GENOME-WIDE ANALYSES OF GENES AFFECTING GROWTH, MUSCLE ACCRETION AND FILLET QUALITY TRAITS IN RAINBOW TROUT

Abstract

Growth performance is one of the most economic important traits for the aquaculture industry. In addition, fillet quality attributes are among the primary determinants of consumer acceptability. To study the genetic architecture of these traits, phenotypic characterization of whole body weight (WBW), muscle yield, fat content, shear force, moisture, protein content, and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. In total, 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, were identified in fish families exhibiting contrasting phenotypes. Expression of many DE lncRNAs (n = 229) was positively correlated with overlapping, neighboring or distantly located protein-coding genes (n = 1,030), resulting in 3,392 interactions. Three DE antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. A 50K SNP chip has been developed and used across four genome-wide association (GWA) studies to identify quantitative trait loci (QTL) explaining variations in fish growth and fillet quality attributes. In the first study, QTL explaining up to 28.40% of the additive genetic variance for muscle yield were identified; particularly on chromosomes 14 and 16. In the second study, 247 QTL associated with bodyweight gain were identified. Most SNPs affecting muscle yield and bodyweight gain exist in genes that act as major regulators of developmental processes. In the third study, the additive genetic variance for fillet firmness and protein content was investigated where RYR3 harbored most SNPs affecting the two traits. In the fourth study, sixty-one common SNPs on chromosomes 19 and 29 affecting the muscle fat and moisture content were identified. SNP-harboring genes, in the common QTL, were mainly involved in lipid metabolic process and cytoskeleton remodeling. Presence of common QTL associated with multiple phenotypes suggests common mechanisms underlying those phenotypes in fish. The present work identified DE genes and genetic markers explaining variations in growth and fillet quality phenotypes in selectively bred trout populations. Such markers could be used for marker-assisted and genomic selection in breeding programs of rainbow trout.