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Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)

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Abstract

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for specified Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor-joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Poncirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identified five populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.

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Acknowledgements

We would like to thank the U.S. Department of Agriculture for the funding to support this project. In addition, we thank the Genetic Graduate Group at the University of California, Riverside for providing partial funding of this project. Also, thanks to Dr. Mark Springer and Dr. Angela Burk-Herrick (University of California, Riverside) for providing assistance on PAUP and phylogenetic interpretation. Thanks to Dr. Tracy Kahn and Ms. Toots Bier for their support in providing historical and morphological information on Citrus varieties from the Citrus Variety Collection (CVC archival data). Lastly, thanks to colleagues at USDA-ARS Plant Genetic Resource Conservation Unit in Griffin, GA, USA for reviewing this manuscript.

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Authors and Affiliations

  1. Department of Botany and Plant Sciences and Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, 92521, USA

    Noelle A. Barkley

  2. Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA

    Mikeal L. Roose & Claire T. Federici

  3. USDA-ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, 92507, USA

    Robert R. Krueger

  4. 1109 Experiment Street, Griffin, GA, 30223, USA

    Noelle A. Barkley

Authors
  1. Noelle A. Barkley
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  2. Mikeal L. Roose
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  3. Robert R. Krueger
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  4. Claire T. Federici
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Correspondence to Noelle A. Barkley.

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Communicated by J. S. Heslop-Harrison

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Barkley, N.A., Roose, M.L., Krueger, R.R. et al. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112, 1519–1531 (2006). https://doi.org/10.1007/s00122-006-0255-9

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  • DOI: https://doi.org/10.1007/s00122-006-0255-9

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