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Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones

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Abstract

Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.

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Acknowledgments

This study was supported by Spain’s Ministerio de Ciencia e Innovación (AGL2009-13273), Consolider Ingenio Aquagenomics (CSD200700002) and Xunta de Galicia (09MMA011261PR; 10MMA200027PR). Samples for cytogenetic analysis were kindly supplied by Cluster de Acuicultura de Galicia. Thanks to Víctor González, Manuel Manchado, and Miguel Hermida for technical support and to María López and Vanessa Pérez for technical assistance. We also thank José Antonio Álvarez-Dios for useful comments on the manuscript. The authors wish to acknowledge to the Department of Biología Celular y Ecología of USC for providing the microscope. Finally, the authors are grateful to the people of the laboratory of Dr. Foresti in Botucatu (Brasil) for their technical help with FISH.

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Correspondence to Carmen Bouza.

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Linkage map of turbot (Hermida et al. 2013a) showing the markers and BAC clones assayed in this study. (M) Multiple or (X) lack of marker-specific clones in the turbot BAC library; (F) Failed BAC probes for BAC-FISH assays. The centromere-linked marker positions were indicated by grey points according to Martínez et al. (2008). (JPEG 247 kb)

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Taboada, X., Pansonato-Alves, J.C., Foresti, F. et al. Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones. Chromosoma 123, 281–291 (2014). https://doi.org/10.1007/s00412-014-0452-2

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