051584

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was funded by Defra grant 2009H. We thank the James Hutton Institute for provision of the European barley germplasm.

Author information

Authors and Affiliations

  1. John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntington Road, Cambridge, CB3 0LE, UK

    James Cockram, Huw Jones, Carol Norris & Donal M. O’Sullivan

Authors
  1. James Cockram
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Huw Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Carol Norris
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Donal M. O’Sullivan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to James Cockram or Donal M. O’Sullivan.

Additional information

Communicated by P. Hayes.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cockram, J., Jones, H., Norris, C. et al. Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.). Theor Appl Genet 125, 1735–1749 (2012). https://doi.org/10.1007/s00122-012-1950-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-012-1950-3

Keywords

Search

Navigation