Theoretical and Applied Genetics

, Volume 107, Issue 5, pp 806–813 | Cite as

Efficient construction of high-density linkage map and its application to QTL analysis in barley

  • K. Hori
  • T. Kobayashi
  • A. Shimizu
  • K. Sato
  • K. Takeda
  • S. Kawasaki
Article

Abstract.

Using a High Efficiency Genome Scanning (HEGS) system and recombinant inbred (RI) lines derived from the cross of Russia 6 and H.E.S. 4, a high-density genetic map was constructed in barley. The resulting 1,595.7-cM map encompassed 1,172 loci distributed on the seven linkage groups comprising 1,134 AFLP, 34 SSR, three STS and vrs1 (kernel row type) loci. Including PCR reactions, gel electrophoresis and data processing, 6 months of work by a single person was sufficient for the whole mapping procedure under a reasonable cost. To make an appraisal of the resolution of genetic analysis for the 95 RI lines based on the constructed linkage map, we measured three agronomic traits: plant height, spike exsertion length and 1,000-kernel weight, and the analyzed quantitative trait loci (QTLs) associated with these traits. The results were compared on the number of detected QTLs and their effects between a high-density map and a skeleton map constructed by selected AFLP and anchor markers. The composite interval mapping on the high-density map detected more QTLs than the other analyses. Closely linked markers with QTLs on the high-density map could be powerful tools for marker-assisted selection in barley breeding programs and further genetic analyses including an advanced backcross analysis or a map-based cloning of QTL.

Keywords.

Barley High Efficiency Genome Scanning (HEGS) Genetic map QTL 

Notes

Acknowledgements.

We thank Drs. Saisho and Tanno, the Research Institute Bioresearch, Okayama University, for excellent technical advice. We also acknowledge all members in the plant physiology department, the National Institute of Agrobiological Science, for their technical advice. This research was supported by the grant from Core Research for the Evolutional Science and Technology, Japan Science and Technology Corporation.

Supplementary material

Table 3.xls (408 kb)
Table 3 (XLS 409 KB)

References

  1. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Biol Rep 9:208–219Google Scholar
  2. Basten CJ, Weir BS, Zeng ZB (1994) Zmap-a QTL cartgrapher. In: Smith C, Gavora JS, Benkel B, Chesnais J, Fairfull W, Gibson JP, Kennedy BW, Burnside EB (eds) The 5th world congress on genetics applied to livestock production: computing strategies and software, vol. 22. The Organizing Committee, 5th World Congress on Genetics Applied to Livestock Production, Ontario, Canada, pp 65–66 (http://statgen.ncsu.edu/qtlcart/cartographer.html)Google Scholar
  3. Becker J, Vos P, Kuiper M, Salamini F, Heun M (1995) Combined mapping of AFLP and RFLP markers in barley. Mol Gen Genet 249:65–73PubMedCrossRefGoogle Scholar
  4. Blake TK, Kadyrzhanova D, Shepherd KW, Islam AKMR, Langridge PL, McDonald CL, Erpelding J, Larson S, Blake NK, Talbert LE (1996) STS-PCR markers appropriate for wheat-barley introgression. Theor Appl Genet 93:826–832CrossRefGoogle Scholar
  5. Castiglioni P, Pozzi C, Heum M, Terzi V, Muller KJ, Rohde W, Salamini F (1998) An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley. Genetics 149:1039–2056Google Scholar
  6. Castiglioni P, Ajmone-Marsan P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: co-dominant scoring and linkage group distribution. Theor Appl Genet 99:425–431CrossRefGoogle Scholar
  7. 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, Vvales MI, Wolfe RI (2001) Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population. Theor Appl Genet 103:415–424CrossRefGoogle Scholar
  8. Frary A, Nesbitt TC, Frary A, Grandillo S, van der Kneep E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88PubMedCrossRefGoogle Scholar
  9. Groh S, Zacharias A, Kianian SF, Penner GA, Chong J, Rines HW, Phillips RL (2001) Comparative AFLP mapping in two hexaploid oat populations. Theor Appl Genet 102:876–884CrossRefGoogle Scholar
  10. Jui PY, Choo TM, Ho KM, Konishi T, Martin RA (1997) Genetic analysis of a two-row × six-row cross of barley using doubled-haploid lines. Theor Appl Genet 94:549–556CrossRefGoogle Scholar
  11. Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J, Obert JA, Morishige DT, Schlueter SD, Childs KL, Ale M, Mullet JE (2000) A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genetic map. Genome Res 10:789–807PubMedCrossRefGoogle Scholar
  12. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  13. Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412PubMedGoogle Scholar
  14. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199PubMedGoogle Scholar
  15. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedCrossRefGoogle Scholar
  16. Langridge P, Karakousis A, Nield J (1997) Practical workshop in the basic recombinant DNA techniques course manual. Waite Agricultural Research Institute, University of AdelaideGoogle Scholar
  17. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:391–401Google Scholar
  18. Liu ZW, Biyashev RM, Saghai Maroof MA (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor Appl Genet 93:869–876Google Scholar
  19. Mano Y, Kawasaki S, Takaiwa F, Komatsuda T (2001) Construction of a genetic map of barley (Hordeum vulgare L.) cross 'Azumamugi' × 'Kanto Nakate Gold' using a simple and efficient amplified fragment-length polymorphism system. Genome 44:284–292PubMedCrossRefGoogle Scholar
  20. Marquez-Cedillo LA, Hayes PM, Jones BL, Kleinhofs A, Legge WG, Rossnagel BG, Sato K, Ullrich SE, Wesenberg DM and the North American Barley Genome Mapping Project (2001) QTL analysis of agronomic traits in barley based on the doubled-haploid progeny of two elite North American varieties representing different germplasm groups. Theor Appl Genet 103:625–637CrossRefGoogle Scholar
  21. Mather DE, Thinker NA, La Berge DE, Edney M, Jones BL, Rossnagel BG, Legge WG, Briggs KG, Irvine RB, Falk DE, Kasha KJ (1997) Regions of the genome that affect grain and malt quality in a North American two-row barley cross. Crop Sci 37:544–554CrossRefGoogle Scholar
  22. Meksem K, Ruben E, Hyten D, Triwitayakorn K, Lightfoot DA (2001) Conversion of AFLP bands into high-throughput DNA markers. Mol Gen Genet 265:207–214Google Scholar
  23. Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE (2002) A high-density genetic map of Sorghum bicolor (L.) Moench based on 2,926 AFLP, RFLP and SSR markers. Plant Mol Biol 48:483–499PubMedCrossRefGoogle Scholar
  24. Murai H, Hashimoto Z, Sharma PN, Shimizu T, Murata K, Takumi S, Mori N, Kawasaki S, Nakamura C (2001) Construction of a high-resolution linkage map of a rice brown planthopper (Nilaparvata lugens Stal) resistance gene bph2. Theor Appl Genet 103:526–532CrossRefGoogle Scholar
  25. Olson M, Hood L, Cantor C, Doststein D (1989) A common language for physical mapping of the human genome. Science 245:1434–1435PubMedCrossRefGoogle Scholar
  26. 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
  27. Ramsay 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
  28. Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233PubMedCrossRefGoogle Scholar
  29. Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1995) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224CrossRefGoogle Scholar
  30. 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 104:54–60PubMedCrossRefGoogle Scholar
  31. Teulat B, Merah O, Souyris I, This D (2001) QTLs for agronomic traits from a Mediterranean barley progeny grown in several environments. Theor Appl Genet 103:774–787CrossRefGoogle Scholar
  32. Ukai Y, Ohsawa R, Saito A, Hayashi T (1995) MAPL: a package of computer programs for construction of DNA polymorphism linkage maps and analysis of QTLs. Breed Sci 45:139–142 (http://wheat.ab.a.u-tokyo.ac.jp/∼ukai/)Google Scholar
  33. Vos P, Hogers R, Bleeker M, Reijan M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  34. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedCrossRefGoogle Scholar
  35. Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Thoer Appl Genet 97:37–44CrossRefGoogle Scholar
  36. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod-sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2483PubMedCrossRefGoogle Scholar
  37. Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer 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 101:1093–1099CrossRefGoogle Scholar
  38. 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? 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 99:1221–1232CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • K. Hori
    • 1
  • T. Kobayashi
    • 1
  • A. Shimizu
    • 2
  • K. Sato
    • 1
  • K. Takeda
    • 1
  • S. Kawasaki
    • 2
  1. 1.Research Institute for BioresourcesOkayama UniversityChuo, KurashikiJapan
  2. 2.National Institute of Agrobiological ResourcesKannondai, TsukubaJapan

Personalised recommendations