Genome Mapping in Cool-Season Forage Grasses

  • Hongwei Cai
  • Maiko Inoue
  • Nana Yuyama
  • Mariko Hirata


Molecular markers, specifically SSR markers, have found wide utility in genomic research. However, in forage grasses, the availability of such markers restricts and restrains the breeder/geneticist from taking full advantage of this frequently utilized technology. In this report, we review recent developments in our laboratory to generate or increase the number and availability of SSR markers for timothy (Phleum pratense), orchardgrass (Dactylis glomerata), Italian ryegrass (Lolium multiflorum) and zoysiagrass (Zoysia japonica). Until now, genomic research (including marker development, gene mapping, and quantitative trait loci (QTL) analysis in most forage grasses, with the exception of Lolium species, lagged behind that performed in major crops species such as rice and maize. To address this deficit, we have developed about 1,000 simple sequence repeat (SSR) markers for Phleum pratense, Dactylis glomerata, Zoysia japonica and Lolium multiflorum from SSR-enriched genomic libraries. Most of these SSR markers are polymorphic in a screening panel that included eight individuals of each species. From the polymorphic SSR makers we constructed a linkage map for hexaploid and diploid timothy. From the multi-alleles of hexaploid timothy SSR markers, we detected seven homologous linkage groups and found a homologous relationship between hexaploid and diploid timothy. We also developed SSR markers for Italian ryegrass of which 11 are specific to 12 Italian ryegrass cultivars developed in Japan. An orchardgrass SSR-linkage map is under construction.


Quantitative Trait Locus Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker Tall Fescue Perennial Ryegrass 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Al-Janabi SM, McClelland M, Petersen C, Sobral BWS (1994) Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae. Theor Appl Genet 88: 933–944CrossRefGoogle Scholar
  2. Arumuganathan K, Tallury SP, Fraser ML, Bruneau AH, Qu R (1999) Nuclear DNA content of thirteen turfgrass species by flow cytometry. Crop Sci 39: 1518–1521Google Scholar
  3. Cai HW, Yuyama N, Tamaki H, Yosizawa A (2003a) Development of SSR markers and detection of homologous linkage groups in hexaploid grass timothy (Phleum pratense L.).Plant, Animal & Microbe Genomes XI Conference, January, San Diego, CAGoogle Scholar
  4. Cai HW, Yuyama N, Tamaki H, Yoshizawa A (2003b) Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pratense L.). Theor Appl Genet 107: 1337–1349CrossRefGoogle Scholar
  5. Cai HW, Inoue M, Yuyama N, Nakayama S (2004) An AFLP-based linkage map of Zoysiagrass (Zoysia japonica Steud.). Plant Breed 123: 543–548CrossRefGoogle Scholar
  6. Cai HW, Inoue M, Yuyama N, Takahashi W, Hirata M, Sasaki T (2005) Isolation, characterization and mapping of simple sequence repeat markers in Zoysiagrass (Zoysia spp.). Theor Appl Genet 112: 158–166CrossRefPubMedGoogle Scholar
  7. Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4: 129–131CrossRefPubMedGoogle Scholar
  8. Forbes I Jr.(1952) Chromosome numbers and hybrids in Zoysia. Agron J 44: 147–151Google Scholar
  9. Fukuoka H (1989) Breeding of Zoysia spp. J Jpn Soc Turfgrass Sci 17: 183–190 (in Japanese)Google Scholar
  10. Hirata M, Cai HW, Inoue M, Yuyama N, Miura Y, Komatsu K, Takamizo T, Fujimori M (2006) Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 113: 270–279CrossRefPubMedGoogle Scholar
  11. Ikeda S (2005) Isolation of disease resistance gene analogs from Italian ryegrass (Lolium multiflorum Lam.). Grassl Sci 51: 63–70CrossRefGoogle Scholar
  12. Inoue M, Cai HW (2004) Sequence analysis and conversion of genomic RFLP markers to STS and SSR markers in Italian Ryegrass (Lolium multiflorum Lam.). Breed Sci 54: 245–251CrossRefGoogle Scholar
  13. Inoue M, Gao ZS, Hirata M, Fujimori M, Cai HW (2004) Construction of a high-density linkage map of Italian ryegrass (Lolium multiflorum Lam.) using restriction fragment length polymorphism, amplified fragment length polymorphism, and telomeric repeat associated sequence markers. Genome 47: 57–65CrossRefPubMedGoogle Scholar
  14. Jones ES, Dupal MP, Kolliker R, Drayton MC, Forster JW (2001) Development and characterization of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102: 405–415CrossRefGoogle Scholar
  15. Kanno A, Watanabe N, Nakamura I, Hirai A (1993) Variations in chloroplast DNA from rice (Oryza sativa): differences between deletions mediated by short direct-repeat sequences within a single species. Theor Appl Genet 86: 579–584CrossRefGoogle Scholar
  16. Kishimoto S, Aida R, Shibata M (2003) Identification of chloroplast DNA variations by PCR-RFLP analysis in Dendranthema. J Jpn Soc Hort Sci 72: 197–204CrossRefGoogle Scholar
  17. Kitamura F (1989) The climate of Japan and its surrounding areas and the distribution and classification of zoysiagrasses. Int Turfgrass Soc Res J 6: 17–21Google Scholar
  18. Miura Y, Hirata M, Fujimori M (2007) Mapping of EST-derived CAPS markers in Italian ryegrass (Lolium multiflorum Lam.). Plant Breed 126: 353–360CrossRefGoogle Scholar
  19. Nakamura I, Kameya N, Kato Y, Yamanaka S, Jomori H, Sato YI (1998) A proposal for identifying the short ID sequence which addresses the plastid subtype of higher plants. Breed Sci 47: 385–388Google Scholar
  20. Robison M, Wolyn D (2002) Complex organization of the mitochondrial genome of petaloid CMS carrot. Mol Genet Genomics 268: 232–239CrossRefPubMedGoogle Scholar
  21. Saha MC, Mian R, Zwonitzer JC, Chekhovskiy K, Hopkins AA (2005) An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.). Theor Appl Genet 110: 323–336CrossRefPubMedGoogle Scholar
  22. Shoji S (1983) Species ecology of Zoysia grass. J Jpn Soc Turfgrass Sci 12: 105–110 (in Japanese)Google Scholar
  23. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105–1109CrossRefPubMedGoogle Scholar
  24. Tsuruta SI, Hashiguchi M, Ebina M, Matsuo T, Yamamoto T, Kobayashi M, Takahara M, Nakagawa H, Akashi R (2005) Development and characterization of simple sequence repeat markers in Zoysia japonica Steud. Grassl Sci 51: 249–257CrossRefGoogle Scholar
  25. Yaneshita M, Kaneko S, Sasakuma T (1999) Allotetraploidy of Zoysia species with 2n=40 based on a RFLP genetic map. Theor Appl Genet 98: 751–756CrossRefGoogle Scholar

Copyright information

© Springer Science + Business Media, LLC 2009

Authors and Affiliations

  • Hongwei Cai
    • 1
    • 2
  • Maiko Inoue
    • 1
  • Nana Yuyama
    • 1
  • Mariko Hirata
    • 1
  1. 1.Forage Crop Research InstituteJapan Grassland Agriculture & Forage Seed AssociationHigashiakataJapan
  2. 2.Department of Plant Genetics & Breeding, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina

Personalised recommendations