INTEGRATED GENOMICS AND METAGENOMICS PREDICTIONS AND MODULATION OF THE GUT MICROBIOTA?MUSCLE AXIS TO IMPROVE FILLET YIELD IN RAINBOW TROUT

The ultimate goal of this project is to improve the muscle/fillet yield and quality traits of rainbow trout fish, thus improvingaquaculture production efficiency, converting fish feed to high-quality fish fillets. This research develops technologies that make animal protein production in the US more efficient, competitive, and environmentally cleaner.Our specific objectives are:1) Utilization of a 50K SNP "functional" chip to genotype fish representing high/low fillet yield genetic lines in addition to profiling their gut microbiome composition using 16S rRNA gene and shotgun metagenomics sequencing. Host genotyping data and microbiome profiles will be utilized in a microbiome GWAS (mGWAS) to identify genetic variants associated with individual taxa and/or the microbiome. Further, we will harness the microbiome high-throughput sequencing data to identify heritable microbial taxa and metagenomics genes/functions associated with the fillet yield/quality traits. Genotype-microbiome and microbiome-phenotype associations will be assessed in genetically selected lines for fillet yield in USDA/NCCCWA and a commercial breeding population from an industry partner. This objective will allow the utility of fecal samples to detect elite breeding candidates.2) Evaluation of improving the prediction accuracy and cost efficiency of fillet yield/quality traits when the joint action of the genomics and microbiota/metagenomics "hologenomics" data are integrated into the prediction model. Each data source's contribution to the fillet yield/qualitytraits will be evaluated by estimating a reduction in the prediction power when one data source is excluded from the prediction model. A five-fold cross-validation strategy will be used to evaluate the prediction performance. The outcome of this objective will allow the availability of prediction methods that use genomic information from the host (i.e., SNP chip) and the microbiome (e.g., microbiota/metagenomics) for the breeders to assess the future performance of fish better.3) Modulating the gut microbial composition to favor beneficial bacterial flora positively influences muscle mass. The gut microbiome composition in a low fillet yield genetic line eggs/larvae will be modulated by performing early-life fecal transplantation from high fillet yield genetic line donors. 16S rRNA gene sequencing will be used to assess the impact of fecal transplantation on modulating the microbiome community to enhance muscle growth and qualitytraits in rainbow trout. This objective will disclose possibilities for manipulating the microbiomein rainbow trout via early-life fecal transplantation.