Identification of a major locus determining a pigmentation defect in cultivated gilthead seabream (Sparus aurata).
FST
aquaculture
depigmentation
discoloration
next-generation sequencing
Journal
Animal genetics
ISSN: 1365-2052
Titre abrégé: Anim Genet
Pays: England
ID NLM: 8605704
Informations de publication
Date de publication:
Mar 2020
Mar 2020
Historique:
accepted:
15
11
2019
pubmed:
5
1
2020
medline:
29
9
2020
entrez:
5
1
2020
Statut:
ppublish
Résumé
The gilthead seabream (Sparus aurata) is an important cultivated species in the Mediterranean area. A major problem for the gilthead seabream aquaculture sector derives from the high frequency of phenotypic abnormalities, including discolorations. In this study, we applied a whole-genome resequencing approach to identify a genomic region affecting a pigmentation defect that occurred in a cultivated S. aurata population. Two equimolar DNA pools were constructed using DNA extracted from 30 normally coloured and 21 non-pigmented fish collected among the offspring of the same broodstock nucleus. Whole-genome resequencing reads from the two DNA pools were aligned to the S. aurata draft genome and variant calling was performed. A whole-genome heterozygosity scan from single pool sequencing data highlighted a peak of reduced heterozygosity of approximately 5 Mbp on chromosome 6 in the non-pigmented pool that was not present in the normally coloured pool. The comparison of the non-pigmented with the normally coloured fish using a whole-genome F
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
319-323Subventions
Organisme : Ensminger Fund
Organisme : State of Iowa Funds
Organisme : University of Bologna RFO Funds
Informations de copyright
© 2020 Stichting International Foundation for Animal Genetics.
Références
Bansal V. (2010) A statistical method for the detection of variants from next generation resequencing of DNA pools. Bioinformatics 26, i318-24.
Baxter L.L., Watkins-Chow D.E., Pavan W.J. & Loftus S.K. (2019) A curated gene list for expanding the horizons of pigmentation biology. Pigment Cell & Melanoma Research 32, 348-58.
Bertolini F., Geraci C., Schiavo G., Sardina M.T., Chiofalo V. & Fontanesi L. (2016) Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach. Marine Genomics 28, 63-70.
Bolger A.M., Lohse M. & Usadel B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-20.
Bovo S., Bertolini F., Schiavo G., Mazzoni G., Dall'Olio S. & Fontanesi L. (2015) Reduced representation libraries from DNA pools analysed with next generation semiconductor based-sequencing to identify SNPs in extreme and divergent pigs for back fat thickness. International Journal of Genomics 2015, 95073.
DePristo M.A., Banks E., Poplin R. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43, 491-8.
Karlsson E.K., Baranowska I., Wade C.M. et al. (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nature Genetics 39, 1321-8.
Kelsh R.N. (2004) Genetics and evolution of pigment patterns in fish. Pigment Cell Research 17, 326-36.
Kim D., Langmead B., Salzberg S.L. (2015) HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12, 357-60.
Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. & 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 15, 2078-9.
Mellgren E.M. & Johnson S.L. (2002) The evolution of morphological complexity in zebrafish stripes. Trends in Genetics 18, 128-34.
Moretti A., Pedini Fernandez-Criado M., Cittolin G., Guidastri R. (1999) Manual on Hatchery Production of Seabass and Gilthead Seabream, pp. 194. FAO, Rome.
Negrín-Báez D., Navarro A., Lee-Montero I., Soula M., Afonso J.M. & Zamorano M.J. (2015) Inheritance of skeletal deformities in gilthead seabream (Sparus aurata) - lack of operculum, lordosis, vertebral fusion and LSK complex. Journal of Animal Science 93, 53-61.
Odenthal J., Rossnagel K., Haffter P. et al. (1996) Mutations affecting xanthophore pigmentation in the zebrafish, Danio rerio. Development 123, 391-8.
Pauletto M., Manousaki T., Ferraresso S. et al. (2018) Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Communications Biology 1, 119.
Pavlidis M.A. & Mylonas C.C. (2011) Sparidae: Biology and Aquaculture of Gilthead Sea Bream and Other Species. Oxford, UK: Blackwell Publishing Ltd.
Pertea M., Pertea G.M., Antonescu C.M., Chang T.C., Mendell J.T. & Salzberg S.L. (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33, 290-5.
Rubin C.J., Zody M.C., Eriksson J. et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-91.
Rubin C.J., Megens H.J., Martinez BarrioA. et al. (2012) Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences USA 109, 19529-36.
Smith C.T., Elfstrom C.M., Seeb L.W. & Seeb J.E. (2005) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology 14, 4193-203.
Sola L., Moretti A., Crosetti D., Karaiskou N., Magoulas A., Rossi A.R., Rye M., Triantafyllidis A. & Tsigenopoulos C.S. (2006) Gilthead seabream-Sparus aurata. In: Genetic Effects of Domestication, Culture and Breeding of Fish and Shellfish, and Their Impacts on Wild Populations (Ed. by D.S.Crosetti, S. Lapègue, I.Olesen & T.Svaasand), GENIMPACT Project: Evaluation of Genetic Impact of Aquaculture Activities on Native Populations. A European Network. WP1 Workshop ‘Genetics of Domestication, Breeding and Enhancement of Performance of Fish and Shellfish’, Viterbo, Italy, 12th-17th June, 2006, 6 pp. http://genimpact.imr.no/
Theodorou J.A., Perdikaris C. & Venou B. (2016) Origin of broodstock and effects on the deformities of gilthead sea bream (Sparus aurata L. 1758) in a Mediterranean commercial hatchery. International Aquatic Research 8, 275.
Whitehead P.J.P., Bauchot M.-L., Hureau J.-C., Nielsen J. & Tortonese E. (1986) Fishes of the North-Eastern Atlantic and the Mediterranean. Paris: UNESCO.
Yan B., Liu B., Zhu C.D., Li K.L., Yue L.J., Zhao J.L., Gong X.L. & Wang C.H. (2013) microRNA regulation of skin pigmentation in fish. Journal of Cell Science 126, 3401-8.