Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population

Autor: John R. MacMillan, Hao Cheng, Breno O. Fragomeni, Richard Towner, Guangtu Gao, Roger L. Vallejo, Yniv Palti, Kristy L. Shewbridge
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Infectious hematopoietic necrosis virus
Technology
Multifactorial Inheritance
lcsh:QH426-470
Breeding program
Dairy & Animal Science
[SDV]Life Sciences [q-bio]
Population
Quantitative Trait Loci
Fisheries
Biology
Quantitative trait locus
Crosses
Breeding
Selective breeding
Fish Diseases
Genetic
Rhabdoviridae Infections
Genetic variation
Genetics
Animals
14. Life underwater
education
Ecology
Evolution
Behavior and Systematics
Crosses
Genetic
lcsh:SF1-1100
Disease Resistance
education.field_of_study
Human Genome
0402 animal and dairy science
Bayes Theorem
04 agricultural and veterinary sciences
General Medicine
Biological Sciences
biology.organism_classification
040201 dairy & animal science
Genetic architecture
lcsh:Genetics
Oncorhynchus mykiss
Animal Science and Zoology
Rainbow trout
lcsh:Animal culture
Research Article
Genome-Wide Association Study
Zdroj: Genetics, Selection, Evolution : GSE
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2019, 51 (1), pp.47. ⟨10.1186/s12711-019-0489-z⟩
Genetics, selection, evolution : GSE, vol 51, iss 1
Genetics Selection Evolution, Vol 51, Iss 1, Pp 1-14 (2019)
ISSN: 1297-9686
0999-193X
DOI: 10.1186/s12711-019-0489-z⟩
Popis: International audience; AbstractBackgroundInfectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been applying selective breeding to improve genetic resistance to IHNV in their rainbow trout breeding program. The goals of this study were to elucidate the genetic architecture of IHNV resistance in this commercial population by performing genome-wide association studies (GWAS) with multiple regression single-step methods and to assess if genomic selection can improve the accuracy of genetic merit predictions over conventional pedigree-based best linear unbiased prediction (PBLUP) using cross-validation analysis.ResultsTen moderate-effect quantitative trait loci (QTL) associated with resistance to IHNV that jointly explained up to 42% of the additive genetic variance were detected in our GWAS. Only three of the 10 QTL were detected by both single-step Bayesian multiple regression (ssBMR) and weighted single-step GBLUP (wssGBLUP) methods. The accuracy of breeding value predictions with wssGBLUP (0.33–0.39) was substantially better than with PBLUP (0.13–0.24).ConclusionsOur comprehensive genome-wide scan for QTL revealed that genetic resistance to IHNV is controlled by the oligogenic inheritance of up to 10 moderate-effect QTL and many small-effect loci in this commercial rainbow trout breeding population. Taken together, our results suggest that whole genome-enabled selection models will be more effective than the conventional pedigree-based method for breeding value estimation or the marker-assisted selection approach for improving the genetic resistance of rainbow trout to IHNV in this population.
Databáze: OpenAIRE
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