Identification of genomic loci associated with growth in rainbow trout

Authors: ALI, ALI - Middle Tennessee State University; AL-TOBASEI, RAFET - Middle Tennessee State University; LOURENCO, DANIELA - University Of Georgia; Leeds, Timothy - Tim; KENNEY, BRETT - West Virginia University; SALEM, MOHAMED - Middle Tennessee State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2020
Publication Date: 3/5/2020
Citation: Ali, A., Al-Tobasei, R., Lourenco, D., Leeds, T.D., Kenney, B., Salem, M. 2020. Identification of genomic loci associated with growth in rainbow trout. Biomed Central (BMC) Genomics. 21(209). https://doi.org/10.1186/s12864-020-6617-x.
DOI: https://doi.org/10.1186/s12864-020-6617-x

Interpretive Summary: Growth performance is an economically-important trait in rainbow trout aquaculture, and the effectiveness of traditional selective breeding to improve growth performance in rainbow trout populations has been clearly demonstrated in commercial and research breeding programs. Sequencing of the rainbow trout genome and development of a genetic map has allowed scientists to begin identifying specific genes that affect growth performance. Scientists recently developed a high-density array (50,000 SNP chip) to genotype for polymorphisms that occur within exons, which are the DNA sequences within a gene that are transcribed into RNA and ultimately translated into proteins. This study used the recently-developed high-density array to genotype fish from a population that was characterized for growth performance to conduct a genome-wide association analysis. Hundreds of polymorphisms were associated with growth performance, giving scientists insights into the genes and biological pathways that are important for growth. Targeting these genes in genomic- and marker-assisted selective breeding approaches is expected to accelerate the rate of genetic improvement for growth performance in rainbow trout populations.

Technical Abstract: BACKGROUND Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost to market-size. However, genes underlying growth have not been fully explored in rainbow trout. RESULTS A 50K, gene-transcribed SNP chip was used to genotype a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs were identified and associated with bodyweight gain. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 46 SNPs were identified in association with bodyweight gain. The highest SNP associated with this trait was identified in a gene coding for thrombospondin-1 (THBS1) (R2 = 0.09). CONCLUSION The majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.