Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar 2:14:1078381.
doi: 10.3389/fgene.2023.1078381. eCollection 2023.

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

Sergio Vela-Avitúa  1 , Benjamin R LaFrentz  2 , Carlos A Lozano  1 , Craig A Shoemaker  2 , Jose Fernando Ospina-Arango  3 , Benjamin H Beck  2 , Morten Rye  1
Affiliations

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

Sergio Vela-Avitúa et al. Front Genet. .

Abstract

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.

Keywords: Nile tilapia; Streptococcus iniae; genome-wide association study (GWAS); marker assisted selection (MAS); quantitative trait loci (QTL); survival.

PubMed Disclaimer

Conflict of interest statement

Authors SV-A, CL, and MR were employed by Benchmark Genetics Norway AS. Author JO-A was employed by Spring Genetics. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Manhattan plot for survival to S. iniae in Nile tilapia. On the y axis is the - log10(p-values) and the x axis is the chromosome (linkage group) position on the Oreochromis niloticus genome, U represents SNPs with unknown chromosome location. The dotted red line marks the genome-wide Bonferroni corrected threshold.
FIGURE 2
FIGURE 2
Quantile-quantile plot with the distribution of observed vs. expected -log10(p).
FIGURE 3
FIGURE 3
Cumulative mortality (%) for S. iniae in QTL validation experiment.
FIGURE 4
FIGURE 4
Kaplan-Meier survival curves for “resistant” group and “susceptible” group during the S. iniae QTL validation experiment.
FIGURE 5
FIGURE 5
Survival to S. iniae at the end of test by haplotypes on the four top markers in QTL validation experiment.
See this image and copyright information in PMC

References

    1. Bentsen H. B., Gjerde B., Eknath A. E., de Vera M. S. P., Velasco R. R., Danting J. C., et al. (2017). Genetic improvement of farmed tilapias: Response to five generations of selection for increased body weight at harvest in Oreochromis niloticus and the further impact of the project. Aquaculture 468, 206–217. 10.1016/J.AQUACULTURE.2016.10.018 - DOI
    1. Boison S., Ding J., Leder E., Gjerde B., Bergtun P. H., Norris A., et al. (2019). QTLs associated with resistance to cardiomyopathy syndrome in atlantic salmon. J. Hered. 110, 727–737. 10.1093/JHERED/ESZ042 - DOI - PMC - PubMed
    1. Chang C. C., Chow C. C., Tellier L. C. A. M., Vattikuti S., Purcell S. M., Lee J. J. (2015). Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience 4, 7. 10.1186/s13742-015-0047-8 - DOI - PMC - PubMed
    1. Conte M. A., Gammerdinger W. J., Bartie K. L., Penman D. J., Kocher T. D. (2017). A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 18, 341. 10.1186/s12864-017-3723-5 - DOI - PMC - PubMed
    1. Danecek P., Bonfield J. K., Liddle J., Marshall J., Ohan V., Pollard M. O., et al. (2021). Twelve years of SAMtools and BCFtools. Gigascience 10, giab008–4. 10.1093/GIGASCIENCE/GIAB008 - DOI - PMC - PubMed

LinkOut - more resources