Identification of Single-Nucleotide Polymorphisms in Differentially Expressed Genes Favoring Soybean Meal Tolerance in Higher-Growth Zebrafish (Danio rerio)

IF 2.6 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Marine Biotechnology Pub Date : 2024-07-03 DOI:10.1007/s10126-024-10343-7
Pilar E. Ulloa, Felipe Jilberto, Natalia Lam, Gonzalo Rincón, Luis Valenzuela, Valentina Cordova-Alarcón, Adrián J. Hernández, Patricio Dantagnan, Maria Cristina Ravanal, Sebastian Elgueta, Cristian Araneda
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Abstract

Genetic variability within the same fish species could confer soybean meal (SBM) tolerance in some individuals, thus favoring growth. This study investigates the single-nucleotide polymorphisms (SNPs) in differentially expressed genes (DEGs) favoring SBM tolerance in higher-growth zebrafish (Danio rerio). In a previous work, nineteen families of zebrafish were fed a fish meal diet (100FM control diet) or SBM-based diets supplemented with saponin (50SBM + 2SPN–experimental diet), from juvenile to adult stages. Individuals were selected from families with a genotype-by-environment interaction higher (170 ± 18 mg) or lower (76 ± 10 mg) weight gain on 50SBM + 2SPN in relation to 100FM. Intestinal transcriptomic analysis using RNA-seq revealed six hundred and sixty-five differentially expressed genes in higher-growth fish fed 50SBM + 2SPN diet. In this work, using these results, 47 SNPs in DEGs were selected. These SNPs were genotyped by Sequenom in 340 zebrafish that were fed with a 50SBM + 2SPN diet or with 100FM diet. Marker-trait analysis revealed 4 SNPs associated with growth in 3 immunity-related genes (aif1l, arid3c, and cst14b.2) in response to the 50SBM + 2SPN diet (p-value < 0.05). Two SNPs belonging to aif1l y arid3c produce a positive (+19 mg) and negative (−26 mg) effect on fish growth, respectively. These SNPs can be used as markers to improve the early selection of tolerant fish to SBM diet or other plant-based diets. These genes can be used as biomarkers to identify SNPs in commercial fish, thus contributing to the aquaculture sustainability.

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鉴定有利于高生长斑马鱼(Danio rerio)耐受豆粕的差异表达基因的单核苷酸多态性。
同一鱼类物种中的遗传变异可能会赋予某些个体对豆粕(SBM)的耐受性,从而有利于生长。本研究调查了有利于高生长斑马鱼(Danio rerio)耐受豆粕的差异表达基因(DEGs)中的单核苷酸多态性(SNPs)。在之前的一项研究中,19 个斑马鱼家族从幼鱼到成鱼阶段都喂食鱼粉饲料(100FM 对照饲料)或添加皂素的 SBM 饲料(50SBM + 2SPN 实验饲料)。从基因型与环境交互作用的家系中选取个体,与 100FM 相比,它们在 50SBM + 2SPN 日粮中的体重增加较高(170 ± 18 mg)或较低(76 ± 10 mg)。使用 RNA-seq 进行的肠道转录组分析显示,在喂食 50SBM + 2SPN 的高生长鱼类中,有六百六十五个不同表达的基因。在这项工作中,利用这些结果选出了 DEGs 中的 47 个 SNPs。Sequenom 对喂食 50SBM + 2SPN 或 100FM 食物的 340 条斑马鱼中的这些 SNP 进行了基因分型。标记性状分析表明,4 个 SNPs 与 3 个免疫相关基因(aif1l、arid3c 和 cst14b.2)的生长有关,这些基因对 50SBM + 2SPN 日粮的反应(p 值为 0.05)。
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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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