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Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies

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Abstract

Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion–deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata.

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Acknowledgments

This research was jointly financed by the grant AGL2008-00596-Ministry of Science and Innovation of Spain-Fondo Europeo de Desarrollo Regional (FEDER) and the grant Prometeo/2008/121 from the Generalitat Valenciana, Spain.

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Authors and Affiliations

  1. Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain

    Andrés García-Lor, Luis Navarro & Patrick Ollitrault

  2. Unité de Recherche GEQA, Institut National de la Recherche Agronomique (INRA), 20230, San Giuliano, France

    François Luro

  3. Department BIOS, TGU AGAP, International Center for of Agricultural Research for Development (CIRAD), Avenue Agropolis, TA A-75/02, 34398, Montpellier Cedex 5, France

    Patrick Ollitrault

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  1. Andrés García-Lor
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Correspondence to Luis Navarro or Patrick Ollitrault.

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García-Lor, A., Luro, F., Navarro, L. et al. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Mol Genet Genomics 287, 77–94 (2012). https://doi.org/10.1007/s00438-011-0658-4

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