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Development of a molecular linkage map of pearl millet integrating DArT and SSR markers

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Abstract

Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F7 Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available.

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Acknowledgments

This study was supported by the ‘Generation Challenge Programme’ of the Consultative Group on International Agricultural Research (CGIAR) and by the Department of Biotechnology, Government of India. The authors thank DArT P/L, Australia for providing technical know-how, software, and helpful discussions and the Council of Scientific and Industrial Research (CSIR), India for providing a Junior Research Fellowship to Mr V. Rajaram.

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Authors and Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India

    A. Supriya, S. Senthilvel, T. Nepolean, K. Eshwar, V. Rajaram, R. Shaw & C. T. Hash

  2. Department of Biotechnology and Molecular Biology, College of Basic Sciences and Humanities, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125 004, India

    A. Supriya & R. C. Yadav

  3. Indian Agricultural Research Institute, New Delhi, 110 012, India

    T. Nepolean

  4. Centre for Biotechnology, IST, JNTUH, Kukatpally, Hyderabad, 500 085, India

    V. Rajaram & M. L. Narasu

  5. Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, Canberra, ACT, 2600, Australia

    A. Kilian

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  1. A. Supriya
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Correspondence to S. Senthilvel.

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Supriya, A., Senthilvel, S., Nepolean, T. et al. Development of a molecular linkage map of pearl millet integrating DArT and SSR markers. Theor Appl Genet 123, 239–250 (2011). https://doi.org/10.1007/s00122-011-1580-1

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