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Identification, validation and cross-species transferability of novel Lavandula EST-SSRs

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Abstract

Main conclusion

We identified and characterized EST-SSRs with strong discrimination power against Lavandula angustifolia and Lavandula x intermedia . The markers also showed considerable cross-species transferability rate into six related Lavandula species.

Abstract

Lavenders (Lavandula) are important economical crops grown around the globe for essential oil production. In an attempt to develop genetic markers for these plants, we analyzed over 13,000 unigenes developed from L. angustifolia and L. x intermedia EST databases, and identified 3,459 simple sequence repeats (SSR), which were dominated by trinucleotides (41.2 %) and dinucleotides (31.45 %). Approximately, 19 % of the unigenes contained at least one SSR marker, over 60 % of which were localized in the UTRs. Only 252 EST-SSRs were 18 bp or longer from which 31 loci were validated, and 24 amplified discrete fragments with 85 % polymorphism in L. x intermedia and L. angustifolia. The average number of alleles in L. x intermedia and L. angustifolia were 3.42 and 3.71 per marker with average PIC values of 0.47 and 0.52, respectively. These values suggest a moderate to strong level of informativeness for the markers, with some loci producing unique fingerprints. The cross-species transferability rate of the markers ranges 50–100 % across eight species. The utility of these markers was assessed in eight Lavandula species and 15 L. angustifolia and L. x intermedia cultivars, and the dendrogram deduced from their similarity indexes successfully delineated the species into their respective sections and the cultivars into their respective species. These markers have potential for application in fingerprinting, diversity studies and marker-assisted breeding of Lavandula.

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Abbreviations

CDS:

Protein coding regions

EST:

Expressed sequence tags

EO:

Essential oil

He :

Genetic diversity

Na :

Number of alleles

PIC:

Polymorphic information content

PFR:

Primer flanking regions

SSR:

Simple sequence repeats

UTR:

Untranslated regions

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Acknowledgments

This work was supported through grants and/or in-kind contributions to SSM by UBC, Genome British Columbia, Natural Sciences and Engineering Research Council of Canada, Agriculture and Agri-Food Canada and the BC Ministry of Agriculture (through programs delivered by the Investment Agriculture Foundation of BC), Downderry Nursery (Hadlow, Tonbridge, UK), Okanagan Lavender and Herb Farm (Kelowna, BC, Canada) and Sacred Mountain Lavender (Salt Spring Islands, BC, Canada). Finally, we appreciate Dr. Michael Russello for his help with manuscript preparation.

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  1. Zerihun A. Demissie

    Present address: Department of Biological Sciences, Brock University, 500 Glenridge Ave, St. Catharines, ON, L2S 3A1, Canada

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  1. Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC, V1V 1V7, Canada

    Ayelign M. Adal, Zerihun A. Demissie & Soheil S. Mahmoud

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Adal, A.M., Demissie, Z.A. & Mahmoud, S.S. Identification, validation and cross-species transferability of novel Lavandula EST-SSRs. Planta 241, 987–1004 (2015). https://doi.org/10.1007/s00425-014-2226-8

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