Quantitative trait loci for precocious parr maturation, early smoltification, and adult maturation in double-backcrossed trans-Atlantic salmon (Salmo salar)

Abstract Cardiomyopathy syndrome (CMS) caused by piscine myocarditis virus is a major disease affecting the Norwegian Atlantic salmon industry. Three different populations of Atlantic salmon from the Mowi breeding program were used in this study. The first 2 populations (population 1 and 2) were naturally infected in a field outbreak, while the third population (population 3) went through a controlled challenged test. The aim of the study was to estimate the heritability, the genetic correlation between populations and perform genome-wide association analysis for resistance to this disease. Survival data from population 1 and 2 and heart atrium histology score data from population 3 was analyzed. A total of 571, 4312, and 901 fish from population 1, 2, and 3, respectively were genotyped with a noncommercial 55,735 Affymetrix marker panel. Genomic heritability ranged from 0.12 to 0.46 and the highest estimate was obtained from the challenge test dataset. The genetic correlation between populations was moderate (0.51–0.61). Two chromosomal regions (SSA27 and SSA12) contained single nucleotide polymorphisms associated with resistance to CMS. The highest association signal (P = 6.9751 × 10−27) was found on chromosome 27. Four genes with functional roles affecting viral resistance (magi1, pi4kb, bnip2, and ha1f) were found to map closely to the identified quantitative trait loci (QTLs). In conclusion, genetic variation for resistance to CMS was observed in all 3 populations. Two important quantitative trait loci were detected which together explain half of the total genetic variance, suggesting strong potential application for marker-assisted selection and genomic predictions to improve CMS resistance.

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A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon

Genetics ◽

10.1534/genetics.103.013227 ◽

2004 ◽

Vol 167 (2) ◽

pp. 851-858 ◽

Cited By ~ 33

Author(s):

Thomas Moen ◽

Kjersti T. Fjalestad ◽

Hege Munck ◽

Luis Gomez-Raya

Keyword(s):

Disease Resistance ◽

Quantitative Trait Loci ◽

Atlantic Salmon ◽

Quantitative Trait ◽

Testing Strategy ◽

Multistage Testing ◽

Trait Loci

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Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon

Frontiers in Genetics ◽

10.3389/fgene.2019.00056 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 20

Author(s):

Diego Robledo ◽

Alejandro P. Gutiérrez ◽

Agustín Barría ◽

Jean P. Lhorente ◽

Ross D. Houston ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Atlantic Salmon ◽

Quantitative Trait ◽

Functional Annotation ◽

Sea Lice ◽

Trait Loci

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Mapping of quantitative trait loci associated with size, shape, and parr mark traits using first- and second-generation backcrosses between European and North American Atlantic salmon (Salmo salar)

Genome ◽

10.1139/gen-2017-0026 ◽

2018 ◽

Vol 61 (1) ◽

pp. 33-42 ◽

Cited By ~ 3

Author(s):

Stephanie Pedersen ◽

Lei Liu ◽

Brian Glebe ◽

Steven Leadbeater ◽

Sigbjørn Lien ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Atlantic Salmon ◽

North American ◽

Quantitative Trait ◽

Restoration Ecology ◽

Second Generation ◽

Physical Map ◽

Skin Pigmentation ◽

Phenotypic Variance ◽

Trait Loci

Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations. GridQTL analyses using low-density female-specific linkage maps detected QTL showing experiment-wide significance on Ssa02, Ssa03, Ssa09, Ssa11, Ssa19, and Ssa26/28 for both length and weight; on Ssa04 and Ssa23 for parr mark number; on Ssa09 and Ssa13 for parr mark contrast; and on Ssa05, Ssa07, Ssa10, Ssa11, Ssa18, Ssa23, and Ssa26/28 for geometric morphometric shape coordinates. Pleiotrophic QTL on Ssa11 affected length, weight, and shape. No QTL was found that explained more than 10% of the phenotypic variance in pigmentation or shape traits. Each QTL was approximately positioned on the physical map of the Atlantic salmon genome. Some QTL locations confirmed previous studies but many were new. Studies like ours may increase the success of salmon restoration projects by enabling better phenotypic and genetic matching between introduced and extirpated strains.

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