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A comparative assessment of the utility of PCR-based marker systems in pearl millet

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Abstract

A set of 22 pearl millet inbred lines including the parents of eleven mapping populations, was screened with 627 markers including 100 pearl millet genomic SSRs (gSSRs), 60 pearl millet EST-SSRs (eSSRs), 410 intron sequence haplotypes (ISHs), and 57 exon sequence haplotypes (ESHs). In all, 267 (59%) of the markers were informative for at least one of the 11 mapping populations, which segregate for traits like drought and salinity tolerance; host plant resistance to downy mildew, rust and blast; fertility restoration and sterility and maintenance of cytoplasmic male sterility etc. An average of 116 polymorphic markers was identified per mapping population. The average PIC values and number of profiles (P) per polymorphic marker were: gSSRs (PIC = 0.62, P = 6.1), ISHs (PIC = 0.39, P = 2.6), eSSRs (PIC = 0.36, P = 3.1) and ESHs (PIC = 0.35, P = 3.1). A high correlation (r > 0.97, P < 0.05) was observed between the patterns of diversity exposed by the different marker systems. The polymorphic markers identified are suitable for the de novo construction, or the supplementation of pearl millet linkage maps. The genetic relationships identified among the panel of inbred lines may be useful in designing strategies to improve the use of available genetic variation in the context of pearl millet breeding.

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Acknowledgements

Authors are thankful to the The Syngenta Foundation for the Sustainable Agriculture (SFSA, www.syngentafoundation.org/), and Department of Biotechnology of the Government of India (DBT, http://dbtindia.nic.in/) for financial support. MT is also thankful to the Council of Scientific and Industrial Research (CSIR) of the Government of India for sponsoring his fellowship.

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Authors and Affiliations

  1. Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, AP, India

    Mahendar Thudi, Senapathi Senthilvel, C. Tom Hash, David A. Hoisington & Rajeev K. Varshney

  2. School of Life Sciences, University of Hyderabad, Hyderabad, 500046, AP, India

    Mahendar Thudi & Arjula R. Reddy

  3. University of Nottingham, University Park, Nottingham, NG7 2RD, UK

    Andrew Bottley

  4. College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA

    Alex F. Feltus

  5. Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA

    Andrew H. Paterson

  6. Genomics Towards Gene Discovery Sub Programme, Generation Challenge Programme, c/o CIMMYT, Int APDO Postal 6-641, 06600, Mexico, DF, Mexico

    Rajeev K. Varshney

Authors
  1. Mahendar Thudi
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  2. Senapathi Senthilvel
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  3. Andrew Bottley
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  4. C. Tom Hash
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  5. Arjula R. Reddy
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  6. Alex F. Feltus
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  7. Andrew H. Paterson
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  8. David A. Hoisington
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  9. Rajeev K. Varshney
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Correspondence to Rajeev K. Varshney.

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Thudi, M., Senthilvel, S., Bottley, A. et al. A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica 174, 253–260 (2010). https://doi.org/10.1007/s10681-010-0148-5

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  • DOI: https://doi.org/10.1007/s10681-010-0148-5

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