Optimizing genomic tools to investigate signatures of resistance in pacu (Piaractus mesopotamicus) to Aeromonas hydrophila infection

Abstract

The development of genomic tools will be useful to the continuing development of native species production in Brazil, maximizing the genetic gain and, consequently, boosting new selective breeding for these species. The aim objective of this study is to develop genomic tolls directed to identify signatures of resistance in pacu (Piaractus mesopotamicus) to Aeromonas hydrophila based in challenged full-sibling individuals. Differential expression analysis between susceptible and resistant phenotypes will be related with an imbalanced expression analysis toThe development of genomic tools will be useful to the continuing development of native species production in Brazil, maximizing the genetic gain and, consequently, boosting new selective breeding for these species. The aim objective of this study is to develop genomic tolls directed to identify signatures of resistance in pacu (Piaractus mesopotamicus) to Aeromonas hydrophila based in challenged full-sibling individuals. Differential expression analysis between susceptible and resistant phenotypes will be related with an imbalanced expression analysis to identify potentially functional SNPs related to host responses. 45 mapped SNPs with allelic imbalances were included in a medium-density SNP array for use in genomic selection of populations of farmed pacu resistant to Aeromonas hydrophila infection. The majority of the included SNPs are associated to pathways responsible by the immune defenses against Aeromonas hydrophila, and will contribute for a functional enriched genomic selection for control of this infection. A low-density SNP array was constructed and will be optimized by genotype imputation. Genome-wide association studies (GWAS) using imputed SNP will be performed relating the genomic regions found in the allelic imbalance analysis enriching the evaluation of genetic architecture of Aeromonas hydrophila resistance in pacu. The medium-density SNP array will be used to detect signatures of selection by runs of homozygosity, using the challenged individuals. The pathways and genomic regions that will be highlighted by this study are potential candidates for functional studies, and downstream applications in pacu production and will be a model for other species. (AU) identify potentially functional SNPs related to host responses. 45 mapped SNPs with allelic imbalances were included in a medium-density SNP array for use in genomic selection of populations of farmed pacu resistant to Aeromonas hydrophila infection. The majority of the included SNPs are associated to pathways responsible by the immune defenses against Aeromonas hydrophila, and will contribute for a functional enriched genomic selection for control of this infection. A low-density SNP array was constructed and will be optimized by genotype imputation. Genome-wide association studies (GWAS) using imputed SNP will be performed relating the genomic regions found in the allelic imbalance analysis enriching the evaluation of genetic architecture of Aeromonas hydrophila resistance in pacu. The medium-density SNP array will be used to detect signatures of selection by runs of homozygosity, using the challenged individuals. The pathways and genomic regions that will be highlighted by this study are potential candidates for functional studies, and downstream applications in pacu production and will be a model for other species. (AU)