Skip to main content

An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum

Theoretical and Applied Genetics volume 109, pages 1485–1493 (2004)Cite this article

Abstract

Over the past 10 years, resources have been established for the genetic analysis of pearl millet, Pennisetum glaucum (L.) R. Br., an important staple crop of the semi-arid regions of India and Africa. Among these resources are detailed genetic maps containing both homologous and heterologous restriction fragment length polymorphism (RFLP) markers, and simple sequence repeats (SSRs). Genetic maps produced in four different crosses have been integrated to develop a consensus map of 353 RFLP and 65 SSR markers. Some 85% of the markers are clustered and occupy less than a third of the total map length. This phenomenon is independent of the cross. Our data suggest that extreme localization of recombination toward the chromosome ends, resulting in gaps on the genetic map of 30 cM or more in the distal regions, is typical for pearl millet. The unequal distribution of recombination has consequences for the transfer of genes controlling important agronomic traits from donor to elite pearl millet germplasm. The paper also describes the generation of 44 SSR markers from a (CA)n-enriched small-insert genomic library. Previously, pearl millet SSRs had been generated from BAC clones, and the relative merits of both methodologies are discussed.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

  • Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1139

    Google Scholar 

  • Allouis S, Qi X, Lindup S, Gale MD, Devos KM (2001) Construction of a BAC library of pearl millet, Pennisetum glaucum. Theor Appl Genet 102:1200–1205

    Google Scholar 

  • Areshchenkova T, Ganal MW (2002) Comparative analysis of polymorphisms and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet 104:229–235

    Google Scholar 

  • Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94:557–563

    Google Scholar 

  • Chao S, Sharp PJ, Kilian A, Gale MD (1989) RFLP based genetic maps of homologous group 7 chromosomes of wheat and barley. AFRC Institute of Plant Science and John Innes Institute annual report. IPSR, Norwich, pp 23–24

  • Close TJ, Kortt AA, Chandler PM (1989) A cDNA-based comparison of dehydration-induced proteins (dehyrdins) in barley and corn. Plant Mol Biol 13:95–108

    Google Scholar 

  • Connell JP, Pammi S, Iqbal MJ, Huizinga T, Reddy AS (1998) A high through-put procedure for capturing microsatellites from complex plant genomes. Plant Mol Biol Rep 16:341–349

    Google Scholar 

  • Devos KM, Atkinson MD, Chinoy CN, Liu C, Gale MD (1992) RFLP based genetic map of the homologous group 3 chromosomes of wheat and rye. Theor Appl Genet 83:931–939

    Google Scholar 

  • Devos KM, Pittaway TS, Reynolds A, Gale MD (2000) Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theor Appl Genet 100:190–198

    Google Scholar 

  • Edwards KG, Varker GHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. BioTechniques 20:758–760

    Google Scholar 

  • Ganal MW, Broun P, Tanksley SD (1992) Genetic mapping of tandemly repeated telomeric DNA sequences in tomato (Lycopersicon esculentum). Genomics 14:444–448

    Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W-L, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    Google Scholar 

  • Jones ES, Liu CJ, Gale MD, Hash CT, Witcombe JR (1995) Mapping quantitative trait loci for downy mildew resistance in pearl millet. Theor Appl Genet 91:448–456

    Google Scholar 

  • Jones ES, Breese WA, Liu CJ, Singh SD, Shaw DS, Witcombe JR (2002) Mapping quantitative trait loci for resistance to downy mildew in pearl millet: field and glasshouse screens detect the same QTL. Crop Sci 42:1316–1323

    Google Scholar 

  • Kijas JMH, Fowler JCS, Garbett CA, Thomas MR (1994) Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. BioTechniques 16:657–662

    Google Scholar 

  • Liu CJ, Witcombe JR, Pittaway TS, Nash M, Busso CS, Hash CT, Gale MD (1994) An RFLP-based genetic map of pearl millet (Pennisetum glaucum). Theor Appl Genet 89:481–487

    Google Scholar 

  • McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:89–99

    Google Scholar 

  • McIntosh RA, Hart GE, Devos KM, Gale MD, Rogers WJ (1998) Catalogue of gene symbols for wheat. In: Slinkard AE (ed) Proceedings of the 9th international wheat genetics symposium. University Extension Press, University of Saskatchewan, Saskatoon, pp 1–325

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Google Scholar 

  • Padi FK (2002) Genetic analysis of adaptive traits in pearl millet (Pennisetum glaucum (L.). R. Br.). Dissertation, University of East Anglia

  • Poncet V, Lamy F, Devos KM, Gale MD, Sarr A, Robert T (2000) Genetic control of domestication traits in pearl millet (Pennisetum glaucum L., Poaceae). Theor Appl Genet 100:147–159

    Google Scholar 

  • Poncet V, Martel E, Allouis S, Devos KM, Lamy F, Sarr A, Robert T (2002) Comparative analysis of QTLs affecting domestication traits between two domesticated × wild pearl millet (Pennisetum glaucum L., Poaceae) crosses. Theor Appl Genet 104:965–975

    Google Scholar 

  • Qi X, Stam P, Lindhout P (1996) Comparison and integration of four barley genetic maps. Genome 39:379–394

    Google Scholar 

  • Qi X, Lindup S, Pittaway TS, Allouis S, Gale MD, Devos KM (2001) Development of simple sequence repeat markers from bacterial artificial chromosomes without subcloning. BioTechniques 31:355–362

    Google Scholar 

  • Röder MS, Lapitan NLV, Sorrells ME, Tanksley SD (1993) Genetic and physical mapping of barley telomeres. Mol Gen Genet 238:294–303

    Google Scholar 

  • Roder MS, Plashk J, Konig SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333

    Google Scholar 

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

    Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    Google Scholar 

  • Stephenson P, Bryan GJ, Kirby J, Collins AJ, Devos KM, Busso CS, Gale MD (1998) Fifty new microsatellite loci for the wheat genetic map. Theor Appl Genet 97:946–949

    Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Govannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND (1992) High-density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans 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 23:4407–4414

    Google Scholar 

  • Wu J, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235

    Google Scholar 

  • Yadav RS, Hash CT, Bidinger FR, Cavan GP, Howarth CJ (2002) Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought stress conditions. Theor Appl Genet 104:67–83

    Google Scholar 

  • Yadav RS, Bidinger FR, Hash CT, Yadav YP, Yadav OP, Bhatnagar SK, Howarth CJ (2003) Mapping and characterization of QTL × E interactions for traits determining grain and stover yield in pearl millet. Theor Appl Genet 106:512–520

    Google Scholar 

  • Yadav RS, Hash CT, Bidinger FR, Devos KM, Howarth CJ, Skot K (2004) Genomic regions associated with grain yield and aspects of post-flowering drought tolerance in pearl millet across stress environments and testers background. Euphytica 136:265–277

    Google Scholar 

Download references

Acknowledgements

This manuscript is largely an output from projects funded by the Plant Science Research Programme (contracts R6951 and R7979) of the UK Department for International Development (DFID) for the benefit of developing countries. The views expressed are not necessarily those of DFID. KMD acknowledges funding from the Biotechnology and Biological Sciences Research Council (BBSRC) through a David Phillips Research Fellowship.

Author information

Affiliations

  1. John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK

    X. Qi, T. S. Pittaway, S. Lindup, H. Liu, E. Waterman, F. K. Padi, J. Zhu, M. D. Gale & K. M. Devos

  2. ICRISAT, Patancheru, 502 324, Andhra Pradesh, India

    C. T. Hash

  3. Scottish Crop Research Institute, Invergowry, Dundee, DD2 5DA, UK

    H. Liu

  4. Savanna Agricultural Research Institute, P.O. Box 52, Nyankpala/Tamale, Northern Region, Ghana

    F. K. Padi

  5. Department of Crop and Soil Sciences and Department of Plant Biology, The University of Georgia, 3111 Miller Plant Sciences Building, Athens, GA, 30602-7271, USA

    K. M. Devos

Authors
  1. X. Qi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T. S. Pittaway
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. Lindup
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. H. Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. E. Waterman
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. F. K. Padi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. C. T. Hash
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. J. Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. M. D. Gale
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. K. M. Devos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to K. M. Devos.

Additional information

Communicated by P. Langridge

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Qi, X., Pittaway, T.S., Lindup, S. et al. An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum. Theor Appl Genet 109, 1485–1493 (2004). https://doi.org/10.1007/s00122-004-1765-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-004-1765-y

Keywords

  • Simple Sequence Repeat Marker
  • Polymorphism Information Content
  • Pearl Millet
  • Restriction Fragment Length Polymorphism Marker
  • Downy Mildew Resistance