Similar Genetic Architecture with Shared and Unique Quantitative Trait Loci for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations

Frontiers in Genetics

Breno O. Fragomeni¹  Alvaro G. Hernandez²  Guangtu Gao³  Jason P. Evenhuis³  Gregory D. Wiens³  Roger L. Vallejo³  Timothy D. Leeds³  Timothy J. Welch³  Yniv Palti³  Sixin Liu³  James E. Parsons⁴  Kyle E. Martin⁴ 

[1] Animal and Dairy Science Department, University of Georgia, Athens, GA, United States;High-Throughput Sequencing and Genotyping Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, United States;National Center for Cool and Cold Water Aquaculture, United States Department of Agriculture, Agricultural Research Service, Kearneysville, WV, United States;Troutlodge, Inc., Sumner, WA, United States;

关键词: aquaculture;    bacterial cold water disease;    genome-wide association study;    quantitative trait loci;    rainbow trout;   

DOI  :  10.3389/fgene.2017.00156

来源: DOAJ

【 摘 要 】

Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57 K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57 K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered.

【 授权许可】

Unknown