利用7337个个体的数据检测大黄鱼有害隐性变异。

IF 2.8 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Zhou Jiang, Ji Zhao, Ning Li, Jiaying Wang, Fei Pu, Hongshu Chi, Peng Xu, Tao Zhou
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引用次数: 0

摘要

在二倍体生物中,有害的隐性等位基因是基因突变的重要组成部分,在纯合状态下往往会导致致命的影响。大黄鱼(Larimichthys crocea)是中国重要的海洋养殖物种,由于其在福建、广东和浙江沿海的自然分布有限,加上人工繁殖的密集,已经出现了近交萧条的迹象。因此,鉴定具有有害隐性纯合基因型的基因座对于产业的可持续发展至关重要。本研究对连续三代1844条大黄鱼进行分析,初步鉴定出131个隐性纯合基因型缺失位点。通过亲本分析排除假阳性后,利用闽东种群4663例和大曲种群830例的基因型数据进行大规模验证。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。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。这些基因参与了关键的生物过程,如信号转导调节、细胞骨架组织、神经功能和聚糖合成。为了进一步验证隐性纯合子基因型缺失位点的可靠性,我们将携带6个随机选择的基因座的杂合子亲本鱼配对建立独立的家系。在这些位点上没有后代表现出隐性纯合基因型,支持先前鉴定的准确性。通过分析大黄鱼种群的基因型数据,本研究确定了隐性纯合基因型缺失的关键位点。这些发现可以为减少致死突变的选择性育种策略提供指导,从而提高种群适合度,支持水产养殖业的可持续发展。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Detecting Deleterious Recessive Variants in Large Yellow Croaker Using Data from 7337 Individuals.

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.

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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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