TiLV infected tilapia: phenotypes and genotypes

Disease resistance is one of the main targets of animal breeding programs. In recent years, incorporating genomic information to accelerate genetic progress has become one of the priorities of the industry. We combined a fine-mapping analysis using population scale whole-genome sequence for resistance to Tilapia Lake Virus (TiLV) in a breeding Nile tilapia (<i>Oreochromis niloticus</i>) GIFT population, with gene differential expression and functional annotation analyses. Here, 950 fish from a natural TiLV outbreak were sampled and genotyped for 5.7M SNPs using whole-genome resequencing and imputation. Our results confirmed a major QTL in the proximal end of <i>Oni22</i>, identifying 555 markers significantly associated with binary survival (BS) within a 10 Mb window, and tightly linked with the most significant marker (p-value = 4.90E-11) located at 311 Kb, presenting a substitution effect of 16 %. Highly associated markers with TiLV resistance confer missense mutations in two anti-viral genes harbored in this region; <i>lgals17</i> and <i>vps52</i>. Host transcriptomic response analyses identified genes differentially expressed between resistant and susceptible genotypes according to the major QTL highlighting <i>ha1f</i>. This is the first study combining whole genome sequencing at population scale with genomic approaches to assess the underlying genomic basis for TiLV resistance. Our results confirm and narrow down a major QTL underlying this key trait in a major aquaculture species worldwide. The identified markers and genes have the potential to improve resistance to TiLV in Nile tilapia, significantly improving animal health and welfare.