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Mining and characterizing microsatellites from citrus ESTs

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Abstract

Freely available computer programs were arranged in a pipeline to extract microsatellites from public citrus EST sequences, retrieved from the NCBI. In total, 3,278 bi- to hexa-type SSR-containing sequences were identified from 56,199 citrus ESTs. On an average, one SSR was found per 5.2 kb of EST sequence, with the tri-nucleotide motifs as the most abundant. Primer sequences flanking SSR motifs were successfully identified from 2,295 citrus ESTs. Among those, a subset (100 pairs) were synthesized and tested to determine polymorphism and heterozygosity between/within two genera, sweet orange (C. sinensis) and Poncirus (P. trifoliata), which are the parents of the citrus core mapping population selected for an international citrus genomics effort. Eighty-seven pairs of primers gave PCR amplification to the anticipated SSRs, of which 52 and 35 appear to be homozygous and heterozygous, respectively, in sweet orange, and 67 and 20, respectively, in Poncirus. By pairing the loci between the two intergeneric species, it was found that 40 are heterozygous in at least one species with two alleles (9), three alleles (28), or four alleles (3), and the remaining 47 are homozygous in both species with either one allele (31) or two alleles (16). These EST-derived SSRs can be a resource used for understanding of the citrus SSR distribution and frequency, and development of citrus EST-SSR genetic and physical maps. These SSR primer sequences are available upon request.

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Acknowledgment

The authors would like to thank Dr. Thomas Thiel and Dr. Lisa Davis for their kind answers to the questions about using the misa Perl scripts for SSR search, and implementing microsatellite analysis on ABI 3100 machine, Mr. Allan Burrage and Mr. Gary Wilhite for their enthusiastic assistance to setup Linux in the VMWare virtual machine, and Mrs. Margie K. Wendell for her excellent technical support. This research was supported in part under Project Number 0110-03I of the Florida Citrus Production Research Advisory Council, and by a grant from USDA-CSREES-NCRI 2002-34399-12765. Florida Agricultural Experiment Station Journal Series Number is R-11027.

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Authors and Affiliations

  1. Institute of Food and Agricultural Sciences, Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL, 33850, USA

    Chunxian Chen, Ping Zhou, Young A Choi, Shu Huang & Fred G. Gmitter Jr

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  1. Chunxian Chen
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  2. Ping Zhou
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  3. Young A Choi
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  4. Shu Huang
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  5. Fred G. Gmitter Jr
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Correspondence to Fred G. Gmitter Jr.

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Communicated by S. J. Knapp

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Chen, C., Zhou, P., Choi, Y.A. et al. Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112, 1248–1257 (2006). https://doi.org/10.1007/s00122-006-0226-1

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  • DOI: https://doi.org/10.1007/s00122-006-0226-1

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