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

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Abstract

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.

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Change history

  • 23 January 2020

    The original version of this article unfortunately contained a mistake in the authorgroup section. Author Zhenmin Bao’s given name was incorrectly spelled as “Zhemin Bao”.

  • 23 January 2020

    The original version of this article unfortunately contained a mistake in the authorgroup section. Author Zhenmin Bao���s given name was incorrectly spelled as ���Zhemin Bao���.

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Funding

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)].

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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.

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Correspondence to Shanshan Lian.

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

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The authors declare that they have no conflict of interest.

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Zhao, L., Li, Y., Lou, J. et al. Transcriptomic Profiling Provides Insights into Inbreeding Depression in Yesso Scallop Patinopecten yessoensis. Mar Biotechnol 21, 623–633 (2019). https://doi.org/10.1007/s10126-019-09907-9

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Keywords

  • Inbreeding depression
  • Bivalves
  • Transcriptome
  • Differential expression analysis
  • WGCNA