Abstract A major problem in smallholder Nile tilapia (Oreochromis niloticus) farms is that the achieved production is much lower than under optimal management. One of the main environmental factors contributing to lower production is dissolved oxygen (DO), because the majority of Nile tilapia production takes place under smallholder farms with no aeration of ponds which leads to large DO fluctuations. On the contrary, breeding programs select fish in aerated ponds. Aerating ponds is currently not an option for smallholder farmers because either it is too expensive or they lack access to cheap electricity supply. Therefore, it is crucial to know the genetic correlation between aerated and non-aerated ponds to optimize breeding programs to select fish that perform well in ponds with fluctuating DO levels. The objectives of this study were 1) to investigate the presence of genotype by environment (GxE) interaction between aerated and non-aerated earthen ponds using a design that minimized common environmental effects and 2) the impact of (non-)aeration on genetic parameters. The experimental fish were mass-produced using natural group spawning and nursed in four 30m2 hapas. A random sample of fingerlings from each hapa was tagged and randomly distributed to aerated and non-aerated ponds for a grow-out period of 217 and 218 days. Body weight and photographs were taken on five consecutive time points during grow-out. Of the stocked fish, 2063 were genotyped-by-sequencing. A genomic relationship matrix was built using 11,929 SNPs to estimate genetic parameters with ASReml. No-aeration significantly reduced mean harvest weight (HW), survival and thermal growth coefficient (TGC) compared to aeration. Substantial heritabilities (0.14–0.45) were found for HW, TGC, surface area (SA) and body shape, expressed as ellipticity, and low heritabilities (0.03–0.04) for survival in aerated and non-aerated ponds. In both ponds, the environmental effect common to full sibs was not significant. Genetic coefficients of variation were 20–41% lower and heritabilities were 19–25% lower in the non-aerated pond compared to the aerated pond, for HW, TGC and survival. Genetic correlations between ponds for HW, standard length, height, SA and TGC were 0.81, 0.80, 0.74, 0.78 and 0.78, respectively. In summary, some GxE interaction between aerated and non-aerated ponds was found and no-aeration decreased genetic coefficients of variation and heritabilities compared to aerated ponds. Breeding programs are recommended to use half sib information from non-aerated farms or to set up a reference population for genomic selection in a non-aerated environment either on-station or in farms.

中文翻译：

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曝气和非曝气池塘之间环境相互作用的基因型以及曝气对尼罗罗非鱼（Oreochromis niloticus）遗传参数的影响

摘要 尼罗罗非鱼（Oreochromis niloticus）小规模养殖场的一个主要问题是实现的产量远低于最佳管理。导致产量下降的主要环境因素之一是溶解氧 (DO)，因为尼罗罗非鱼的大部分生产发生在小农养殖场，池塘没有曝气，这会导致溶解氧大幅波动。相反，育种计划在曝气池中选择鱼。曝气池目前不是小农的选择，因为要么太贵，要么他们无法获得廉价的电力供应。因此，了解曝气和非曝气池塘之间的遗传相关性对于优化育种计划以选择在 DO 水平波动的池塘中表现良好的鱼类至关重要。本研究的目的是 1) 使用一种将常见环境影响降至最低的设计，研究曝气和非曝气土池之间环境 (GxE) 相互作用基因型的存在，以及 2)（非）曝气对遗传参数的影响. 实验鱼采用自然群体产卵的方式大量生产，并在4条30平方米的hapas中进行饲养。对来自每个鱼塘的随机鱼种样本进行标记并随机分配到曝气和非曝气池塘，养成期分别为 217 天和 218 天。在养成期间的五个连续时间点拍摄体重和照片。在放养的鱼中，2063 条是通过测序进行基因分型的。使用 11,929 个 SNP 构建基因组关系矩阵，以使用 ASReml 估计遗传参数。无曝气显着降低了平均收获重量 (HW)，与曝气相比，存活率和热生长系数 (TGC)。发现 HW、TGC、表面积 (SA) 和体形的显着遗传力 (0.14–0.45)，表示为椭圆度，以及在充气和非充气池塘中存活的低遗传力 (0.03–0.04)。在两个池塘中，全同胞共同的环境影响并不显着。与曝气池相比，非曝气池的 HW、TGC 和存活率的遗传变异系数低 20-41%，遗传力低 19-25%。池塘之间的 HW、标准长度、高度、SA 和 TGC 的遗传相关性分别为 0.81、0.80、0.74、0.78 和 0.78。总之，发现了曝气和非曝气池塘之间的一些 GxE 相互作用，与曝气池塘相比，不曝气降低了变异的遗传系数和遗传力。