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.
复制标题
DOI：
10.1186/s12864-021-07671-6
复制
发表时间：
2021-05-13
期刊：
影响因子：
4.4
通讯作者：
Houston RD
中科院分区：
文献类型：
--
作者：
Gervais O;Barria A;Papadopoulou A;Gratacap RL;Hillestad B;Tinch AE;Martin SAM;Robledo D;Houston RD
传染性鲑鱼贫血病毒 (ISAV) 会引起一种法定疾病，对全球大西洋鲑鱼 (Salmo salar) 水产养殖构成巨大威胁。目前还没有完全有效的治疗方法或疫苗，因此通过选择性育种来增强对 ISAV 的抵抗力是一种有前景的疾病预防途径。基因组选择和潜在的基因组编辑可用于增强宿主抵抗力，这些方法受益于对目标性状遗传和功能基础的了解的提高。本研究的目的是表征商业大西洋鲑鱼种群中 ISAV 抗性的遗传结构，并使用 RNA 测序研究其潜在的功能基因组基础。属于 194 个家庭的总共 2833 条大西洋鲑鱼在同居挑战中暴露于 ISAV，55 天内累计死亡率达到 63%。使用 55 K SNP 阵列对总共 1353 只动物进行了基因分型，二元生存性状的遗传力估计为 0.13–0.33（谱系基因组）。全基因组关联分析证实，对 ISAV 的抗性是一种多基因性状，尽管染色体 Ssa13 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 4927 个和 2437 个差异表达基因。受感染的鱼的补体和凝血途径下调，而一些代谢途径上调。干扰素通路在感染后 7 天几乎没有上调的证据，但在 14 天时被轻度激活，表明宿主和病毒之间存在潜在的串扰。对具有高抗性育种值和低抗性育种值的鱼类的转录组反应进行比较，突出显示 TRIM25 在抗性鱼类中表达上调。 ISAV 抗性显示出具有多基因结构的中等遗传力，但在 13 号染色体上检测到显着的 QTL。干扰素途径的轻度上调表征了来自大西洋鲑鱼种群的心脏样本中对病毒的反应，并鉴定了在抗性育种值高和低的样本之间表现出差异表达的候选基因。在线版本包含可在 10.1186/s12864-021-07671-6 获取的补充材料。
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. 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. 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. The online version contains supplementary material available at 10.1186/s12864-021-07671-6.
登录
查看更多内容
DOI：
10.1534/g3.118.200053
发表时间：
2018-03-28
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Barría A;Christensen KA;Yoshida GM;Correa K;Jedlicki A;Lhorente JP;Davidson WS;Yáñez JM
通讯作者：
Yáñez JM
影响因子：
5.2
作者：
Agrawal P;Nawadkar R;Ojha H;Kumar J;Sahu A
通讯作者：
Sahu A
影响因子：
3.5
作者：
Aguilar, I.;Misztal, I.;Lawlor, T. J.
通讯作者：
Lawlor, T. J.
影响因子：
3.3
作者：
Gjoen, HM;Bentsen, HB
通讯作者：
Bentsen, HB
影响因子：
4.5
作者：
Gjerde, Bjarne;Evensen, Oystein;Storset, Arne
通讯作者：
Storset, Arne