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QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

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Abstract

Fifty-eight F2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P ≤ 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make it easier to target particular loci for map-based cloning and marker-assisted selection studies.

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Acknowledgments

This work was supported by a Career Project (TUBITAK 104T224) from the Scientific and Technical Research Council of Turkey to Sami Doğanlar. This execution of the AFLP marker work was financially supported by DeRuiterZonen C.V., Rijk Zwaan Zaadteelt and Zaadhandel B.V., and Vilmorin Clause & Cie S.A. The AFLP® technology is covered by patents and/or patent applications of Keygene N.V. AFLP and KeyGene are registered trademarks of Keygene N.V. Other trademarks are the property of their respective owners.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, 01075, USA

    Amy Frary

  2. Plant Molecular Genetics Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce Campus, Urla, Izmir, 35430, Turkey

    Anne Frary & Sami Doğanlar

  3. Unité de Génétique et Amélioration des Fruits et Légumes, INRA, Domaine Saint Maurice, BP 94, 84143, Montfaved Cedex, France

    Marie-Christine Daunay

  4. Keygene N.V., Agro Business Park 90, 6708 PW, Wageningen, The Netherlands

    Koen Huvenaars & Rolf Mank

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  1. Amy Frary
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  2. Anne Frary
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  3. Marie-Christine Daunay
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  4. Koen Huvenaars
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Correspondence to Sami Doğanlar.

Additional information

The localization of QTL for 32 morphological traits on the high-resolution map of the eggplant genome has allowed hotspots and putative orthologs with other solanaceous species to be identified.

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Frary, A., Frary, A., Daunay, MC. et al. QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis. Euphytica 197, 211–228 (2014). https://doi.org/10.1007/s10681-013-1060-6

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