Identifying a genome-wide QTL interval controlling for ammonia-nitrogen tolerance on chrLG1 of Nile tilapia

Abstract

Ammonia‑nitrogen in aquaculture environment is one of the important factors affecting survival of tilapia. Understanding the genetic basis of tilapia controlling for the ammonia‑nitrogen tolerance is significant for selection of tilapia elite lines. In this study, we successfully identified a QTL interval across chrLG1 associated with ammonia‑nitrogen tolerance in the GIFT line of Nile tilapia (Oreochromis niloticus) using ddRAD-Seq based genome-wide association studies (GWAS). Most of the associated SNPs are located between 21,578,770–22,661,799 bp on chrLG1. We validated there exists significant correlations between their genotypes and ammonia‑nitrogen tolerance (p < 0.01) by Sanger sequencing. Four differentially expressed genes (usp10, cgnl1, cog4, gnao1b) in the RNA-seq datasets at 6 h post challenge of ammonia‑nitrogen are found within the QTL interval of the GWAS dataset. It is interesting that the SNP mutation (C/T; position: chrLG1:22632460) in the exon of cog4 located at the peak region of the QTL caused an amino acid change from threonine to proline in the mapping populations. To our knowledge, this is the first GWAS based study focusing on ammonia‑nitrogen tolerance in tilapia. Our finding lays a foundation for molecular marker-assisted selection and functional analysis of ammonia‑nitrogen tolerance in tilapia.