Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing
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利用 RNA 测序表征大西洋鲑鱼阿米巴鳃病遗传抗性的机制
DOI：
10.1101/699561
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Robledo D
中科院分区：
文献类型：
--
作者：
Robledo D
鳃健康是大西洋鲑鱼养殖的主要问题之一，阿米巴鳃病（Amoebic Gill Disease，AGD）是由阿米巴（Neoparamoeba perurans）感染引起的常见疾病。在缺乏预防措施的情况下，通过选择性育种提高鲑鱼对AGD的遗传抗性可以降低疾病的发生率并减轻鳃损伤。了解导致AGD抗性的机制和潜在的致病基因组特征可以帮助这一努力，同时也为其他控制策略的发展提供关键信息。AGD抗性被认为是中度遗传的，并且已经鉴定了几个推定的QTL。本研究的目的是提高对AGD抗性机制的理解，并确定潜在QTL的推定致病基因组因素。为了实现这一点，RNA提取从鳃和头肾AGD抗性和敏感动物后，挑战与N。结果抗性和易感动物之间的比较主要突出了主要在鳃的局部免疫反应的差异，涉及红细胞基因和免疫功能和细胞粘附相关的基因。差异表达的免疫基因指出了Th2和Th17反应的对比，这与阿米巴连续挑战后观察到的遗传性增加一致。5个QTL区域候选基因表现出差异表达，包括与干扰素反应相关的基因（GVINP1）、参与全身炎症的基因（MAP4K4）和凋亡的正调节因子（TRIM39）。等位基因特异性表达的分析突出了17号染色体上QTL区域的一个基因，E1A刺激基因1（CREG 1）的细胞阻遏物，显示了提示顺式作用调节变体的等位基因差异表达。并强调了进一步功能研究的候选基因，这些基因可以进一步阐明导致抗性的基因组机制，并有助于通过改进的基因组选择来增强鲑鱼的健康。
BackgroundGill health is one of the main concerns for Atlantic salmon aquaculture, and Amoebic Gill Disease (AGD), attributable to infection by the amoebaNeoparamoeba perurans,is a frequent cause of morbidity. In the absence of preventive measures, increasing genetic resistance of salmon to AGD via selective breeding can reduce the incidence of the disease and mitigate gill damage. Understanding the mechanisms leading to AGD resistance and the underlying causative genomic features can aid in this effort, while also providing critical information for the development of other control strategies. AGD resistance is considered to be moderately heritable, and several putative QTL have been identified. The aim of the current study was to improve understanding of the mechanisms underlying AGD resistance, and to identify putative causative genomic factors underlying the QTL. To achieve this, RNA was extracted from the gill and head kidney of AGD resistant and susceptible animals following a challenge withN. perurans, and sequenced.ResultsComparison between resistant and susceptible animals primarily highlighted differences mainly in the local immune response in the gill, involving red blood cell genes and genes related to immune function and cell adhesion. Differentially expressed immune genes pointed to a contrast in Th2 and Th17 responses, which is consistent with the increased heritability observed after successive challenges with the amoeba. Five QTL-region candidate genes showed differential expression, including a gene connected to interferon responses (GVINP1), a gene involved in systemic inflammation (MAP4K4), and a positive regulator of apoptosis (TRIM39). Analyses of allele-specific expression highlighted a gene in the QTL region on chromosome 17, cellular repressor of E1A-stimulated genes 1 (CREG1), showing allelic differential expression suggestive of a cis-acting regulatory variant.ConclusionsIn summary, this study provides new insights into the mechanisms of resistance to AGD in Atlantic salmon, and highlights candidate genes for further functional studies that can further elucidate the genomic mechanisms leading to resistance and contribute to enhancing salmon health via improved genomic selection.
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