Gene expression analysis between rainbow trout strains with different susceptibility to enteritis when reared on plant-based diets

Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, and as growth was a major factor in the selection program, both muscle and liver gene expression were examined for differential regulation between commercial and selected trout strains when fed alternative diets. After three months of rearing on either a fishmeal (FM) or plant protein-based (PM) diet, muscle and liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then aligned to the rainbow trout transcriptome. Read-counts were used to assess differential expression between strains and treatments. Significant differentially expressed genes between comparisons were assessed. Overall design: Rainbow trout strain selected for tolerance to plant-based diets (ARS-KO) and control fish strain (House Creek) were fed either a fish meal (FM) or plant meal (PM) based diet in replicate tanks over a 12-week period. After this time, muscle and liver tissues were sampled. A total of 80 samples were taken: ten biological replicates, sampling two tissues, with two treatment groups, for each of the two trout strains.

虹鳟（Oncorhynchus mykiss）及其他鲑科鱼类均为肉食性鱼类。在水产养殖领域，鱼源性饲料原料因需求持续攀升与供应日渐缩减，正快速丧失可持续性。使用植物蛋白完全替代鱼粉会引发严重的肠道肠炎，导致生长受阻与饲料利用效率降低。通过选择性育种，我们成功培育出一种虹鳟品系：该品系在饲喂高大豆植物蛋白日粮时不会出现远端肠道肠炎，且相较于其他品系生长速度显著提升。由于中枢代谢在日粮调整过程中发挥核心调控作用，且生长速度是本次育种筛选的关键指标，因此我们针对饲喂替代日粮的商品养殖虹鳟与选育虹鳟品系，检测了肌肉与肝脏组织的基因表达差异调控情况。在分别饲喂鱼粉（fishmeal, FM）日粮与植物蛋白日粮（plant protein, PM）饲养3个月后，我们采集了未选育的国内品系（House Creek，可发生肠炎）与选育品系（ARS-KO，无肠炎症状）的肌肉与肝脏组织，提取组织样品并制备用于Illumina RNA测序（Illumina RNA-seq）的样本。对原始测序读段进行质量筛查后，将其比对至虹鳟转录组；利用读段计数评估不同品系与处理组间的基因表达差异，并对各组比较中的显著差异表达基因进行分析。实验设计概况：针对植物基日粮耐受性选育的虹鳟品系（ARS-KO）与对照品系（House Creek），分别饲喂鱼粉（FM）或植物粕（PM）日粮，设置重复养殖池，饲养周期为12周。饲养结束后采集肌肉与肝脏组织。共计采集80份样品：两个虹鳟品系各设10个生物学重复，每个重复采集两种组织，并对应两个处理组。