Jiang Zhou, Zhao Ji, Li Ning, Wang Jiaying, Pu Fei, Chi Hongshu, Xu Peng, Zhou Tao
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
Mar Biotechnol (NY). 2025 Jun 26;27(4):105. doi: 10.1007/s10126-025-10486-1.
In diploid organisms, deleterious recessive alleles represent a significant component of genetic mutations and often result in lethal effects when in a homozygous state. Large yellow croaker (Larimichthys crocea), a critical marine aquaculture species in China, has shown signs of inbreeding depression due to its limited natural distribution along the coasts of Fujian, Guangdong, and Zhejiang provinces, combined with intensive artificial propagation practices. Identifying loci with deleterious recessive homozygous genotypes is therefore crucial for sustainable industry development. In this study, 1844 large yellow croaker across three consecutive generations were analyzed, resulting in the preliminary identification of 131 loci with missing recessive homozygous genotypes. After excluding false positives through parentage analysis, large-scale validation was conducted using genotype data from 4663 individuals from the MinDong population and 830 individuals from the Daqu population. Ultimately, 22 loci with complete absence of homozygous recessive genotypes were identified across 7337 individuals. The average minor allele frequency (MAF) of these loci was 0.16. Except for LG17_2296176 and LG17_4414232, which exhibited moderate linkage disequilibrium, the remaining 20 loci were largely independent with no observed linkage disequilibrium. Annotation of the 22 loci identified 12 associated genes, including vegfa, sntg2, tcf7, kif2a, lage3, ano10, mpdu1, and others. These genes are involved in key biological processes such as signal transduction regulation, cytoskeletal organization, neural function, and glycan synthesis. To further verify the reliability of the loci with missing recessive homozygous genotypes, heterozygous parental fish carrying 6 randomly selected loci were paired to establish independent families. None of the offspring exhibited recessive homozygous genotypes at these loci, supporting the accuracy of the prior identification. By analyzing genotype data from large yellow croaker populations, this study identifies key loci with missing recessive homozygous genotypes. These findings may offer guidance for selective breeding strategies aimed at minimizing lethal mutations, thereby enhancing population fitness and supporting the sustainable development of the aquaculture industry.
在二倍体生物中，有害隐性等位基因是基因突变的重要组成部分，当处于纯合状态时往往会导致致死效应。大黄鱼（Larimichthys crocea）是中国重要的海水养殖鱼类，由于其自然分布局限于福建、广东和浙江沿海，加上密集的人工繁殖，已出现近亲繁殖衰退的迹象。因此，识别具有有害隐性纯合基因型的位点对于该产业的可持续发展至关重要。在本研究中，对连续三代的1844尾大黄鱼进行了分析，初步鉴定出131个具有缺失隐性纯合基因型的位点。通过亲权分析排除假阳性后，利用闽东群体的4663个个体和岱衢群体的830个个体的基因型数据进行了大规模验证。最终，在7337个个体中鉴定出22个完全不存在纯合隐性基因型的位点。这些位点的平均次要等位基因频率（MAF）为0.16。除LG17_2296176和LG17_4414232表现出中度连锁不平衡外，其余20个位点基本独立，未观察到连锁不平衡。对这22个位点的注释鉴定出12个相关基因，包括vegfa、sntg2、tcf7、kif2a、lage3、ano10、mpdu1等。这些基因参与信号转导调控、细胞骨架组织、神经功能和聚糖合成等关键生物学过程。为进一步验证具有缺失隐性纯合基因型位点的可靠性，将携带6个随机选择位点的杂合亲本鱼配对建立独立家系。后代在这些位点均未表现出隐性纯合基因型，支持了先前鉴定的准确性。通过分析大黄鱼群体的基因型数据，本研究识别出具有缺失隐性纯合基因型的关键位点。这些发现可为旨在最小化致死突变的选择性育种策略提供指导，从而提高种群适应性，支持水产养殖业的可持续发展。
