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Genetic diversity and population structure analysis of mandarin germplasm by nuclear, chloroplastic and mitochondrial markers

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Abstract

The mandarin horticultural varietal group (a basic taxon of the cultivated citrus (Citrus reticulata)) is highly polymorphic. It includes also genotypes introgressed by other species. The precise contribution of ancestral species to the mandarin group is not known. The goals of this work were (1) to characterise the mandarin germplasm using nuclear (simple sequence repeat (SSR), indel, single nucleotide polymorphism (SNP)), chloroplastic and mitochondrial markers; (2) to evaluate genetic diversity and detect redundancies; (3) to determine the possible presence of citrus ancestral genome introgressions into the mandarin genome; and (4) to determine the genetic structure within the mandarin group. Fifty microsatellites (SSRs), 24 insertion-deletions (indels), 67 SNPs, 8 chloroplastic SSRs (cpDNA) and 4 mitochondrial (mtDNA) indel markers were analysed for 191 genotypes, including the 4 main citrus ancestral species (C. reticulata, C. maxima, C. medica and C. micrantha) and Fortunella. C. maxima was the main genome introgressed in the mandarin germplasm. Seven clusters were revealed by Structure analysis at the nuclear level (N) within the mandarin germplasm. At least four of these clusters showed a clear introgression from other ancestral species. Moreover, most of the mandarins appeared to be complex mixtures of these groups. The maternal indel analysis (mtDNA and cpDNA) revealed ten cytotypes in which mandarins were represented in seven of them. This work provides new insights into the organisation of the mandarin germplasm and its structure at the nuclear and cytoplasmic levels and will be useful to design more efficient breeding programmes and management of citrus germplasm collections.

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Acknowledgments

This work was supported by a grant (AGL2011-26490) from the Ministry of Economy and Innovation-Fondo Europeo de Desarrollo Regional (FEDER), 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

    Andres Garcia-Lor, Patrick Ollitrault & Luis Navarro

  2. UMR AGAP Institut National de la Recherche Agronomique (INRA Corse), 20230, San Giuliano, France

    François Luro

  3. UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de Roujol, 97170, Petit-Bourg, Guadeloupe

    Patrick Ollitrault

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  1. Andres Garcia-Lor
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  2. François Luro
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  3. Patrick Ollitrault
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  4. Luis Navarro
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Correspondence to Luis Navarro.

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Communicated by W.-W Guo

This article is part of the Topical Collection on Population Structure

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Garcia-Lor, A., Luro, F., Ollitrault, P. et al. Genetic diversity and population structure analysis of mandarin germplasm by nuclear, chloroplastic and mitochondrial markers. Tree Genetics & Genomes 11, 123 (2015). https://doi.org/10.1007/s11295-015-0951-1

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