Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus

Abstract Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP...

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Autores principales:	Vito A. Mastrochirico-Filho, Raquel B. Ariede, Milena V. Freitas, Carolina H. S. Borges, Lieschen V. G. Lira, Natália J. Mendes, John F. G. Agudelo, Pablo Cáceres, Milthon H. M. Berrocal, Gustavo A. L. Sucerquia, Fabio Porto-Foresti, José M. Yáñez, Diogo T. Hashimoto
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dd25570e14b44299b68f833b6b3a129a
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spelling	oai:doaj.org-article:dd25570e14b44299b68f833b6b3a129a2021-12-02T19:16:47ZDevelopment of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus10.1038/s41598-021-98885-x2045-2322https://doaj.org/article/dd25570e14b44299b68f833b6b3a129a2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98885-xhttps://doaj.org/toc/2045-2322Abstract Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.Vito A. Mastrochirico-FilhoRaquel B. AriedeMilena V. FreitasCarolina H. S. BorgesLieschen V. G. LiraNatália J. MendesJohn F. G. AgudeloPablo CáceresMilthon H. M. BerrocalGustavo A. L. SucerquiaFabio Porto-ForestiJosé M. YáñezDiogo T. HashimotoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vito A. Mastrochirico-Filho Raquel B. Ariede Milena V. Freitas Carolina H. S. Borges Lieschen V. G. Lira Natália J. Mendes John F. G. Agudelo Pablo Cáceres Milthon H. M. Berrocal Gustavo A. L. Sucerquia Fabio Porto-Foresti José M. Yáñez Diogo T. Hashimoto Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
description	Abstract Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.
format	article
author	Vito A. Mastrochirico-Filho Raquel B. Ariede Milena V. Freitas Carolina H. S. Borges Lieschen V. G. Lira Natália J. Mendes John F. G. Agudelo Pablo Cáceres Milthon H. M. Berrocal Gustavo A. L. Sucerquia Fabio Porto-Foresti José M. Yáñez Diogo T. Hashimoto
author_facet	Vito A. Mastrochirico-Filho Raquel B. Ariede Milena V. Freitas Carolina H. S. Borges Lieschen V. G. Lira Natália J. Mendes John F. G. Agudelo Pablo Cáceres Milthon H. M. Berrocal Gustavo A. L. Sucerquia Fabio Porto-Foresti José M. Yáñez Diogo T. Hashimoto
author_sort	Vito A. Mastrochirico-Filho
title	Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
title_short	Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
title_full	Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
title_fullStr	Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
title_full_unstemmed	Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus
title_sort	development of a multi-species snp array for serrasalmid fish colossoma macropomum and piaractus mesopotamicus
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/dd25570e14b44299b68f833b6b3a129a
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Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus

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