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Microsatellite identification and characterization in peanut (A. hypogaea L.)

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Abstract

A major constraint to the application of biotechnology to the improvement of the allotetraploid peanut, or groundnut (Arachis hypogaea L.), has been the paucity of polymorphism among germplasm lines using biochemical (seed proteins, isozymes) and DNA markers (RFLPs and RAPDs). Six sequence-tagged microsatellite (STMS) markers were previously available that revealed polymorphism in cultivated peanut. Here, we identify and characterize 110 STMS markers that reveal genetic variation in a diverse array of 24 peanut landraces. The simple-sequence repeats (SSRs) were identified with a probe of two 27,648-clone genomic libraries: one constructed using PstI and the other using Sau3AI/BamHI. The most frequent, repeat motifs identified were ATT and GA, which represented 29% and 28%, respectively, of all SSRs identified. These were followed by AT, CTT, and GT. Of the amplifiable primers, 81% of ATT and 70.8% of GA repeats were polymorphic in the cultivated peanut test array. The repeat motif AT showed the maximum number of alleles per locus (5.7). Motifs ATT, GT, and GA had a mean number of alleles per locus of 4.8, 3.8, and 3.6, respectively. The high mean number of alleles per polymorphic locus, combined with their relative frequency in the genome and amenability to probing, make ATT and GA the most useful and appropriate motifs to target to generate further SSR markers for peanut.

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Acknowledgements

The authors are grateful to Scott Lee, Manisha Singh, and Shiwanand Varma for technical assistance. The project was funded under a USAID linkage grant to ICRISAT.

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Author notes

  1. M. D. Burow

    Present address: Texas Agricultural Experiment Station, Texas A&M University, Rte. 3, Box 219, Lubbock, TX 79403, USA

  2. M. E. Ferguson

    Present address: International Institute for Tropical Agriculture (IITA), c/o ILRI, P.O. Box 30709, Nairobi, Kenya

Authors and Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Andhra Pradesh, India

    M. E. Ferguson

  2. Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA

    M. D. Burow

  3. Departments of Crop and Soil Science, Botany and Genetics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA

    S. R. Schulze & A. H. Paterson

  4. KISR, c/o Dr. John Peacock, P.O. Box 24885, 13109 , Safat, Kuwait

    P. J. Bramel

  5. Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA

    S. Kresovich & S. Mitchell

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  1. M. E. Ferguson
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Correspondence to M. E. Ferguson.

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Communicated by J.S. Heslop-Harrison

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Ferguson, M.E., Burow, M.D., Schulze, S.R. et al. Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108, 1064–1070 (2004). https://doi.org/10.1007/s00122-003-1535-2

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  • DOI: https://doi.org/10.1007/s00122-003-1535-2

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