Molecular Breeding

, 38:51 | Cite as

Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike

  • Ana M. CasasEmail author
  • Bruno Contreras-Moreira
  • Carlos P. Cantalapiedra
  • Shun Sakuma
  • María Pilar Gracia
  • Marian Moralejo
  • José Luis Molina-Cano
  • Takao Komatsuda
  • Ernesto Igartua


Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and has been often associated to phenotypic traits beyond spike type. Comprehensive re-sequencing Vrs1 revealed three two-rowed alleles (Vrs1.b2; Vrs1.b3; Vrs1.t1) and four six-rowed (vrs1.a1; vrs1.a2; vrs1.a3; vrs1.a4) in the natural population. However, the current knowledge about Vrs1 alleles and its distribution among Spanish barley subpopulations is still underexploited. We analyzed the gene in a panel of 215 genotypes, made of Spanish landraces and European cultivars. Among 143 six-rowed accessions, 57 had the vrs1.a1 allele, 83 were vrs1.a2, and three showed the vrs1.a3 allele. Vrs1.b3 was found in most two-rowed accessions, and a new allele was observed in 7 out of 50 two-rowed Spanish landraces. This allele, named Vrs1.b5, contains a ‘T’ insertion in exon 2, originally proposed as the causal mutation giving rise to the six-row vrs1.a2 allele, but has an additional upstream deletion that results in the change of 15 amino acids and a potentially functional protein. We conclude that eight Vrs1 alleles (Vrs1.b2, Vrs1.b3, Vrs1.b5, Vrs1.t1, vrs1.a1, vrs1.a2, vrs1.a3, vrs1.a4) discriminate two and six-rowed barleys. The markers described will be useful for DUS identification, plant breeders, and other crop scientists.


Barley Landraces Vrs1 SNP 



The authors would like to thank Dr. Alessandro Tondelli, who provided data for marker 12_30896 on the barley genotypes tested by Digel et al. (2016). This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness grants AGL2010-21929, AGL2013-48756-R, RFP2012-00015-00-00, RTA2012-00033-C03-02, and EUI2009-04075 (national code for Plant-KBBE project ExpResBar). CPC was funded by the Spanish Ministry of Economy, Industry and Competitiveness grant no. BES-2011-045905 (linked to project AGL2010-21929). TK and SS were supported by a research fund by the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics for Agricultural Innovation grants no. TRS1002). SS was supported by a Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellow for Research Abroad and a Grant-in-Aid for Young Scientists (B) (no. 16 K18635).

Authors’ contributions

AMC, EI, and TK conceived this work. PG, MM, and JMC selected and provided the plant accessions. AMC and SS performed laboratory work. AMC, CPC, and BCM analyzed the DNA sequence data. BCM was responsible for the phylogenetic analysis. AMC, BCM, EI, and TK drafted the document. All the authors read and approved the manuscript.

Supplementary material

11032_2018_816_MOESM1_ESM.xlsx (53 kb)
ESM 1 (XLSX 52 kb)
11032_2018_816_MOESM2_ESM.pdf (74 kb)
ESM 2 Multiple alignment of genomic sequences of 1135 bp from different haplotypes of the Vrs1 gene, computed with clustal-omega-1.2.1. The gaps in positions 383 (which corresponds to the new allele found in accession SBCC153) and 869 (Morex) were manually corrected. Variants in positions of Morex_contig_135757 listed in Table 2 (1067, 1239, 1246, 1287, 1393, 1608, 1724, 1818, 1961) correspond to the following alignment coordinates (210, 383, 389, 431, 537, 752, 869, 963, 1106), respectively. (PDF 74 kb).


  1. Alqudah AM, Koppolu R, Wolde GM, Graner A, Schnurbusch T (2016) The genetic architecture of barley plant stature. Front Genet 7:117. CrossRefPubMedPubMedCentralGoogle Scholar
  2. Baba T, Tanno K, Furusho M, Komatsuda T (2011) Allelic variation at the EF-G locus among northern Moroccan six-rowed barleys. Plant Genet Resour: Charact Util 9:240–242. CrossRefGoogle Scholar
  3. Banks WE, Antunes N, Rigaud S, d'Errico F (2013) Ecological constraints on the first prehistoric farmers in Europe. J Archaeol Sci 40:2746–2753. CrossRefGoogle Scholar
  4. Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, Ramsay L, Russell J, Shaw PD, Thomas W, Waugh R (2017) Development and evaluation of a barley 50k iSelect SNP array. Front Plant Sci 8:1792. CrossRefPubMedPubMedCentralGoogle Scholar
  5. Berger GL, Liu S, Hall MD, Brooks WS, Chao S, Muehlbauer GJ, Baik BK, Steffenson B, Griffey CA (2013) Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping. Theor Appl Genet 126:693–710. CrossRefPubMedGoogle Scholar
  6. Bull H, Casao MC, Zwirek M, Flavell AJ, Thomas WTB, Guo W, Zhang R, Rapazote-Flores P, Kyriakidis S, Russell J, Druka A, McKim SM, Waugh R (2017) Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility. Nat Commun 8:936. CrossRefPubMedPubMedCentralGoogle Scholar
  7. 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 9:2. CrossRefGoogle Scholar
  8. Casas AM, Yahiaoui S, Ciudad F, Igartua E (2005) Distribution of MWG699 polymorphism in Spanish European barleys. Genome 48:41–45. CrossRefPubMedGoogle Scholar
  9. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6:80–92. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659. CrossRefPubMedGoogle Scholar
  11. 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 125:1735–1749. CrossRefPubMedGoogle Scholar
  12. 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 44:1388–1392. CrossRefPubMedGoogle Scholar
  13. 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 Genomics 11:707. CrossRefPubMedPubMedCentralGoogle Scholar
  14. Digel B, Tavakol E, Verderio G, Tondelli A, Xu X, Cattivelli L, Rossini L, von Korff M (2016) Photoperiod-H1 (Ppd-H1) locus controls leaf size. Plant Physiol 172:405–415. CrossRefPubMedPubMedCentralGoogle Scholar
  15. dos Santos AM, Cabezas MP, Tavares AI, Xavier R, Branco M (2016) tcsBU: a tool to extend TCS network layout and visualization. Bioinformatics 32:627–628. CrossRefGoogle Scholar
  16. Evans LT, Wardlaw IF (1976) Aspects of the comparative physiology of grain yield in cereals. Adv Agron 28:301–359. CrossRefGoogle Scholar
  17. Fischbeck G (2003) Diversification through breeding. In: von Bothmer R, van Hintum TH, Knüpffer H, Sato K (eds) Diversity in barley (Hordeum vulgare). Elsevier Science BV, Amsterdam, pp 29–52CrossRefGoogle Scholar
  18. Igartua E, Gracia MP, Lasa JM, Medina B, Molina-Cano JL, Montoya JL, Romagosa I (1998) The Spanish barley core collection. Genet Resour Crop Evol 45:475–481. CrossRefGoogle Scholar
  19. Komatsuda T, Nakamura I, Takaiwa F, Oka S (1998) Development of STS markers closely linked to the vrs1 locus in barley, Hordeum vulgare. Genome 41:680–685. CrossRefGoogle Scholar
  20. Komatsuda T, Li W, Takaiwa F, Oka S (1999) High resolution map around the vrs1 locus controlling two- and six-rowed spike in barley, Hordeum vulgare. Genome 42:248–2535.
  21. 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 U S A 104:1424–1429. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Koppolu R, Anwar N, Sakuma S, Tagiri A, Lundqvist U, Pourkheirandish M, Rutten T, Seiler C, Himmelbach A, Ariyadasa R, Youssef HM, Stein N, Sreenivasulu N, Komatsuda T, Schnurbusch T (2013) Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc Natl Acad Sci U S A 110:13198–13203. CrossRefPubMedPubMedCentralGoogle Scholar
  23. Leino MW, Hagenblad J (2010) Nineteenth century seeds reveal the population genetics of landrace barley (Hordeum vulgare). Mol Biol Evol 27:964–973. CrossRefPubMedGoogle Scholar
  24. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25:1754–1760. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAM tools. Bioinformatics 25:2078–2079. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Liller CB, Neuhaus R, von Korff M, Koornneef M, van Esse W (2015) Mutations in barley row type genes have pleiotropic effects on shoot branching. PLoS One 10:e0140246. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Lister DL, Jones H, Jones MK, O’Sullivan DM, Cockram J (2013) Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform. Taxon 62:779–789. CrossRefGoogle Scholar
  28. 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 (2013) Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J 76:494–505. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A, Hübner S, Korol A, David M, Reiter E, Riehl S, Schreiber M, Vohr SH, Green RE, Dawson IK, Russell J, Kilian B, Muehlbauer GJ, Waugh R, Fahima T, Krause J, Weiss E, Stein N (2016) Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat Genet 48:1089–1093. CrossRefPubMedGoogle Scholar
  30. 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, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín 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, Doležel 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. CrossRefPubMedGoogle Scholar
  31. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Molina-Cano JL, Gómez-Campo C, Conde J (1982) Hordeum spontaneum C. Koch as a weed of barley fields in Morocco. Z Pflanzenzüchtg 88:161–167Google Scholar
  33. Molina-Cano JL, Russell JR, Moralejo MA, Escacena JL, Arias G, Powell W (2005) Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley. Theor Appl Genet 110:613–619. CrossRefPubMedGoogle Scholar
  34. Moralejo M, Romagosa I, Salcedo G, Sánchez-Monge R, Molina-Cano JL (1994) On the origin of Spanish two-rowed barleys. Theor Appl Genet 87:829–836. CrossRefPubMedGoogle Scholar
  35. Müller J (2015) Movement of plants, animals, ideas, and people in South-East Europe. In: Fowler C, Harding J, Hofmann D (eds.) The Oxford handbook of neolithic Europe, pp 63–80. Oxford University Press.
  36. Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, Chao S, Russell J, Waugh R, Hayes PM, Muehlbauer GJ (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 9:e94688. CrossRefPubMedPubMedCentralGoogle Scholar
  37. Pujol-Andreu J (2011) Wheat varieties and technological change in Europe, 19th and 20th centuries: new issues in economic history. Hist Agrar 54:71–103Google Scholar
  38. 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 43:169–172. CrossRefPubMedGoogle Scholar
  39. Russell J, Mascher M, Dawson IK, Kyriakidis S, Calixto C, Freund F, Bayer M, Milne I, Marshall-Griffiths T, Heinen S, Hofstad A, Sharma R, Himmelbach A, Knauft M, van Zonneveld M, Brown JWS, Schmid K, Kilian B, Muehlbauer GJ, Stein N, Waugh R (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 48:1024–1030. CrossRefPubMedGoogle Scholar
  40. Saisho D, Pourkheirandish M, Kanamori H, Matsumoto T, Komatsuda T (2009) Allelic variation of row type gene Vrs1 in barley and implication of the functional divergence. Breed Sci 59:621–628. CrossRefGoogle Scholar
  41. Sakuma S, Pourkheirandish M, Matsumoto T, Koba T, Komatsuda T (2010) Duplication of a well-conserved homeodomain-leucine zipper transcription factor gene in barley generates a copy with more specific functions. Funct Integr Genomics 10:123–133. CrossRefPubMedGoogle Scholar
  42. Sakuma S, Pourkheirandish M, Hensel G, Kumlehn J, Stein N, Tagiri A, Yamaji N, Ma JF, Sassa H, Koba T, Komatsuda T (2013) Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley. New Phytol 197:939–948. CrossRefPubMedGoogle Scholar
  43. Sakuma S, Lundqvist U, Kakei Y, Thirulogachandar V, Suzuki T, Hori K, Wu J, Tagiri A, Rutten T, Koppolu R, Shimada Y, Houston K, Thomas WTB, Waugh R, Schnurbusch T, Komatsuda T (2017) Extreme suppression of lateral floret development by a single amino acid change in the VRS1 transcription factor. Plant Physiol 175:1720–1731. CrossRefPubMedPubMedCentralGoogle Scholar
  44. Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Tanno K, Takaiwa F, Oka S, Komatsuda T (1999) A nucleotide sequence linked to the vrs1 locus for studies of differentiation in cultivated barley (Hordeum vulgare L.). Hereditas 130:77–82. CrossRefPubMedGoogle Scholar
  46. Tanno K, Taketa S, Takeda K, Komatsuda T (2002) A DNA marker closely linked to the vrs1 locus (row-type gene) indicates multiple origins of six-rowed cultivated barley (Hordeum vulgare L.). Theor Appl Genet 104:54–60. CrossRefPubMedGoogle Scholar
  47. Thirulogachandar V, Alqudah AM, Koppolu R, Rutten T, Graner A, Hensel G, Kumlehn J, Bräutigam A, Sreenivasulu N, Schnurbusch T, Kuhlmann M (2017) Leaf primordium size specifies leaf width and vein number among row-type classes in barley. Plant J 91:601–612. CrossRefPubMedGoogle Scholar
  48. van Esse GW, Walla A, Finke A, Koornneef M, Pecinka A, von Korff M (2017) Six-rowed spike3 (VRS3) is a histone demethylase that controls lateral spikelet development in barley. Plant Physiol 174:2397–2408. CrossRefPubMedPubMedCentralGoogle Scholar
  49. von Bothmer R, Sato K, Komatsuda T, Yasuda Y, Fischbeck G (2003) The domestication of cultivated barley. In: von Bothmer R, van Hintum TH, Knüpffer H, Sato K (eds) Diversity in barley (Hordeum vulgare). Elsevier Science BV, Amsterdam, pp 9–27CrossRefGoogle Scholar
  50. Youssef HM, Koppolu R, Schnurbusch T (2012) Re-sequencing of vrs1 and int-c loci shows that labile barleys (Hordeum vulgare convar. labile) have a six-rowed genetic background. Genet Resour Crop Evol 59:1319–1328. CrossRefGoogle Scholar
  51. Youssef HM, Eggert K, Koppolu R, Alqudah AM, Poursarebani N, Fazeli A, Sakuma S, Tagiri A, Rutten T, Govind G, Lundqvist U, Graner A, Komatsuda T, Sreenivasulu N, Schnurbusch T (2017a) VRS2 regulates hormone-mediated inflorescence patterning in barley. Nat Genet 49:157–161. CrossRefPubMedGoogle Scholar
  52. Youssef HM, Mascher M, Ayoub MA, Stein N, Kilian B, Schnurbusch T (2017b) Natural diversity of inflorescence architecture traces cryptic domestication genes in barley (Hordeum vulgare L.). Genet Resour Crop Evol 64:843–853. CrossRefGoogle Scholar
  53. Zilhao J (2000) From the Mesolithic to the Neolithic in the Iberian Peninsula. In: Price TD (ed) Europe’s first farmers. Cambridge University Press, Cambridge, pp 144–182CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Ana M. Casas
    • 1
    Email author
  • Bruno Contreras-Moreira
    • 1
    • 2
  • Carlos P. Cantalapiedra
    • 1
  • Shun Sakuma
    • 3
    • 4
  • María Pilar Gracia
    • 1
  • Marian Moralejo
    • 5
  • José Luis Molina-Cano
    • 6
  • Takao Komatsuda
    • 7
  • Ernesto Igartua
    • 1
  1. 1.Estación Experimental de Aula DeiConsejo Superior de Investigaciones Científicas (CSIC)ZaragozaSpain
  2. 2.Fundación ARAIDZaragozaSpain
  3. 3.Faculty of AgricultureTottori UniversityTottoriJapan
  4. 4.Leibniz Institute of Plant Genetics and Crop Plant Research, IPKGaterslebenGermany
  5. 5.Universitat de LleidaLleidaSpain
  6. 6.Institut de Recerca i Tecnología Agroalimentàries, (IRTA)LleidaSpain
  7. 7.Institute of Crop ScienceNational Agriculture and Food Research OrganisationTsukubaJapan

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