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

• Published in: Planta Vol. 241; no. 4; pp. 987 - 1004
• Main Authors: Adal, Ayelign M, Demissie, Zerihun A, Mahmoud, Soheil S
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01-04-2015; Springer Berlin Heidelberg; Springer Nature B.V
• Subjects: Agriculture; Alleles; Biomedical and Life Sciences; crops; Cultivars; DNA, Plant - genetics; Ecology; Essential oils; Expressed Sequence Tags; Forestry; Genetic markers; Genetic Markers - genetics; Lavandula - genetics; Lavandula angustifolia; Lavandula intermedia; Life Sciences; loci; marker-assisted selection; microsatellite repeats; Microsatellite Repeats - genetics; Original Article; Phylogeny; Plant Sciences; Species Specificity; unigenes; Genetic marker; EST-SSR; Polymorphism
• ISSN: 0032-0935; 1432-2048
• DOI: 10.1007/s00425-014-2226-8

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. 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.