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

Authors: VELA-AVITÚA, SERGIO - Benchmark Genetics; Lafrentz, Benjamin; LOZANO, CARLOS - Benchmark Genetics; Shoemaker, Craig; OSPINA-ARANGO, JOSE FERNANDO - Spring Genetics; Beck, Benjamin; RYE, MORTEN - Benchmark Genetics

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2023
Publication Date: 3/2/2023
Citation: Vela-Avitúa, S., Lafrentz, B.R., Lozano, C.A., Shoemaker, C.A., Ospina-Arango, J., Beck, B.H., Rye, M. 2023. Genome-wide association study for Streptococcus iniae in Nile Tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance. Frontiers in Genetics. 14:1078381. https://doi.org/10.3389/fgene.2023.1078381.
DOI: https://doi.org/10.3389/fgene.2023.1078381

Interpretive Summary: Streptococcus iniae is a causative agent of streptococcal disease in farm raised tilapia and contributes to large economic losses. Our collaborative research team demonstrated substantial genetic variation for resistance to S. iniae and confirmed the ability to improve resistance through selective breeding. The goal of the present research was to investigate whether there were any genetic markers (i.e., unique DNA sequences) that are associated with Nile tilapia that are resistant to disease. DNA was extracted from tissue samples of tilapia that were infected with S. iniae and genotyped. Analysis of the genotypes of resistant and susceptible fish identified a genetic marker that was associated with resistance to the pathogen. The identification of this marker was a significant finding and suggested that it may be possible to breed tilapia for resistance to S. iniae based on the presence of that marker (MAS; marker assisted selection). The effectiveness of the genetic marker was confirmed experimentally wherein offspring of tilapia positive for the marker and negative for the marker were produced. These fish were then infected with S. iniae and the results demonstrated offspring of fish positive for the marker exhibited 100 % survival compared to only 27 % survival for fish negative for the marker. This was a significant milestone and implies that candidate families no longer need to be routinely infected with S. iniae to assess their level of resistance to this pathogen. Rather, their DNA can be analyzed and if they carry the favorable genetic marker, they will produce the more disease resistant offspring. This is the first time that a genetic marker has been associated with resistance to a bacterial pathogen in Nile tilapia and will greatly contribute to breeding of fish with resistance to S. iniae and reduce losses associated with this pathogen in global tilapia aquaculture.

Technical 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, 9085 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.