利用 GWAS 在红鳍石斑鱼中鉴定与抗 RGNNV 相关的候选 SNP 和基因。
Identification of candidate SNPs and genes associated with anti-RGNNV using GWAS in the red-spotted grouper, Epinephelus akaara.
机构信息
Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong, Institute of Applied Biological Resources, Guangzhou, 510260, China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong, Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
出版信息
Fish Shellfish Immunol. 2021 May;112:31-37. doi: 10.1016/j.fsi.2021.02.010. Epub 2021 Feb 18.
The red-spotted grouper, Epinephelus akaara, has been cultured widely in China, and in several countries of Southeast Asia, due to its important economic value. However, in recent years the outbreak of disease caused by red-spotted grouper nervous necrosis virus (RGNNV) has caused mass mortality in the stage of the grouper lifecycle from fry to juvenile, resulting in considerable economic loss in commercial aquaculture. However, the molecular mechanism underlying anti-RGNNV infection in red-spotted grouper has never been fully understood. To identify the anti-RGNNV related markers and candidate genes, we performed a genome-wide association study (GWAS) on a natural population of 100 individuals for a full-genome screen of the red-spotted grouper. In this research, 36,311 single, high quality nucleotide polymorphisms (SNPs) were developed. Two significantly associated SNPs and three suggestively associated SNPs were identified at the genome level. From these identified SNPs, five candidate genes were annotated: EPHA7, Osbpl2, GPC5, CDH4 and Pou3f1. These genes are involved in nervous system development, retinal formation, and lipid metabolism regulation. In combination with studies on the characteristics of NNV infection, it was speculated that in the fry stage of the grouper lifecycle, the immune system is not fully developed. Therefore, improved resistance to RGNNV may come through regulating nervous system development or lipid metabolism related pathways. In addition, the genotypes of SNPs associated with disease-resistant traits were analyzed. The markers and genes obtained in this study may facilitate a marker-assisted selection for red-spotted grouper aiming at disease resistance to RGNNV.
赤点石斑鱼（Epinephelus akaara）由于其重要的经济价值，已在中国和东南亚的几个国家广泛养殖。然而，近年来，赤点石斑鱼神经坏死病毒（RGNNV）爆发导致了鱼苗到幼鱼阶段的大量死亡，给商业养殖造成了相当大的经济损失。然而，赤点石斑鱼抗 RGNNV 感染的分子机制尚未完全阐明。为了鉴定抗 RGNNV 的相关标记和候选基因，我们对 100 个自然种群进行了全基因组关联研究（GWAS），对赤点石斑鱼进行了全基因组筛选。在这项研究中，开发了 36311 个单核苷酸、高质量多态性（SNP）。在基因组水平上鉴定出两个显著相关的 SNP 和三个提示相关的 SNP。从这些鉴定出的 SNP 中，注释了五个候选基因：EPHA7、Osbpl2、GPC5、CDH4 和 Pou3f1。这些基因参与神经系统发育、视网膜形成和脂质代谢调节。结合 NNV 感染的特征研究，推测在石斑鱼鱼苗阶段，免疫系统尚未完全发育。因此，通过调节神经系统发育或脂质代谢相关途径，可能会提高对 RGNNV 的抵抗力。此外，还分析了与抗病特性相关的 SNP 基因型。本研究获得的标记和基因可能有助于赤点石斑鱼对 RGNNV 的抗病性进行标记辅助选择。
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