Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China.
Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
Mar Biotechnol (NY). 2019 Oct;21(5):623-633. doi: 10.1007/s10126-019-09907-9. Epub 2019 Jul 13.
Inbreeding often causes a decline in biological fitness, known as inbreeding depression. In genetics study, inbreeding coefficient f gives the proportion by which the heterozygosity of an individual is reduced by inbreeding. With the development of high-throughput sequencing, researchers were able to perform deep approaches to investigate which genes are affected by inbreeding and reveal some molecular underpinnings of inbreeding depression. As one commercially important species, Yesso scallop Patinopecten yessoensis confront the same dilemma of inbreeding depression. To examine how inbreeding affects gene expression, we compared the transcriptome of two experimentally selfing families with inbreeding coefficient f reached 0.5 as well as one natural population (f ≈ 0) of P. yessoensis. A total of 24 RNA-Seq libraries were constructed using scallop adductor muscle, and eventually 676.56 M (96.85%) HQ reads were acquired. Based on differential gene analysis, we were able to identify nine common differentially expressed genes (DEGs) across the top-ranked 30 DEGs in both selfing families in comparation with the natural population. Remarkable, through weighted gene co-expression network analysis (WGCNA), five common DEGs were found enriched in the most significant inbreeding related functional module M14 (FDR = 1.64E-156), including SREBP1, G3BP2, SBK1, KIAA1161, and AATs-Glupro. These five genes showed significantly higher expression in self-bred progeny. Suggested by the genetic functional analysis, up-regulated SREBP1, G3BP2, and KIAA1161 may suggest a perturbing lipid metabolism, a severe inframammary reaction or immune response, and a stress-responsive behavior. Besides, the significant higher SBK1 and AATs-Glupro may reflect the abnormal cellular physiological situation. Together, these genetic aberrant transcriptomic performances may contribute to inbreeding depression in P. yessoensis, deteriorating the stress tolerance and survival phenotype in self-bred progeny. Our results would lay a foundation for further comprehensive understanding of bivalve inbreeding depression, which may potentially benefit the genetic breeding for scallop aquaculture.
近亲繁殖通常会导致生物适应性下降，这被称为近交衰退。在遗传学研究中，近交系数 f 表示个体因近亲繁殖而导致杂合性降低的比例。随着高通量测序技术的发展，研究人员能够深入研究哪些基因受到近亲繁殖的影响，并揭示近交衰退的一些分子基础。作为一种具有商业重要性的物种，虾夷扇贝（Patinopecten yessoensis）面临着同样的近交衰退困境。为了研究近亲繁殖如何影响基因表达，我们比较了两个实验性自交家系（近交系数 f 达到 0.5）和一个虾夷扇贝自然种群（f≈0）的转录组。使用虾夷扇贝的肌肉组织构建了总共 24 个 RNA-Seq 文库，最终获得了 676.56M（96.85%）HQ 读数。基于差异基因分析，我们能够在两个自交家系中识别出前 30 个差异表达基因（DEG）中排名最高的 9 个共同差异表达基因（DEG），并与自然种群进行比较。值得注意的是，通过加权基因共表达网络分析（WGCNA），在与近交关系最显著的功能模块 M14（FDR=1.64E-156）中发现了 5 个共同的 DEG，包括 SREBP1、G3BP2、SBK1、KIAA1161 和 AATs-Glupro。这些 5 个基因在自交后代中表现出显著更高的表达水平。通过遗传功能分析表明，上调的 SREBP1、G3BP2 和 KIAA1161 可能提示脂质代谢紊乱、严重的乳腺下反应或免疫反应以及应激反应行为。此外，SBK1 和 AATs-Glupro 的显著上调可能反映了异常的细胞生理状况。总的来说，这些遗传异常的转录组表现可能导致虾夷扇贝的近交衰退，降低自交后代的应激耐受和生存表型。我们的研究结果为进一步全面理解双壳类动物的近交衰退奠定了基础，这可能为贝类养殖的遗传育种提供帮助。
