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Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance

Streptococcus iniae is a problematic gram-positive bacterium negatively affecting Nile tilapia (Oreochromis niloticus), one of the main aquacultural species produced worldwide. The aim of this study was to identify the genetic architecture of survival to S. iniae and identify single nucleotide polym...

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Autores principales: Vela-Avitúa, Sergio, LaFrentz, Benjamin R., Lozano, Carlos A., Shoemaker, Craig A., Ospina-Arango, Jose Fernando, Beck, Benjamin H., Rye, Morten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10017449/
https://www.ncbi.nlm.nih.gov/pubmed/36936431
http://dx.doi.org/10.3389/fgene.2023.1078381
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author Vela-Avitúa, Sergio
LaFrentz, Benjamin R.
Lozano, Carlos A.
Shoemaker, Craig A.
Ospina-Arango, Jose Fernando
Beck, Benjamin H.
Rye, Morten
author_facet Vela-Avitúa, Sergio
LaFrentz, Benjamin R.
Lozano, Carlos A.
Shoemaker, Craig A.
Ospina-Arango, Jose Fernando
Beck, Benjamin H.
Rye, Morten
author_sort Vela-Avitúa, Sergio
collection PubMed
description Streptococcus iniae is a problematic gram-positive bacterium negatively affecting Nile tilapia (Oreochromis niloticus), one of the main aquacultural species produced worldwide. The aim of this study was to identify the genetic architecture of survival to S. iniae and identify single nucleotide polymorphism (SNPs) linked to quantitative trait loci (QTL) related to survival to S. iniae challenge. With this purpose, Nile tilapia from the Spring Genetics breeding program were sent to a controlled S. iniae challenge test where phenotypes were scored as dead for fish that died during challenge test and survivors for the fish alive at the termination of the test. Additionally, fin-clip samples from all fish in the test were collected for DNA extraction. Out of 1904 fish in the challenge test, tissue samples of 321 fish were sent for genotyping using double digest restriction site associated DNA sequencing (ddRADseq). After quality control and filtering, 9,085 SNPs were used to perform a genome-wide association study (GWAS). A significant signal in LG8 was observed indicating association with survival to S. iniae challenge, with SNPs explaining from 12% to 26% of the genetic variance. To demonstrate the usefulness of marker assisted selection (MAS) to selectively breed fish for survival to S. iniae, offspring of breeding candidates classified as “resistant” and “susceptible” based on haplotypes of the four most significant markers were sent to a controlled S. iniae challenge test. At the end of the test, the differences in mortality between the two groups were strikingly different with a final cumulative percent mortality of less than 1% and 73% for offspring from “resistant” and “susceptible” parents, respectively. These results demonstrate that MAS for improved resistance to S. iniae is feasible.
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spelling pubmed-100174492023-03-17 Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance Vela-Avitúa, Sergio LaFrentz, Benjamin R. Lozano, Carlos A. Shoemaker, Craig A. Ospina-Arango, Jose Fernando Beck, Benjamin H. Rye, Morten Front Genet Genetics Streptococcus iniae is a problematic gram-positive bacterium negatively affecting Nile tilapia (Oreochromis niloticus), one of the main aquacultural species produced worldwide. The aim of this study was to identify the genetic architecture of survival to S. iniae and identify single nucleotide polymorphism (SNPs) linked to quantitative trait loci (QTL) related to survival to S. iniae challenge. With this purpose, Nile tilapia from the Spring Genetics breeding program were sent to a controlled S. iniae challenge test where phenotypes were scored as dead for fish that died during challenge test and survivors for the fish alive at the termination of the test. Additionally, fin-clip samples from all fish in the test were collected for DNA extraction. Out of 1904 fish in the challenge test, tissue samples of 321 fish were sent for genotyping using double digest restriction site associated DNA sequencing (ddRADseq). After quality control and filtering, 9,085 SNPs were used to perform a genome-wide association study (GWAS). A significant signal in LG8 was observed indicating association with survival to S. iniae challenge, with SNPs explaining from 12% to 26% of the genetic variance. To demonstrate the usefulness of marker assisted selection (MAS) to selectively breed fish for survival to S. iniae, offspring of breeding candidates classified as “resistant” and “susceptible” based on haplotypes of the four most significant markers were sent to a controlled S. iniae challenge test. At the end of the test, the differences in mortality between the two groups were strikingly different with a final cumulative percent mortality of less than 1% and 73% for offspring from “resistant” and “susceptible” parents, respectively. These results demonstrate that MAS for improved resistance to S. iniae is feasible. Frontiers Media S.A. 2023-03-02 /pmc/articles/PMC10017449/ /pubmed/36936431 http://dx.doi.org/10.3389/fgene.2023.1078381 Text en Copyright © 2023 Vela-Avitúa, LaFrentz, Lozano, Shoemaker, Ospina-Arango, Beck and Rye. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Vela-Avitúa, Sergio
LaFrentz, Benjamin R.
Lozano, Carlos A.
Shoemaker, Craig A.
Ospina-Arango, Jose Fernando
Beck, Benjamin H.
Rye, Morten
Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance
title Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance
title_full Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance
title_fullStr Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance
title_full_unstemmed Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance
title_short Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance
title_sort genome-wide association study for streptococcus iniae in nile tilapia (oreochromis niloticus) identifies a significant qtl for disease resistance
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10017449/
https://www.ncbi.nlm.nih.gov/pubmed/36936431
http://dx.doi.org/10.3389/fgene.2023.1078381
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