PDF(Pubmed)
Abstract：
Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.
摘要：
海洋动物具有相当复杂和杂合性的基因组。他们独特的生殖系统，其特点是繁殖力高，早期死亡率高，增加了近亲繁殖的风险，在各个幼虫发育阶段可能导致严重的近亲繁殖抑郁症。在这项研究中,我们建立了一套中国明对虾的近交系，近交系数为0.25，并研究了主要幼虫发育阶段的消除方式和近交抑郁的表现。利用减少代表性的基因组测序来探索跨两个典型消除阶段的基因型频率特征。结果表明，在孵化和变态进入菌丝和幼虫后阶段时，死亡率显着。近交抑郁在这些发育阶段也很明显，抑郁率为24.36%,29.23%,和45.28%。SNP的分离分析表明孵化前配子选择的重要作用，占zoea阶段偏差的45.95%。在幼虫发育的合子选择阶段，纯合子缺乏和杂合子过量是主要的选择类型。两种类型的总和解释了在Mysis和幼虫后阶段的合子选择的82.31％和89.91％，分别。在发育后期，总体变形率从22.37％下降到12.86％。通过选择性扫描分析鉴定了总共783个基因座。我们还发现，在幼虫后阶段，同一位点的变形类型可能会发生变化。主要的变化包括配子选择向正常分离和其他形式的变形向杂合过量的过渡。这可能归因于对有害等位基因的高强度选择和遗传搭便车效应。幼虫消除后，保留了更大比例的杂合个体。我们检测到遗传多样性参数的增加，如预期杂合性，观察到的杂合性，和后幼虫阶段的多态信息含量。这些发现表明存在许多隐性有害等位基因及其连锁，并表明部分优势假说的主要作用。研究结果为海洋动物近亲繁殖抑制的机制提供了有价值的见解，并为制定虾种群的育种策略提供了指导。
