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

Sergio Vela-Avitúa; Benjamin R LaFrentz; Carlos A Lozano; Craig A Shoemaker; Jose Fernando Ospina-Arango; Benjamin H Beck; Morten Rye

doi:10.3389/fgene.2023.1078381

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

Front Genet. 2023 Mar 2:14:1078381. doi: 10.3389/fgene.2023.1078381. eCollection 2023.

Authors

Sergio Vela-Avitúa¹, Benjamin R LaFrentz², Carlos A Lozano¹, Craig A Shoemaker², Jose Fernando Ospina-Arango³, Benjamin H Beck², Morten Rye¹

Affiliations

¹ Benchmark Genetics Norway AS, Bergen, Norway.
² United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aquatic Animal Health Research Unit, Auburn, AL, United States.
³ Spring Genetics, Miami, FL, United States.

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.

Grants and funding

The Nile tilapia families and funding for this research were provided under a Material Transfer Agreement–Cooperative Research and Development Agreement (MTA-CRADA No. 58-6010-6-005) between Spring Genetics and USDA-ARS. This research was also supported by USDA-ARS CRIS Project No. 6010-32000-027-00D, Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture.