Performing Department
(N/A)
Non Technical Summary
Muscle/fillet is the most valuable product of fish. Improving fillet yield and quality can enhance the efficiency of aquaculture production and customer satisfaction and have significant economic benefits.Classical breeding has limited success in improving fillet yield and requires several generations. The aquaculture industry is eager to adopt innovative genetic selection methods to increase the efficiency of genetic improvement, i.e., increasing the accuracy of breeding values and reducing generation intervals, consequently increasing genetic gain. Gut microbiota have recently shown a role in maintaining and regulating host physiology, including muscle gain and functions in mammals. However, host genetics' role on the gut microbiota-muscle axis remains to be discovered in Agri-animal species, including fish.A recent study in our laboratory showed that fillet yield genetic lines produced at USDA/ARS/NCCCWA are predictive of the gut microbiome composition in rainbow trout, indicating the presence of heritable fillet yield-associated microbiome components.In the proposed study, we will assess novel approaches to improve fillet yield in trout breeding programs at NCCCWA and one of the world's leading commercial producers of rainbow trout eggs. We will use host genotypes along with high-throughput gut microbiome/metagenomics data in microbiome genome-wide association studies to 1) identify gene variants associated with the microbiomeand detect heritable microbial groups associated with improved fillet yield that could be used as markers to develop improved fish for breeding purposes, 2) assess the feasibility of improving the genetic prediction accuracy and genotyping cost efficiency when the microbiome data and the genomic relationship information are integrated into genomics-metagenomics analyses.Additionally, we plan to assess the effects of modulating the gut microbial composition in favoring beneficial microbial flora to increase fillet yield via early-life fecal transplantation.
Animal Health Component
0%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Goals / Objectives
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.
Project Methods
In the project, we will assess novel approaches to improve fillet yield in trout breeding programs at NCCCWA and a commercial producer, one of the world's leading suppliers of rainbow trout eggs.Methods for each 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.Dr. Al-Tobasei, Middle Tennessee State University. He will help with the bioinformatics work of theSNP/mGWAS analyses.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.Drs. Daniela and Jeferson Lourenco, University of Georgia. will consult the GWAS and Genomicselection statistical analysis providing biostatistics expertise for this objective.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.