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      ddRADseq reveals determinants for temperature-dependent sex reversal in Nile tilapia on LG23

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          Abstract

          Background

          In Nile tilapia sex determination is governed by a male heterogametic system XX/XY either on LG1 or LG23. The latter carries a Y-specific duplicate of the amh gene, which is a testis-determining factor. Allelic variants in the amh gene demonstrated to be major triggers for autosomal and temperature-dependent sex reversal. Further, QTL on LG23 and LG20 show a temperature-responsiveness with influence on the phenotypic sex relative to the sex chromosomes. Here we present a ddRADseq based approach to identify genomic regions that show unusual large differentiation in terms of fixation index (F ST) between temperature-treated pseudomales and non-masculinized females using a comparative genome-scan. Genome-wide associations were identified for the temperature-dependent sex using a genetically all-female population devoid of amh-ΔY.

          Results

          Twenty-two thousand three hundred ninety-two SNPs were interrogated for the comparison of temperature-treated pseudomales and females, which revealed the largest differentiation on LG23. Outlier F ST-values (0.35–0.44) were determined for six SNPs in the genomic interval (9,190,077–11,065,693) harbouring the amh gene (9,602,693–9,605,808), exceeding the genome-wide low F ST of 0.013. Association analysis with a set of 9104 selected SNPs confirmed that the same genomic region on LG23 exerts a significant effect on the temperature-dependent sex.

          Conclusions

          This study highlights the role of LG23 in sex determination, harbouring major determinants for temperature-dependent sex reversal in Nile tilapia. Furthermore F ST outlier detection proves a powerful tool for detection of sex-determining regions in fish genomes.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12864-017-3930-0) contains supplementary material, which is available to authorized users.

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          Most cited references 3

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          Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands.

          To increase the yield of DNA sequence generated by the 454 technology from small amounts of starting DNA, we investigated the efficiency of each step in the 454 library preparation process. We find that the last step, when the single-stranded library is released by NaOH, is inefficient and highly variable. When this step is replaced with heat treatment, library amounts dramatically increase. Furthermore, when sequencing templates are first isolated by NaOH treatment and subsequently by heat treatment, the sequences of both strands of individual template DNA molecules can be determined. Using this approach, we confirm that C/G base pairs observed as T/A base pairs in Neanderthal DNA sequences are due to a modification of the cytosine rather than guanine residues.
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            Evidence for two unlinked “sex reversal” loci in the Nile tilapia, Oreochromis niloticus, and for linkage of one of these to the red body colour gene

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              Short communication A YY-male Oreochromis niloticus strain developed from an exceptional mitotic gynogenetic male and growth performance testing of genetically all-male progenies

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                Author and article information

                Contributors
                swessel@gwdg.de
                ina.krause@agr.uni-goettingen.de
                cfloren@gwdg.de
                esc@chronixbiomedical.de
                jbeck@chronixbiomedical.de
                cknorr@gwdg.de
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                14 July 2017
                14 July 2017
                2017
                : 18
                Affiliations
                [1 ]ISNI 0000 0001 2364 4210, GRID grid.7450.6, Department of Animal Sciences, Division of Aquaculture and Water Ecology, , University of Goettingen, ; Albrecht-Thaer-Weg 3, 37075 Goettingen, Germany
                [2 ]ISNI 0000 0001 2364 4210, GRID grid.7450.6, Department of Animal Sciences, Division of Livestock Biotechnology and Reproduction, , University of Goettingen, ; Burckhardtweg 2, 37077 Goettingen, Germany
                [3 ]ISNI 0000 0001 2364 4210, GRID grid.7450.6, Institute of Veterinary Medicine, , University of Goettingen, ; 37077 Goettingen, Germany
                [4 ]Chronix Biomedical GmbH, 37077 Goettingen, Germany
                Article
                3930
                10.1186/s12864-017-3930-0
                5513378
                28705237
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: WE4434/2-1
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Genetics

                ddradseq, fst, temperature, sex reversal, lg23, nile tilapia, sex chromosomes

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