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Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot

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Abstract

According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean π sil = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F ST = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r 2 = 0.635) within the 700–1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.

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Acknowledgments

We would like to thank Françoise Gros and Marie-France Le Cunff, of the ‘Plate-forme de séquençage & de génotypage’ (IFR26, Nantes) for sequencing PCR products. We are grateful to Domenica Manicacci for providing script for LD decay analysis. We wish to thank Gérard Simon for his critical reading of this paper. This study was supported by grants from the region Pays de la Loire. This project is part of collaboration with Vilmorin SA, Clause Vegetable Seeds and Diana Naturals. Jérémy Clotault is a PhD student funded by the French Ministry of Research. Ethical standards: Authors declare that the experiments carried out comply with the current laws of the country in which they were performed, i.e., France.

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Authors and Affiliations

  1. Agrocampus Ouest, INHP, IFR 149 Quasav, UMR 1259 GenHort, 2 Rue Le Nôtre, 49045, Angers, France

    Jérémy Clotault, Emmanuel Geoffriau & Mathilde Briard

  2. Clause Vegetable Seeds, 49070, Beaucouzé, France

    Eric Lionneton

  3. Université d’Angers, IFR 149 Quasav, UMR 1259 GenHort, 49045, Angers, France

    Didier Peltier

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  1. Jérémy Clotault
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Correspondence to Emmanuel Geoffriau.

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Communicated by M. Havey.

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Clotault, J., Geoffriau, E., Lionneton, E. et al. Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot. Theor Appl Genet 121, 659–672 (2010). https://doi.org/10.1007/s00122-010-1338-1

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