A Major QTL for Resistance to Vibrio anguillarum in Rainbow Trout

Karami, Asma M.; Ødegård, Jørgen; Marana, Moonika Haahr; Zuo, Shaozhi; Jaafar, Rzgar M.; Mathiessen, Heidi; Jørgensen, Louise von Gersdorff; Kania, Per W.; Dalsgaard, Inger; Nielsen, Torben; Buchmann, Kurt

doi:10.3389/fgene.2020.607558

Cited by 29 publications

(33 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The early infection (3 dpc) triggered a strong transcriptional up-regulation of many immune genes in different organs including those encoding pro-inflammatory cytokines IL-1β, IL-6 and TNFα and other cytokines involved in the development of adaptive immunity (IL-8, IL-10, IL-22, IL-17C2, INFγ). The clear up-regulation of previously mentioned immune markers is consistent with earlier studies in trout exposed to A. salmonicida 47,52,53 and other bacterial pathogens 12,35 . Along with the inflammation induced we saw a marked up-regulation of SAA, C3 and several other components of the innate immune system (lysozyme and cathelicidins).…”

Section: Discussionsupporting

confidence: 90%

“…Fish showing clinical signs (653) were sampled as susceptible and at 13 dpc all fish surviving the challenge (145) were sampled as resistant. For DNA-typing, a circular tissue piece (Ø 2.75 mm) was taken from the tail fin of each fish using punching scissors (AgnTho's AB, Lidingö, Sweden) and transferred to lysis buffer (Vaxxinova Norge, Bergen, Norway) for subsequent DNA purification and genotyping according to Karami et al 12 .…”

Section: Methodsmentioning

confidence: 99%

“…SNPs included in the study were restricted to 32 205 loci and showed all three possible genotype clusters (PolyHighRes) by Thermo Fisher Array Power Tools software. Statistical www.nature.com/scientificreports/ analysis was performed according to our latest QTL study 12 . Shortly, the genomic relationship matrix (GRM) was computed using the Genome-Wide Complex Trait Analysis (GCTA) software 60 .…”

Section: Genetic Analysismentioning

confidence: 99%

See 2 more Smart Citations

Whole-genome association study searching for QTL for Aeromonas salmonicida resistance in rainbow trout

Marana

Karami

Ødegård

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis, has extensive negative effects on wild and farmed salmonids worldwide. Vaccination induces some protection under certain conditions but disease outbreaks occur even in vaccinated fish. Therefore, alternative disease control approaches are required to ensure the sustainable expansion of rainbow trout aquaculture. Selective breeding can be applied to enhance host resistance to pathogens. The present work used genome-wide association study (GWAS) to identify quantitative trait loci (QTL) associated with A. salmonicida resistance in rainbow trout. A total 798 rainbow trout exposed to A. salmonicida by bath challenge revealed 614 susceptible and 138 resistant fish. Genotyping was conducted using the 57 K single nucleotide polymorphism (SNP) array and the GWAS was performed for survival and time to death phenotypes. We identified a QTL on chromosome 16 and located positional candidate genes in the proximity of the most significant SNPs. In addition, samples from exposed fish were examined for expression of 24 immune-relevant genes indicating a systematic immune response to the infection. The present work demonstrated that resistance to A. salmonicida is moderately heritable with oligogenic architecture. These result will be useful for the future breeding programs for improving the natural resistance of rainbow trout against furunculosis.

show abstract

Section: Discussionsupporting

confidence: 90%

Section: Methodsmentioning

confidence: 99%

Section: Genetic Analysismentioning

confidence: 99%

See 1 more Smart Citation

Whole-genome association study searching for QTL for Aeromonas salmonicida resistance in rainbow trout

Marana

Karami

Ødegård

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Thus, genes encoding IL-8 (cytokine/ chemokine attracting neutrophils and other leukocytes), cathelicidin 1 and 2 (antimicrobial peptides), lysozyme and complement factors are expressed following Vibrio anguillarum exposure of rainbow trout gills. 15 External environmental factors influence the neutrophil response as temperature is a main regulator of fish physiology due to the poikilothermic nature of this animal group. Some studies have shown a temperature-dependent positive correlation between peripheral blood neutrophil concentrations in Atlantic salmon blood between 10 and 18°C.…”

Section: Regulation Of Neutrophil Responsesmentioning

confidence: 99%

Neutrophils and aquatic pathogens

Buchmann

2022

Parasite Immunology

Self Cite

View full text Add to dashboard Cite

Introduction Neutrophilic granulocytes are short‐lived cells continuously circulating in the vascular system of vertebrates. They play a basic and decisive role in the innate immune defence of the hosts against all types of pathogenic microorganisms. Methods Based on a literature study, the functions of neutrophils and cells with similar functions are described. The study places special emphasis on organisms in the aquatic environment and the pathogens occurring in that particular environment. Results The evolutionary origin of this specific cell type is not clear, but its most basic traits (recognition of foreign elements, extracellular trap release, phagocytosis and elimination of ingested material) are found in phagocytes in members of evolutionary ancient invertebrate groups spanning from amoebae, sponges, sea‐anemones, mollusks (snails and mussels), arthropods (crustaceans and insects) to echinoderms (sea stars and sea urchins). Their functions as innate immune sentinels and effector cells in these groups are well described. Neutrophilic granulocytes with elongated and lobed nuclei (possibly allowing cell movements through narrow extracellular spaces and leaving space for phagosomes) occur in vertebrates including fish, amphibians, reptiles, birds and mammals although the morphology of the nucleus, stainability of cytoplasmic granula, and the antimicrobial armament vary among groups. Following the pathogen invasion of a fish host, the neutrophils migrates from the vascular system into the infection focus. They apply their PRRs (including TLRs) to recognize the invader as non‐self, produce netosis by casting extracellular chromatin containing traps in the microenvironment. These nets assist the immobilization of invading microbes and prevents their further spread. The cells attach to and engulf the microbes by phagocytosis, whereafter they eliminate the pathogen in phagolysosomes equipped with a range of killing mechanisms and attract, by release of chemokines, additional immune cells (monocytes, macrophages and lymphocytes) to the site of invasion. Their role in innate immunity of fish hosts towards aquatic pathogens has been elucidated by in vivo and in vitro studies. Neutrophils interact with virus (e.g. IPNV and VHSV), bacteria (e.g. Aeromonas, Vibrio, Edwardsiella, Mycobacterium and Renibacterium) and parasites, including monogeneans (Gyrodactylus), cestodes (Diphyllobothrium), trematodes (Diplostomum) and ciliates (Ichthyophthirius and Philasterides). Despite the decisive function of neutrophils in innate immunity and early protection, the excessive production of ROS, RNS and NETs may lead to pathological disturbances in the host, which are exacerbated if the pathogens evolve immune evasion mechanisms. Conclusion Neutrophils in aquatic organisms play a central role in innate immunity but may serve as a toll and a support in acquired protection. The strong impact of the cellular reactions not only on pathogen but also on host tissues emphasizes that an optimal immune reaction is balanced, involv...

show abstract

“…A first commercial medium-density Axiom® Trout Genotyping array (hereafter termed 57K chip) has then been developed (Palti et al, 2015) and produced by Affymetrix (Thermofisher). Since then it has been largely used in population genetics studies (Larson et al, 2018; D’Ambrosio et al, 2019; Paul et al, 2021), GWAS and GS accuracy works for various traits in farmed populations (Gonzalez-Pena et al, 2016; Vallejo et al, 2017, 2019; Reis Neto et al, 2019; Rodríguez et al, 2019; Yoshida et al, 2019; Fraslin et al, 2019, 2020; Karami et al, 2020; D’Ambrosio et al, 2020; Blay et al, 2021a, 2021b). However, out of the 57,501 SNPs included in this chip, nearly 20,000 were found to be unusable because they were either duplicated due to the ancestral genome duplication or showing primer polymorphism in 5 French commercial or experimental lines (D’Ambrosio et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Bernard

Dehaullon

Gao

et al. 2022

Preprint

View full text Add to dashboard Cite

Single nucleotide polymorphism (SNP) arrays, also named "SNP chips", enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.

show abstract

A Major QTL for Resistance to Vibrio anguillarum in Rainbow Trout

Cited by 29 publications

References 78 publications

Whole-genome association study searching for QTL for Aeromonas salmonicida resistance in rainbow trout

Whole-genome association study searching for QTL for Aeromonas salmonicida resistance in rainbow trout

Neutrophils and aquatic pathogens

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

Contact Info

Product

Resources

About