Skip to main content
Log in

EST derived SSR markers for comparative mapping in wheat and rice

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Structural and functional relationships between the genomes of hexaploid wheat (Triticum aestivum L.) (2n=6x=42) and rice (Oryza sativa L.) (2n=2x=24) were evaluated using linkage maps supplemented with simple sequence repeat (SSR) loci obtained from publicly available expressed sequence tags (ESTs). EST-SSR markers were developed using two main strategies to design primers for each gene: (1) primer design for multiple species based on supercluster analysis, and (2) species-specific primer design. Amplification was more consistent using the species-specific primer design for each gene. Forty-four percent of the primers designed specifically for wheat sequences were successful in amplifying DNA from both species. Existing genetic linkage maps were enhanced for the wheat and rice genomes using orthologous loci amplified with 58 EST-SSR markers obtained from both wheat and rice ESTs. The PCR-based anchor loci identified by these EST-SSR markers support previous patterns of conservation between wheat and rice genomes; however, there was a high frequency of interrupted colinearity. In addition, multiple loci amplified by these primers made the comparative analysis more difficult. Enhanced comparative maps of wheat and rice provide a useful tool for interpreting and transferring molecular, genetic, and breeding information between these two important species. These EST-SSR markers are particularly useful for constructing comparative framework maps for different species, because they amplify closely related genes to provide anchor points across species.

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

Access this article

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

  • Ahn S, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90:7980–7997

    CAS  PubMed  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayers N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    CAS  Google Scholar 

  • Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross-transferable to erianthus and sorghum. Plant Sci 160:1115–1123

    CAS  PubMed  Google Scholar 

  • Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922

    CAS  PubMed  Google Scholar 

  • Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12:637–646

    CAS  PubMed  Google Scholar 

  • Dunford RP, Yano M, Kurata N, Sasaki T, Huestis G, Rocheford T, Laurie DA (2002) Comparative mapping of the barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Genetics 161:825–834

    Google Scholar 

  • Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for phenotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    CAS  Google Scholar 

  • Foote T, Roberts M, Kurata N, Sasaki T, Moore G (1997) Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat. Genetics 147:801–807

    CAS  PubMed  Google Scholar 

  • Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971–1974

    CAS  PubMed  Google Scholar 

  • Gallego F, Feuillet C, Messmer M, Penger A, Graner A, Yano M, Sasaki T, Keller B (1998) Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome 41:328–336

    Article  CAS  PubMed  Google Scholar 

  • Gao L, Tang J, Li H, Jia J (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261

    Article  CAS  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Boyko EV (1996) Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143:1001–1012

    CAS  PubMed  Google Scholar 

  • Goff SA, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    CAS  PubMed  Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    Article  CAS  PubMed  Google Scholar 

  • Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121:17–25

    CAS  Google Scholar 

  • Harushima Y, et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494

    CAS  PubMed  Google Scholar 

  • Holloway JL, Knapp SJ (1993) Gmendel 3.0 Users Guide. Department of Crop and Soil Science, Oregon State University, Corvallis, Ore.

  • Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71

    CAS  Google Scholar 

  • Hulbert SH, Richter TE, Axtell JD, Bennetzen JL (1990) Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci USA 87:4251–4255

    CAS  PubMed  Google Scholar 

  • Kantety RV, Rota ML, Matthews DE, Sorrells MS (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  CAS  PubMed  Google Scholar 

  • Kilian A, Chen J, Han F, Steffenson B, Kleinhofs A (1997) Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol Biol 35:187–195

    CAS  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Kurata N, Moore G, Nagamura T, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Biotechnology 12:276–278

    CAS  Google Scholar 

  • La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics, in press

  • Laurie DA (1997) Comparative genetics of flowering time. Plant Mol Biol 35:167–177

    CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Liu S, Anderson JA (2003) Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. Genome 46:817–823

    Article  CAS  PubMed  Google Scholar 

  • Marino CL, Nelson JC, Lu YH, Sorrells ME, Leroy P (1996) Molecular genetic maps of the group 6 chromosomes of hexaploid wheat (Triticum aestivum L. em. Thell). Genome 39: 359–366

    CAS  Google Scholar 

  • Miller RT, Christoffels AG, Gopalakrishnan C, Burke J, Ptitsyn AA, Broveak TR, Hide WA (1999) A comprehensive approach to clustering of the expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res 9:1143–1155

    CAS  PubMed  Google Scholar 

  • Moore G (2000) Cereal chromosome structure, evolution, and pairing. Annu Rev Plant Physiol Plant Mol Biol 51:195–222

    Article  CAS  PubMed  Google Scholar 

  • Moore G, Devos KM, Wang Z, Gale MD (1995) Grasses, line up and form a circle. Curr. Biol. 5:737–739

    Google Scholar 

  • Nelson JC, Van Deynze AE, Autrique E, Sorrells ME, Lu Y, Merlino M, Atkinson M, Leroy P (1995a) Molecular mapping of wheat: homoeologous group 2. Genome 38:516–524

    CAS  Google Scholar 

  • Nelson JC, Van Deynze AE, Autrique E, Sorrells ME, Lu YH, Negre S, Bernard M, Leroy P (1995b) Molecular mapping of wheat: homoeologous group 3. Genome 38:525–533

    CAS  Google Scholar 

  • Nelson JC, Sorrells ME, Van Deynze AE, Lu YH, Atkinson M, Bernard M, Leroy P, Faris JD, Anderson JA (1995c) Molecular mapping of wheat: major genes and rearrangements in homoeologous groups 4, 5, and 7. Genetics 141:721–731

    CAS  PubMed  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier N-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Sarma RN, Fish L, Gill BS, Snape JW (2000) Physical characterization of the homoeologous group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes. Genome 43:191–198

    Article  CAS  PubMed  Google Scholar 

  • Scarth R, Law CN (1983) The location of the photoperiodic gene Ppd2 and an additional genetic factor, ear-emergence , on chromosome 2B of wheat. Heredity 51:607–619

    Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    CAS  Google Scholar 

  • Shindo C, Tsujimoto H, Sasakuma T (2003) Segregation analysis of heading traits in hexaploid wheat utilizing recombinant inbred lines. Heredity 90:56–63

    Article  CAS  PubMed  Google Scholar 

  • Sorrells ME, et al (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1817–1827

    Google Scholar 

  • Taylor C, Madsen K, Borg S, Moller MG, Boelt B, Holm PB (2001) The development of sequence-tagged sites (STSs) in Lolium perenne L.: the application of primer sets derived from other genera. Theor Appl Genet 103:648–658

    CAS  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    CAS  PubMed  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    CAS  PubMed  Google Scholar 

  • Van Deynze AE, Dubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Appels R (1995a) Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome 38:45–59

    CAS  Google Scholar 

  • Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME (1995b) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248:744–754

    PubMed  Google Scholar 

  • Van Deynze AE, Sorrells ME, Park WD, Ayres NM, Fu H, Cartinhour SW, Paul E, McCouch SR (1998) Anchor probes for comparative mapping of grass genera. Theor Appl Genet 97:356–369

    Article  Google Scholar 

  • Ware D, Stein L (2003) Comparison of genes among cereals. Curr Opin Plant Biol 6:121–127

    Article  CAS  PubMed  Google Scholar 

  • Wilson WA, Harrington SE, Woodman WL, Lee M, Sorrells ME, McCouch SR (1999) Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated Panicoids. Genetics 153:453–473

    CAS  PubMed  Google Scholar 

  • Wu J, Kurata N, Tanoue H, Shimokawa T, Umehara Y, Yano M, Sasaki T (1998) Physical mapping of duplicated genomic regions of two chromosome ends in rice. Genetics 150:1595–1603

    Google Scholar 

  • Wu J, et al (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525–535

    CAS  PubMed  Google Scholar 

  • 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. Theor Appl Genet 97:37–44

    CAS  Google Scholar 

  • Yu J-K, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME (2004) Development and mapping of EST-derived simple sequence repeat (SSR) markers for hexaploid wheat. Genome, in press

Download references

Acknowledgements

We are grateful to Drs. Susan McCouch and Svetlana Temnykh for providing the DH lines of rice mapping population IR64 × Azucena and map data; Drs. Bikram Gill and Sukhwinder Singh for wheat EST-SSR primer sequences, and Doug Valenta for technical assistance. We thank Dr. David E. Matthews and Hugh Edwards for providing advice and information regarding integration of new maps and data into the GrainGenes database (http://www.wheat.pw.usda.gov). The present work was supported by grants from the USDA/NRI Project No. 2001-35301-10612 and Hatch Project 149419.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to M. E. Sorrells.

Additional information

Communicated by R. Hagemann

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yu, JK., La Rota, M., Kantety, R.V. et al. EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271, 742–751 (2004). https://doi.org/10.1007/s00438-004-1027-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-004-1027-3

Keywords

Navigation