Genome wide analysis of infectious salmon anemia resistance in commercial Saint John River Atlantic salmon

Holborn, Melissa K.; Ang, Keng Pee; Powell, Frank C.; Boulding, Elizabeth G.

doi:10.1016/j.aquaculture.2019.734514

Cited by 14 publications

(15 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Higher heritability estimates using genomic relationships have been observed compared to pedigree-based estimates in previous studies investigating disease resistance in aquaculture species [ 42 , 43 ], potentially due to high linkage disequilibrium due to recent selective breeding causing overestimation of additive genetic variance using genomic markers [ 43 ]. Nonetheless, these results are in line with the range of previous heritability estimates for resistance to ISAV in Atlantic salmon (0.13–0.40 [ 23 – 28 ]). The genetic architecture of resistance to ISAV in this population was polygenic, and major QTL were not observed, as is common for disease resistance traits [ 43 – 48 ].…”

Section: Discussionsupporting

confidence: 91%

“…A previous study investigating host resistance to ISAV also detected a SNP marker associated with survival to ISAV on Ssa13, however the most signifiant SNPs in the two putative QTL are almost 50 Mb apart [ 28 ]. Together with two additional previous studies, putative QTL affecting resistance to ISAV have been mapped on 12 different chromosomes [ 28 – 30 ], none of which were significantly associated with resistance in the current study.…”

Section: Discussionmentioning

confidence: 99%

“…Genomic selection exploits both between and within family genetic variation to improve the innate resistance of aquaculture stocks via selective breeding, with cumulative benefits every generation [ 21 ]. Several studies have shown that host resistance to ISAV has a significant additive genetic component in Atlantic salmon, with heritability estimates ranging from 0.13 to 0.40 [ 23 – 28 ]. Furthermore, studies using molecular markers to investigate the genetic architecture underlying this heritability have revealed putative minor QTL [ 28 – 30 ], and a comparative genomic analysis highlighted potential underlying genes [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

“…Several studies have shown that host resistance to ISAV has a significant additive genetic component in Atlantic salmon, with heritability estimates ranging from 0.13 to 0.40 [ 23 – 28 ]. Furthermore, studies using molecular markers to investigate the genetic architecture underlying this heritability have revealed putative minor QTL [ 28 – 30 ], and a comparative genomic analysis highlighted potential underlying genes [ 31 ]. Several studies have also examined the host response to ISAV by profiling gene expression in tissues and cell lines [ 32 – 37 ].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

et al. 2021

View full text Add to dashboard Cite

Background Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing. Results A total of 2833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1353 animals were genotyped using a 55 K SNP array, and the estimate of heritability for the trait of binary survival was 0.13–0.33 (pedigree-genomic). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome Ssa13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4927 and 2437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated in infected fish, while several metabolic pathways were up-regulated. The interferon pathway showed little evidence of up-regulation at 7 days post infection but was mildly activated at 14 days, suggesting a potential crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance highlighted TRIM25 as being up-regulated in resistant fish. Conclusions ISAV resistance shows moderate heritability with a polygenic architecture, but a significant QTL was detected on chromosome 13. A mild up-regulation of the interferon pathway characterises the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.

show abstract

Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

et al. 2021

View full text Add to dashboard Cite

show abstract

“…We also identified a selective sweep on Chr 5 (positions 8,550,000–8,800,000) which contains a SNP previously found to explain 5.83% of phenotype variation in resistance to infectious salmon anemia (ISA) in commercial Saint John River Atlantic salmon (Holborn et al., 2020). The sweep contains the two genes sh3 domain‐containing ring finger 1 ( sh3rf1 ) and kinesin family member 3a ( kif3a ).…”

Section: Resultsmentioning

confidence: 77%

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Kjærner-Semb

Edvardsen

Ayllón

et al. 2020

Evolutionary Applications

View full text Add to dashboard Cite

show abstract

Genome-wide association study toward efficient selection breeding of resistance to Vibrio alginolyticus in Pacific oyster, Crassostrea gigas

et al. 2022

View full text Add to dashboard Cite

Genome wide analysis of infectious salmon anemia resistance in commercial Saint John River Atlantic salmon

Cited by 14 publications

References 54 publications

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Genome-wide association study toward efficient selection breeding of resistance to Vibrio alginolyticus in Pacific oyster, Crassostrea gigas

Contact Info

Product

Resources

About