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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2023
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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. |
format | Online Article Text |
id | pubmed-10017449 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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