Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

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Abstract

Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout.

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The variant call format and VCFtools

Petr Danecek, Adam Auton, Gonçalo R Abecasis … (2011)

Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk

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Second-generation PLINK: rising to the challenge of larger and richer datasets

Christopher Chang, Carson Chow, Laurent Tellier … (2015)

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

Pablo E. Cingolani, Adrian E. Platts, Le Lily Wang … (2012)

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w(1118); iso-2; iso-3 strain and the reference y(1); cn(1) bw(1) sp(1) strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5' and 3' UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.

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Author and article information

Contributors

Clémence Fraslin: clemence.fraslin@roslin.ed.ac.uk

Florence Phocas: florence.phocas@inrae.fr

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 19 October 2020

Publication date PMC-release: 19 October 2020

Publication date Collection: 2020

Volume: 10

Electronic Location Identifier: 17693

Affiliations

[1 ]GRID grid.420312.6, ISNI 0000 0004 0452 7969, Université Paris-Saclay, , INRAE, AgroParisTech, GABI, ; 78350 Jouy-en-Josas, France

[2 ]GRID grid.462558.8, ISNI 0000 0004 0450 5110, SYSAAF, , Station LPGP/INRAE, ; Campus de Beaulieu, 350002 Rennes, France

[3 ]GRID grid.507621.7, INRAE, SIGENAE, ; 78350 Jouy-en-Josas, France

[4 ]Allice, MNE, 149 rue de Bercy, 75595 Paris, France

[5 ]GRID grid.452770.3, ISNI 0000 0001 2226 6748, Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, ; 75013 Paris, France

[6 ]GRID grid.507621.7, INRAE, US 1426, GeT-PlaGe, ; 31326 Castenet-Tolosan, France

[7 ]GRID grid.507621.7, INRAE, UMR1095, Gentyane, ; 63000 Clermont-Ferrand, France

[8 ]Charles MURGAT Pisciculture, 38270 Beaufort, France

[9 ]GRID grid.462558.8, ISNI 0000 0004 0450 5110, INRAE, LPGP, ; 35000 Rennes, France

[10 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, Present Address: The Roslin Institute and Royal (Dick) School of Veterinary Studies, , The University of Edinburgh, ; Midlothian, UK

Article

Publisher ID: 74757

DOI: 10.1038/s41598-020-74757-8

PMC ID: 7573577

PubMed ID: 33077766

SO-VID: 9b39eff2-1bc6-4cd9-8c05-9c6dc20c17e5

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 30 April 2020

Date accepted : 6 October 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100014510, European Maritime and Fisheries Fund;

Award ID: R FEA470016FA1000008

Award Recipient : Clémence Fraslin

Funded by: FundRef http://dx.doi.org/10.13039/501100003199, France AgriMer;

Award ID: R FEA470016FA1000008

Award Recipient : Clémence Fraslin

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ScienceOpen disciplines: Uncategorized

Keywords: genome-wide association studies,animal breeding,genomics

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ScienceOpen disciplines: Uncategorized

Keywords: genome-wide association studies, animal breeding, genomics

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Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

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Most cited references 40

The variant call format and VCFtools

Second-generation PLINK: rising to the challenge of larger and richer datasets

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

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Cited by 8

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