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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #369715

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: Heritability estimates and genome-wide association analysis of egg quality traits in commercial rainbow trout breeding populations

item Palti, Yniv
item Vallejo, Roger
item Gao, Guangtu
item Long, Roseanna
item Shewbridge, Kristy
item Leeds, Timothy - Tim
item MARTIN, KYLE - Troutlodge, Inc

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2019
Publication Date: 1/10/2020
Citation: Palti, Y., Vallejo, R.L., Gao, G., Long, R., Shewbridge, K., Leeds, T.D., Martin, K. 2020. Heritability estimates and genome-wide association analysis of egg quality traits in commercial rainbow trout breeding populations. Plant and Animal Genome Conference. 28th International Plant and Animal Genome Conference held in San Diego, CA, January 11, 2020. P.No.PO0433

Interpretive Summary:

Technical Abstract: Egg quality traits including survival rate to eyeing stage, fecundity and egg siize are important to rainbow trout breeding companies, but present challenges for genetic analyses becaue they are measured on only sexually-mature fish and the number of phenotyped fish is usually limited. This study used pedigrees and phenotypes (N=7,905 records) from multiple generations in eight cohorts (4 strains × 2 year classes) from Troutlodge, Inc to estimate heritabilities and genetic correlations. In addition, ~100 phenotyped fish from each cohort were genotyped (57K SNP chip) to elucidate genetic architecture using multiple regression single-step genome-wide association analyses. Heritability estimates were 0.27 plus or minus 0.04, 0.49 plus or minus 0.04, and 0.51 plus or minus 0.04 for eyeing rate, fecundity and egg size, respectively. Significant negative genetic correlation (-0.34 plus or minus 0.06) was observed between fecundity and egg size with dam spawning weight having a significant positive genetic correlation with fecundity (0.31 plus or minus 0.08). Weak positive genetic correlations were observed between eyeing rate and either fecundity or egg size (0.19 plus or minus 0.08 for both). The genetic architecture of the traits was polygenic with some moderate-large effects QTL. One large-effect fecundity QTL with effective genetic variance (EGV) of 26% was identified on Omy05 within the double-inversion region that covers most of the chromosome. The strongest-effect eyeing rate QTL was on Omy26 (EGV=14.5%) and on Omy25 (EGV=9.7%) and Omy28 (EGV=8.2%) for egg size. Our results indicate that progress can be accomplished through pedigree-based selective breeding for those egg quality traits. In addition, the approach of combining genotyping and phenotyping data across-populations for genomic selection models may improve accuracy of genetic merit estimates.