Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

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

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2018
Publication Date: 9/19/2018
Citation: Salem, M., Al-Tobasei, R., Ali, A., Lourenco, D., Gao, G., Palti, Y., Kenney, B., Leeds, T.D. 2018. Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout. Frontiers in Genetics [serial online]. 9:387. doi:10.3389/fgene.2018.00387.
DOI: https://doi.org/10.3389/fgene.2018.00387

Interpretive Summary: Increasing the proportion of a whole fish that is edible fillet, or fillet yield, is a means to improve production efficiency, and thus is of interest to both fish farmers and consumers. However, fillet yield poses a challenge to animal breeders aiming to improve this trait through selective breeding, because it cannot be directly measured in breeding candidates. The continued development of rainbow trout genomics resources now allow breeders and scientists to accurately predict the genetic merit of fish lacking phenotypic data based on analysis of their DNA, and also to identify the genes or chromosomal loci that affect the trait of interest. In this study, a new tool was developed for genomic and genetic assays and used for a genome-wide association analysis with a population of rainbow trout that was characterized for fillet yield and other carcass and body weight traits. The analysis identified chromosome regions harboring genes that affected fillet yield, including some with substantial impact on the trait that were not previously identified in rainbow trout. Most of the genetic variation for this trait still appears to be affected by a large number of loci, each with a small effect. Thus, this study suggests that although genomic selection based on high-density genotypic data will likely increase the accuracy of selection for improving fillet yield, some genes and chromosome loci can be further investigated to better understand their function and role in the physiological pathways that control and affect fillet yield in rainbow trout aquaculture. In addition, the effects of the gene sequence variants identified in this population can be verified in other aquaculture population and that information can be then used for genetic improvement in commercial breeding programs.

Technical Abstract: Detection of coding/functional SNPs that change the biological function of a gene may lead to the identification of putative causative alleles within QTL regions and the development of genetic markers with large-effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic-imbalances associated with important aquaculture production traits including WBW, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from a growth- and 54 families from BCWD resistance-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1,728 fish. The average SNP calling-rate for samples passing QC (1,641 fish) was greater than or equal to 98.5%. Genome-wide association analysis on 878 fish (representing 200 families from two generations) genotyped with 35K polymorphic markers (passing QC) identified several QTL regions explaining up to 25% of the additive genetic variance for muscle yield in this rainbow trout aquaculture breeding population. Most of the genes in the QTL regions were previously reported as important regulators of muscle yield including the citrate synthase, tumor protein p53 inducible nuclear protein 2, and activin receptor type-1B genes. These results demonstrate the utility of transcribed gene SNP-chips for genome-wide association studies seeking to identify QTL affecting important aquaculture production traits in rainbow trout.