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
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通过全基因组关联和 RNA 测序探索大西洋鲑鱼对传染性鲑鱼贫血病毒的遗传抗性
DOI：
10.1101/2020.09.08.287052
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Gervais O
中科院分区：
文献类型：
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作者：
Gervais O
传染性鲑贫血病毒（ISAV）是一种严重威胁大西洋鲑（萨尔莫salar）养殖业的重要传染病。目前还没有完全有效的治疗方法或疫苗，因此选择性育种以增加对ISAV的抗性是预防疾病的一个有希望的途径。基因组选择和潜在的基因组编辑可用于增强宿主抗性，这些方法受益于对目标性状的遗传和功能基础的更好了解。本研究的目的是在一个商业大西洋鲑鱼种群的抗ISAV的遗传结构，并研究其潜在的功能基因组基础，使用RNA Sequencing.ResultsA共2833大西洋鲑鱼parr属于194个家庭暴露于ISAV在同居的挑战，累计死亡率达到63%，超过55天。使用55 K SNP阵列对总共1353头动物进行基因分型，二元存活性状的遗传力估计值为0.13-0.33（家系-基因组）。全基因组关联分析证实，抗ISAV是一个多基因性状，虽然染色体Ssa 13中的基因组区域与抗性显着相关，并解释了3%的遗传变异。对16条感染鱼（感染后7天和14天）和8条对照鱼的心脏进行RNA测序，分别在感染后7天和14天突出显示了4927个和2437个差异表达基因。补体和凝血途径在感染鱼中下调，而几种代谢途径上调。干扰素途径在感染后7天几乎没有上调的证据，但在14天被轻度激活，表明宿主和病毒之间存在潜在的串扰。高和低育种值的电阻突出TRIM 25的鱼的转录组反应的比较被上调在resistant fish.ConclusionsISAV电阻显示中等遗传力与多基因结构，但一个显着的QTL检测到13号染色体上。干扰素途径的轻度上调表征了来自该大西洋鲑鱼种群的心脏样品中对病毒的应答，并且鉴定了在具有高和低抗性育种值的样品之间显示差异表达的候选基因。
BackgroundInfectious 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.ResultsA 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.ConclusionsISAV 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.