BSA-seq and transcriptome analysis identification candidate genes associated with Pseudomonas plecoglossicida resistance in the large yellow croaker (Larimichthys crocea)

IF 4.1 2区农林科学 Q1 FISHERIES

Fish & shellfish immunology Pub Date : 2025-06-28 DOI:10.1016/j.fsi.2025.110533

Ting Ye , Feng Liu , Xiao Liang , Dandan Guo , Wei Zhan , Guoer Shao , Bao Lou

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引用次数: 0

Abstract

Visceral white-nodule disease (VWND), caused by Pseudomonas plecoglossicida, poses a significant threat to the development of the Larimichthys crocea aquaculture industry. Breeding disease-resistant strains offers a potential solution, but the underlying mechanisms of disease resistance in L. crocea remain unclear, and relevant functional markers are still lack. In the present study, 243 full-sibling F₁ populations of L. crocea were infected with P. plecoglossicida. Whole-genome resequencing, bulk segregant analysis (BSA) mapping, and spleen transcriptome analysis were performed on two extreme phenotype pools, which defined by survival time (AT) and spleen bacterial load (BL) as disease-resistance indicators. Candidate genes were validated through infection experiments. A total of 5,576,771 SNPs were identified, and Δ(SNP-index), Euclidean distances (ED), and G-statistics were applied to locate two stable disease resistance-related QTLs on Chr 02 (2.6 Mb) and Chr 24 (4.9 Mb) with 99 % confidence, containing 278 candidate genes. Transcriptomic analysis revealed 4811 genes involved in the immune response, with 949 genes linked to P. plecoglossicida resistance variation in L. crocea. Integrated analysis identified 17 core immune gene, and subsequent validation confirmed that 6 genes (Phf11, CYBB, PTK2B, STAT1, Adamts1, and NRP2) play a consistent role in L. crocea resistance. Our findings highlight the utility of BSA-seq for genetic analysis of disease resistance and provide insights for molecular-assisted breeding in L. crocea.

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BSA-seq和转录组分析鉴定大黄鱼耐假单胞菌相关基因

由绒舌假单胞菌引起的内脏白结节病（VWND）严重威胁着鳜鱼养殖业的发展。培育抗病菌株提供了一种潜在的解决方案，但crocea抗病的潜在机制尚不清楚，相关的功能标记仍然缺乏。在本研究中，243个crocea全兄弟F1群体感染了pleclossicida。以生存时间（AT）和脾脏细菌负荷（BL）作为抗病指标，对两个极端表型池进行全基因组重测序、大体积分离分析（BSA）作图和脾脏转录组分析。候选基因通过感染实验进行验证。共鉴定出5,576,771个snp，并应用Δ（SNP-index）、Euclidean距离（ED）和G-statistics在Chr 02 （2.6 Mb）和Chr 24 （4.9 Mb）上定位了两个稳定的抗病相关qtl，置信度为99%，包含278个候选基因。转录组学分析显示，4811个基因参与了免疫应答，其中949个基因与水蛭抗性变异有关。综合分析鉴定出17个核心免疫基因，随后的验证证实了6个基因（Phf11、CYBB、PTK2B、STAT1、Adamts1和NRP2）在L. crocea抗性中发挥一致的作用。我们的研究结果强调了BSA-seq在遗传抗病分析中的应用，并为L. crocea的分子辅助育种提供了见解。

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来源期刊

Fish & shellfish immunology 农林科学-海洋与淡水生物学

CiteScore

7.50

自引率

19.10%

发文量

750

审稿时长

68 days

期刊介绍： Fish and Shellfish Immunology rapidly publishes high-quality, peer-refereed contributions in the expanding fields of fish and shellfish immunology. It presents studies on the basic mechanisms of both the specific and non-specific defense systems, the cells, tissues, and humoral factors involved, their dependence on environmental and intrinsic factors, response to pathogens, response to vaccination, and applied studies on the development of specific vaccines for use in the aquaculture industry.