Nile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2) map the genomic regions associated with these traits and identify candidate genes, 3) evaluate the accuracy of breeding value prediction using genomic data, and 4) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; −0.60 and −0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a, ghrh and eif4e3. The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes.

尼罗罗非鱼是全球产量最高的重要水产养殖品种之一。通过选择性育种对饲料效率进行遗传改进是一个重要目标，基因组选择可能会加速这一过程。本研究的目的是1) 剖析尼罗罗非鱼养殖种群饲料效率性状的遗传结构， 2) 绘制与这些性状相关的基因组区域并确定候选基因， 3) 使用基因组数据评估育种价值预测的准确性，以及 4) 评估遗传标记密度对基因组预测准确性的影响。使用实验性视频记录试验，在 GIFT（遗传改良农场）的 40 个全兄弟家庭中记录了饲料转化率（FCR）、体重增加（BWG）、剩余采食量（RFI）和采食量（FI）性状。罗非鱼) 尼罗罗非鱼养殖种群。使用 ThermoFisher Axiom 65 K 尼罗罗非鱼 SNP 阵列对鱼进行基因分型。使用基因组关系矩阵估计所有评估性状的显着遗传力，范围从 0.12 到 0.22。在 BWG 和饲料效率相关性状之间发现了负但有利的遗传相关性；FCR 和 RFI 分别为 -0.60 和 -0.63。虽然全基因组关联分析表明所有测量性状的多基因遗传结构，但分别在第 7 和第 5 号染色体上鉴定了 BWG 和 FI 的重要 QTL。先前发现与饲料效率性状相关的候选基因位于这些 QTL 区域，包括ntrk3a, 生长激素 和 eif4e3. 使用基因组数据预测育种价值的准确性比使用谱系记录高出 34%。大约 5,000 个 SNP 的 SNP 密度足以实现与完整基因型数据集相似的预测准确性。我们的结果突出了基因组选择在改善尼罗罗非鱼育种计划中饲料效率性状方面的潜力。