Theoretical and Applied Genetics

, Volume 108, Issue 1, pp 73–78 | Cite as

Efficient fine mapping of the naked caryopsis gene (nud) by HEGS (High Efficiency Genome Scanning)/AFLP in barley

  • S. Kikuchi
  • S. Taketa
  • M. Ichii
  • S. Kawasaki


The hulled or naked caryopsis character of barley (Hordeum vulgare L.) is an important trait for edibility and to follow its domestication process. A single recessive gene, nud, controls the naked caryopsis character, and is located on the long arm of chromosome 7H. To develop a fine map around the nud locus efficiently, the HEGS (High Efficiency Genome Scanning) electrophoresis system was combined with amplified fragment length polymorphism (AFLP). From bulked segregant analysis of 1,894 primer combinations, 12 AFLP fragments were selected as linked markers. For mapping, an F2 population of 151 individuals derived from a cross between Kobinkatagi (naked type) and Triumph (hulled type) was used. Seven AFLP markers were localized near the nud region. A fine map was developed with one-order higher resolution than before, along with the seven anchor markers. Among the seven linked AFLP markers (KT1–7), KT1, KT2 and KT6 were co-dominant, and the former two were detected for their single-nucleotide polymorphisms (SNPs) in the same length of fragments after electrophoresis with the non-denaturing gels of HEGS. The nud locus has co-segregated with KT3 and KT7, and was flanked by KT2 and KT4, at the 0.3-cM proximal and the 1.2-cM distal side, respectively. Four of these AFLP markers were converted into sequence-characterized amplified region (SCAR) markers, one of which was a dominant marker co-segregating with the nud gene.


AFLP Bulked segregant analysis HEGS (High Efficiency Genome Scanning) Hordeum vulgare L. Naked barley 



The authors are grateful to Mr. K. Nagai, Mr. T. Awayama and Mr. S. Yamamoto for their technical assistance. This research was supported in part by Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology, and a Grant-in-Aid for Scientific Research (C) (15580007) from the Ministry of Education, Science, Culture and Sports, Japan.


  1. Becker J, Heun M (1995) Barley microsatellites: allele variation and mapping. Plant Mol Biol 27:835–845PubMedGoogle Scholar
  2. Costa JM, Corey A, Hayes PM, Jobet C, Kleinhofs A, Kopisch-Obusch A, Kramer SF, Kudrna D, Li M, Riera-Lizarazu, 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 103:415–424Google Scholar
  3. Fedak G, Tsuchiya T, Helgason SB (1972) Use of monotelotrisomics for linkage mapping in barley. Can J Genet Cytol 14: 949–957Google Scholar
  4. Franckowiack JD (1996) Revised linkage maps for morphological markers in barley, Hordeum vulgare. Naked caryopsis. Special Issue Barley Genet Newslett 26:51–52Google Scholar
  5. Graner A, Bauer E, Kellermann A, Kirchner S, Muraya JK, Jahoor A, Wenzel G (1994) Progress of RFLP-map construction in winter barley. Barley Genet Newslett 23:53–59Google Scholar
  6. Heun M, Kennedy AE, Anderson JA, Lapitan NLV, Sorrells ME Tanksley SD (1991) Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34:437–447Google Scholar
  7. Islam AKMR (1983) Ditelosomic additions of barley chromosomes to wheat. In: Sakamoto S (ed) Proc 6th Int Wheat Genet Symp, Maruzen, Kyoto, pp 233–238Google Scholar
  8. Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174Google Scholar
  9. Kawasaki S, Murakami Y (2000) Genome analysis of Lotus japonicus. J Plant Res 113:497–506Google Scholar
  10. Kawasaki S, Kamihara K, Motomura T, Kodama O (2000) Compact high density AFLP enabled high efficiency genome scanning. 4th Int Rice Genet Symp Abstract, p 73Google Scholar
  11. Kawasaki S, Murakami Y, Imaizumi H, Shimizu A, Mikami I (in press) High Efficiency Genome Scanning (HEGS) and its applications to genome analyses of Lotus japonicus and other crops. Construction of the high-density map, genome library, and saturation-mapping of nodulation genes in Brassicas and Legumes. In: Nagata Y, Tabata S (eds) Genome Structure to Breeding. Springer-Verlag, Berlin Heidelberg New YorkGoogle Scholar
  12. Komatsuda T, Nakamura I, Takaiwa F, Oka S (1998) Development of STS markers closely linked to the vrs1 locus in barley, Hordeum vulgare. Genome 41:680–685CrossRefGoogle Scholar
  13. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  14. Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412Google Scholar
  15. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedGoogle Scholar
  16. Linde-Laursen I, Heslop-Harrison KW, Taketa S (1997) The barley genome and its relationship with the wheat genomes. A survey with an internationally agreed recommendation for barley chromosome nomenclature. Hereditas 126:1–16Google Scholar
  17. Liu CT, Wesenberg DM, Hunt CW, Branen AL, Robertson LD, Burrup DE, Dempster KL, Haggerty RJ (1996) Hulless barley: a new look for barley in Idaho. Resources for Idaho
  18. Meksem K, Leister D, Peleman J, Zabeau M, Salamini F, Gebhardt C (1995) A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers. Mol Gen Genet 249:74–81PubMedGoogle Scholar
  19. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832PubMedGoogle Scholar
  20. Murai H, Hashimoto Z, Sharma PN, Shimizu T, Murata S, Takumi S, Mori N, Kawasaki S, Nakamura C (2001) Construction of a high-resolution linkage map of a rice brown planthopper (Nilaparvata lugens Stål), resistance gene bph2. Theor Appl Genet 103:526–532CrossRefGoogle Scholar
  21. Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–993Google Scholar
  22. Qi X, Stam P, Lindhout P (1998) Use of locus-specific AFLP markers to construct a high-density molecular map in barley. Theor Appl Genet 96:376–384CrossRefGoogle Scholar
  23. Ramsey L, Macaulay M, degli Ivanissevich S, 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 156:1997–2005PubMedGoogle Scholar
  24. Sayed-Tabatabaei BE, Komatsuda T, Takaiwa F, Graner A (1998) DNA sequencing and primer designing for RFLP clones evenly distributed in the barley genome. Barley Genet Newslett 28:15–18Google Scholar
  25. Scholz F (1955) Mutationsversuche an Kulturpflanzen. IV. Kulturpflanze 3:69–89Google Scholar
  26. Serizawa N, Nasuda S, Shi F, Endo TR, Prodanovic S, Schubert I, Künzel G (2001) Deletion-based physical mapping of barley chromosome 7H. Theor Appl Genet 103:827–834CrossRefGoogle Scholar
  27. Simons G, Van der Lee T, Diergaarde P, Van Daelen R, Groenendijk J, Frijters A, Büschges R, Hollricher K, Töpsch S, Schulze-Lefert P, Salamini F, Zabeau M, Vos P (1997) AFLP-based fine mapping of the Mlo gene to a 30-kb DNA segment of the barley genome. Genomics 44:61–70CrossRefPubMedGoogle Scholar
  28. Taketa S, Takeda K (2001) Production and characterization of a complete set of wheat-wild barley (Hordeum vulgare ssp. spontaneum) chromosome addition lines. Breed Sci 51:199–206CrossRefGoogle Scholar
  29. Vos P, Hogers R, Bleeker M, Reijans M, Lee TVD, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedGoogle Scholar
  30. Wen L, Tang HV, Chen W, Chang R, Pring DR, Klein PE, Childs KL, Klein RR (2002) Development and mapping of AFLP markers linked to the sorghum fertility restorer gene rf4. Theor Appl Genet 104:577–585CrossRefGoogle Scholar
  31. Zohary D, Hopf M (2000) Domestication of plants in the old world: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley. Clarendon Press, OxfordGoogle Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  1. 1.Faculty of AgricultureKagawa UniversityKagawaJapan
  2. 2.National Institute of Agrobiological SciencesIbarakiJapan

Personalised recommendations