Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss)

Author(s)

Reis Neto, Rafael Vilhena ^{[1, 2]} ; Yoshida, Grazyella Massako ^{[1, 3]} ; Paul Lhorente, Jean ^[4] ; Manuel Yanez, Jose ^{[5, 1, 4]}

Affiliation

^[1] Univ Chile, Fac Ciencias Vet & Pecuarias, Santa Rosa 11735, Santiago - Chile

^[2] Univ Estadual Paulista, Dept Engn Pesca, Campus Expt Registro, Av Nelso Briho Badur 430, BR-11900000 Registro, SP - Brazil

^[3] Sao Paulo State Univ Unesp, Sch Agr & Veterinarian Sci, Via Acesso Prof Paulo Donato Castellane, BR-14884900 Jaboticabal - Brazil

^[4] Benchmark Genet Chile SA, Puerto Montt - Chile

^[5] Nucleo Milenio INVASAL, Concepcion - Chile

• Document type: Journal article
• Source: Molecular Genetics and Genomics; v. 294, n. 3, p. 563-571, JUN 2019.
• Web of Science Citations: 7

Abstract

Growth is one of the most important traits from both aphysiological and economic perspective in aquaculture species. Thus, identifying the genomic regions and genes underpinning genetic variation for this trait is of particular interest in several fish species, including rainbow trout. In this work, we perform a genome-wide association study (GWAS) to identify the genomic regions associated withbody weight at tagging (BWT) and at 18 months (BW18M) using a dense SNP panel (57k) and 4596 genotyped rainbow trout from 105 full-sib families belonging to a Chilean breeding population. Analysis was performed by means of single-step GBLUP approach. Genetic variance explained by 20 adjacent SNP windows across the whole genome is reported. To further explore candidate genes, we focused on windows that explained the highest proportion of genetic variance in the top 10 chromosomes for each trait. The main window from the top 10 chromosomes was explored by BLAST using the first and last SNP position of each window to determine the targetnucleotide sequence. As expected,thepercentage of genetic variance explained by windows was relatively low, due to the polygenic nature of body weight. The most important genomic region for BWT and BW18M were located on chromosomes 15 and 24 and they explained 2.14% and 3.02% of the genetic variance for each trait, respectively. Candidate genes including several growth factors, genes involved in development of skeletal muscle and bone tissue and nutrient metabolism were identified within the associated regions for both traits BWT and BW18M. These results indicate that body weight is polygenic in nature in rainbow trout, with the most important loci explaining as muchas 3% of the genetic variance for the trait. The genes identified here represent good candidates for further functional validation to uncover biological mechanisms underlying variation for growth in rainbow trout. (AU)

• FAPESP's process: 17/00123-6 - Genome Wide Association Study (GWAS) for carcass traits of tilapia Oreochromis sp
• Grantee: Rafael Vilhena Reis Neto
• Support Opportunities: Scholarships abroad - Research