Why some rainbow trout genotypes grow better with a complete plant-based diet? A transcriptomic and physiological analyses on three isogenic lines

We have investigated the mechanisms behind the response to a plant based diet over a long term period by comparing the transcriptome of 3 isogenic lines (R23h, AB1h, A22h) of rainbow trout. These families represent an interesting genetic materiel to work on as they have similar responses when fed marine based-diet (M diet) but highly different responses when fed a plant-based diet (V diet). Fish were fed since 1st feeding with either a plant-based diet, or a marine diet (ad libitum (M diet) or restricted (MR)). We showed that differences in the ability to grow with the V diet observed amongst genotypes was not due to higher feed intake, but to higher feed efficiencies. The comparison of transcriptome profiles revealed 575, 1770 and 2973 probes differentially expressed amongst the three genotypes when fed the V diet. Interestingly, genotypes which were the less affected by the V diet had exhibited the highest growth. These results demonstrated that those fish were able to maintain energy production and protein synthesis. Moreover, those genotypes were also able to activate pathways linked to lipid and cholesterol metabolism, such as the biosynthesis of omega 3 LC-PUFA. Finally, as it has already been demonstrated, immunity seems also to play an important role in the ability of fish to use the V diet, and further investigations are needed to understand by which ways immunity interacts with growth. Transcriptomic response were studied in the liver of 3 isogenic lines (R23h, AB1h, A22h). Fish were fed since the 1st feeding with either a plant-based diet completly devoid of fish oil and fish meal (V diet) or a marine resources based diet (ad libitum: M diet or restricted: MR diet). Sampling took place after 6 months of feeding (n=6/condition).

本研究通过比较3株虹鳟同基因系（isogenic lines）R23h、AB1h、A22h的转录组（transcriptome），解析了长期植物基日粮响应背后的分子机制。该批家系为极具研究价值的遗传材料：在饲喂海洋源日粮（marine diet）时，各基因型的生理响应高度一致；但在饲喂植物源日粮（plant-based diet）时，其响应差异显著。实验鱼自开口摄食起，分别饲喂植物源日粮或海洋源日粮，其中海洋源日粮分为自由采食（ad libitum）组（M diet）与限饲组（MR diet）。研究发现，不同基因型个体在饲喂V日粮时的生长能力差异，并非源于摄食量的不同，而是由饲料利用效率差异导致。转录组比较分析显示，在饲喂V日粮的条件下，3个基因型间分别存在575、1770和2973个差异表达探针。值得注意的是，受V日粮影响最小的基因型，其生长性能最高。上述结果表明，该类个体能够维持正常的能量产生与蛋白质合成过程。此外，此类基因型还可激活与脂质及胆固醇代谢相关的通路，例如ω-3长链多不饱和脂肪酸（omega 3 LC-PUFA）的生物合成。最后，与已有研究结论一致，免疫系统在鱼类利用V日粮的能力中同样发挥关键作用，未来仍需进一步探究免疫系统与生长发育的互作机制。本研究针对3株虹鳟同基因系（R23h、AB1h、A22h）的肝脏转录组响应展开分析：实验鱼自开口摄食起，分别饲喂完全不含鱼油与鱼粉的植物源日粮（V diet），或以海洋资源为原料的日粮（自由采食组M diet与限饲组MR diet）；饲喂6个月后进行采样，每组样本量为6（n=6/condition）。