Transcriptomic Profiling Provides Insights into Inbreeding Depression in Yesso Scallop Patinopecten yessoensis

  • Liang Zhao
  • Yangping Li
  • Jiarun Lou
  • Zhihui Yang
  • Huan Liao
  • Qiang Fu
  • Zhenyi Guo
  • Shanshan LianEmail author
  • Xiaoli Hu
  • Zhemin Bao
Original Article


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.


Inbreeding depression Bivalves Transcriptome Differential expression analysis WGCNA 


Author Contributions

SL, XH, and ZB conceived and designed the experiments; QF and LZ performed the experiments; YL analyzed the data; JL, ZY, HL, and ZG contributed reagents/materials/analysis tools; SL and LZ wrote the paper.


This work was supported by the National Natural Science Foundation of China [grant no. (31802295)], and Youth Talent Program Supported by Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao) [grant no. (2018-MFS-T06)].

Compliance with Ethical Standards

Data Availability

The transcriptomic data used in the present research can be achieved on SRA database (PRJNA515834).

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

10126_2019_9907_MOESM1_ESM.xlsx (472 kb)
ESM 1 (XLSX 471 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Key Laboratory of Marine Genetics and Breeding (Ministry of Education)Ocean University of ChinaQingdaoChina
  2. 2.Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoChina

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