Data from: Resistance to RHD virus in wild Australian rabbits: comparison of susceptible and resistant individuals using a genomewide approach

Deciphering the genes involved in disease resistance is essential if we are to understand host–pathogen coevolutionary processes. The rabbit haemorrhagic disease virus (RHDV) was imported into Australia in 1995 as a biocontrol agent to manage one of the most successful and devastating invasive species, the European rabbit (Oryctolagus cuniculus). During the first outbreaks of the disease, RHDV caused mortality rates of up to 97%. Recently, however, increased genetic resistance to RHDV has been reported. Here, we have aimed to identify genomic differences between rabbits that survived a natural infection with RHDV and those that died in the field using a genomewide next-generation sequencing (NGS) approach. We detected 72 SNPs corresponding to 133 genes associated with survival of a RHD infection. Most of the identified genes have known functions in virus infections and replication, immune responses or apoptosis, or have previously been found to be regulated during RHD. Some of the genes identified in experimental studies, however, did not seem to play a role under natural selection regimes, highlighting the importance of field studies to complement the genomic background of wildlife diseases. Our study provides a set of candidate markers as a tool for the future scanning of wild rabbits for their resistance to RHDV. This is important both for wild rabbit populations in southern Europe where RHD is regarded as a serious problem decimating the prey of endangered predator species and for assessing the success of currently planned RHDV variant biocontrol releases in Australia.解析参与疾病抗性的基因，是阐明宿主-病原体共进化过程的核心前提。兔出血症病毒（Rabbit Haemorrhagic Disease Virus, RHDV）于1995年作为生物防治制剂被引入澳大利亚，用以管控一种极具破坏力的成功入侵物种——欧洲兔（Oryctolagus cuniculus）。在疫情首次暴发阶段，RHDV的致死率高达97%。然而近期有研究报道，宿主对RHDV的遗传抗性已显著提升。本研究采用全基因组下一代测序（Next-Generation Sequencing, NGS）技术，旨在筛选野外自然感染RHDV后存活个体与死亡个体之间的基因组差异。我们共检测到72个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，关联至133个与RHDV感染存活相关的基因。多数已鉴定的基因已知参与病毒感染与复制、免疫应答或细胞凋亡过程，或此前被证实可在RHDV感染过程中被调控表达。然而部分在实验研究中鉴定出的基因，在自然选择环境下似乎并未发挥关键作用，这凸显了野外研究对补充野生动物疾病基因组背景认知的重要价值。本研究筛选得到一组候选标记，可用于未来野外兔群的RHDV抗性检测。这一研究成果兼具双重重要意义：既可为南欧地区的野生兔种群提供防控支撑——当地兔出血症疫情被视为严重威胁濒危捕食者物种猎物种群的重大问题，同时也能为评估澳大利亚当前计划释放的RHDV变体生物防治制剂的防控成效提供科学依据。