Growth selection in fish is essential for aquaculture; however, long generation times and artificial breeding limitations present challenges for breeding endeavors. The tomato grouper (Cephalopholis sonnerati) is an emerging aquaculture species with a generation cycle of at least 5 to 10 years. Mixed culture of broodstocks and natural mating are commonly employed in hatcheries. To expedite the selection process for tomato grouper, we utilized ISSRseq technology for assisted future growth selection. After 6 months of rearing, we selected 48 individuals, including 24 fast-growing and 24 slow-growing individuals (representing the top and bottom 10% of samples). These samples produced 932 SNPs. Although specific broodstock pairing information is unavailable, our results suggest that these fry likely originated from multiple broodstock exhibiting considerable diversity. Further analysis of genetic relationships among individuals revealed three main clades. One clade contained a higher proportion of faster-growing individuals (80%), while another featured a lower proportion of rapidly growing individuals (28.6%). Through the relatedness network and further exclusion of individuals, the faster-growth clade comprised 92.3% of fast-growing individuals. The faster-growth clade is appropriate for further development into a high-growth strain. Our findings demonstrate that molecular markers can advance population selective breeding to family selection in aquaculture breeding research.

中文翻译：

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利用 ISSRseq 基因分型协助番茄石斑鱼 (Cephalopholis sonnerati) 的生长选择，无需亲鱼信息

鱼类的生长选择对于水产养殖至关重要；然而，较长的世代时间和人工育种的限制给育种工作带来了挑战。番茄石斑鱼（Cephalopholis sonnerati）是一种新兴的水产养殖品种，世代周期至少为5至10年。孵化场通常采用亲鱼混合养殖和自然交配。为了加快番茄石斑鱼的选择过程，我们利用 ISSRseq 技术来辅助未来的生长选择。经过6个月的饲养，我们选择了48只个体，其中24只快速生长个体和24只慢速生长个体（代表样本的顶部和底部10%）。这些样本产生了 932 个 SNP。尽管没有具体的亲鱼配对信息，但我们的结果表明这些鱼苗可能起源于表现出相当大多样性的多种亲鱼。对个体之间遗传关系的进一步分析揭示了三个主要分支。一个进化枝包含较高比例的快速生长个体（80%），而另一个进化枝则包含较低比例的快速生长个体（28.6%）。通过关联网络和进一步排除个体，快速生长分支占快速生长个体的 92.3%。生长较快的进化枝适合进一步发育成高生长菌株。我们的研究结果表明，分子标记可以将水产养殖育种研究中的群体选择育种推进到家系选择。