DOI QR코드

DOI QR Code

Whole-genome sequence association study identifies cyclin dependent kinase 8 as a key gene for the number of mummified piglets

  • Pingxian, Wu (Chongqing Academy of Animal Sciences) ;
  • Dejuan, Chen (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Kai, Wang (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Shujie, Wang (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Yihui, Liu (Sichuan Animal Husbandry Station) ;
  • Anan, Jiang (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Weihang, Xiao (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Yanzhi, Jiang (College of Life Science, Sichuan Agricultural University) ;
  • Li, Zhu (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Xu, Xu (Sichuan Animal Husbandry Station) ;
  • Xiaotian, Qiu (National Animal Husbandry Service) ;
  • Xuewei, Li (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University) ;
  • Guoqing, Tang (Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University)
  • Received : 2022.03.22
  • Accepted : 2022.08.14
  • Published : 2023.01.01

Abstract

Objective: Pigs, an ideal biomedical model for human diseases, suffer from about 50% early embryonic and fetal death, a major cause of fertility loss worldwide. However, identifying the causal variant remains a huge challenge. This study aimed to detect single nucleotide polymorphisms (SNPs) and candidate genes for the number of mummified (NM) piglets using the imputed whole-genome sequence (WGS) and validate the potential candidate genes. Methods: The imputed WGS was introduced from genotyping-by-sequencing (GBS) using a multi-breed reference population. We performed genome-wide association studies (GWAS) for NM piglets at birth from a Landrace pig populatiGWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase on. A total of 300 Landrace pigs were genotyped by GBS. The whole-genome variants were imputed, and 4,252,858 SNPs were obtained. Various molecular experiments were conducted to determine how the genes affected NM in pigs. Results: A strong GWAS peak located on SSC11: 0.10 to 7.11 Mbp (Top SNP, SSC11:1,889,658 bp; p = 9.98E-13) was identified in cyclin dependent kinase 8 (CDK8) gene, which plays a crucial role in embryonic retardation and lethality. Based on the molecular experiments, we found that Y-box binding protein 1 (YBX1) was a crucial transcription factor for CDK8, which mediated the effect of CDK8 in the proliferation of porcine ovarian granulosa cells via transforming growth factor beta/small mother against decapentaplegic signaling pathway, and, as a consequence, affected embryo quality, indicating that this pathway may be contributing to mummified fetal in pigs. Conclusion: A powerful imputation-based association study was performed to identify genes associated with NM in pigs. CDK8 was suggested as a functional gene for the proliferation of porcine ovarian granulosa cells, but further studies are required to determine causative mutations and the effect of loci on NM in pigs.

Keywords

Acknowledgement

This study was supported by grants from the Sichuan Science and Technology Program (2020YFN0024), the Sichuan Innovation Team of Pig (sccxtd-2021-08), Performance Incentive and Guidance Special Project of Scientific Research Organization of Chongqing Science and Technology Committee (cstc2021jxjl8001), Chongqing Special Financial Fund Project (22514C), the National key R&D Program of China #2018YFD0501204, the National Natural Science Foundation of China (31530073, C170102) and the Earmarked fund for the China Agriculture Research System (No. CARS-35-01A).

References

  1. Derks MFL, Gjuvsland AB, Bosse M, et al. Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS Genet 2019;15:e1008055. https://doi.org/10.1371/journal.pgen.1008055 
  2. Chen Z, Ye S, Teng J, et al. Genome-wide association studies for the number of animals born alive and dead in duroc pigs. Theriogenology 2019;139:36-42. https://doi.org/10.1016/j.theriogenology.2019.07.013 
  3. Das S, Abecasis GR, Browning BL. Genotype imputation from large reference panels. Annu Rev Genomics Hum Genet 2018;19:73-96. https://doi.org/10.1146/annurev-genom-083117-021602 
  4. Daetwyler HD, Capitan A, Pausch H, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet 2014;46:858-65. https://doi.org/10.1038/ng.3034 
  5. Akoulitchev S, Chuikov S, Reinberg D. TFIIH is negatively regulated by cdk8-containing mediator complexes. Nature 2000;407:102-6. https://doi.org/10.1038/35024111 
  6. McDermott MS, Chumanevich AA, Lim CU, et al. Inhibition of CDK8 mediator kinase suppresses estrogen dependent transcription and the growth of estrogen receptor positive breast cancer. Oncotarget 2017;8:12558-75. https://doi.org/10.18632/oncotarget.14894 
  7. Brabazon ED, Bree RT, Carton MW, Grealy M, Byrnes L. Cyclin-dependent kinase 8 is expressed both maternally and zygotically during zebrafish embryo development. Biochim Biophys Acta 2002;1576:203-8. https://doi.org/10.1016/s0167-4781(02)00302-0 
  8. Westerling T, Kuuluvainen E, Makela TP. Cdk8 is essential for preimplantation mouse development. Mol Cell Biol 2007;27:6177-82. https://doi.org/10.1128/MCB.01302-06 
  9. Shibahara K, Uchiumi T, Fukuda T, et al. Targeted disruption of one allele of the Y-box binding protein-1 (YB-1) gene in mouse embryonic stem cells and increased sensitivity to cisplatin and mitomycin C. Cancer Sci 2004;95:348-53. https://doi.org/10.1111/j.1349-7006.2004.tb03214.x 
  10. Chatterjee M, Rancso C, Stuhmer T, et al. The Y-box binding protein YB-1 is associated with progressive disease and mediates survival and drug resistance in multiple myeloma. Blood 2008;111:3714-22. https://doi.org/10.1182/blood-2007-05-089151 
  11. Ito K, Tsutsumi K, Kuzumaki T, Gomez PF, Otsu K, Ishikawa K. A novel growth-inducible gene that encodes a protein with a conserved cold-shock domain. Nucleic Acids Res 1994;22:2036-41. https://doi.org/10.1093/nar/22.11.2036 
  12. Lu ZH, Books JT, Ley TJ. YB-1 is important for late-stage embryonic development, optimal cellular stress responses, and the prevention of premature senescence. Mol Cell Biol 2005;25:4625-37. https://doi.org/10.1128/mcb.25.11.4625-4637.2005 
  13. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60. https://doi.org/10.1093/bioinformatics/btp324 
  14. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011;43:491-8. https://doi.org/10.1038/ng.806 
  15. Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics 2011; 27:2156-8. https://doi.org/10.1093/bioinformatics/btr330 
  16. Browning BL, Zhou Y, Browning SR. A One-Penny imputed genome from next-generation reference panels. Am J Hum Genet 2018;103:338-48. https://doi.org/10.1016/j.ajhg.2018.07.015 
  17. Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet 2012;44:821-4. https://doi.org/10.1038/ng.2310 
  18. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001;25:402-8. https://doi.org/10.1006/meth.2001.1262 
  19. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008;26:1367-72. https://doi.org/10.1038/nbt.1511 
  20. Onteru SK, Fan B, Du ZQ, Garrick DJ, Stalder KJ, Rothschild MF. A whole-genome association study for pig reproductive traits. Anim Genet 2012;43:18-26. https://doi.org/10.1111/j.1365-2052.2011.02213.x 
  21. Wei LU, Tian ML, Wang ZR, Liu C, Qing-Yun YU. Research on Relation between placental efficiency and IUGR piglet. J Xinjiang Agric Univ 2010;33:307-11. https://doi.org/10.3969/j.issn.1007-8614.2010.04.006 
  22. Meurens F, Summerfield A, Nauwynck H, Saif L, Gerdts, V. The pig: a model for human infectious diseases. Trends Microbiol 2012;20:50-7. https://doi.org/10.1016/j.tim.2011.11.002 
  23. Guo YM, Lee GJ, Archibald AL, Haley CS. Quantitative trait loci for production traits in pigs: a combined analysis of two Meishan x Large White populations. Anim Genet 2008;39:486-95. https://doi.org/10.1111/j.1365-2052.2008.01756.x 
  24. Rosendo A, Iannuccelli N, Gilbert H, et al. Microsatellite mapping of quantitative trait loci affecting female reproductive tract characteristics in Meishan x Large White F(2) pigs. J Anim Sci 2012;90:37-44. https://doi.org/10.3969/j.issn.1007-8614.2010.04.006 
  25. Liu H, Johnson EM. Distinct proteins encoded by alternative transcripts of the PURG gene, located contrapodal to WRN on chromosome 8, determined by differential termination/polyadenylation. Nucleic Acids Res 2002;30:2417-26. https://doi.org/10.1093/nar/30.11.2417 
  26. Johnson EM, Daniel DC, Gordon J. The pur protein family: genetic and structural features in development and disease. J Cell Physiol 2013;228:930-7. https://doi.org/10.1002/jcp.24237 
  27. Huo N, Yu M, Li X, Zhou C, Jin X, Gao X. PURB is a positive regulator of amino acid-induced milk synthesis in bovine mammary epithelial cells. J Cell Physiol 2019;234:6992-7003. https://doi.org/10.1002/jcp.27452 
  28. Su L, Hershberger RJ, Weissman IL. LYAR, a novel nucleolar protein with zinc finger DNA-binding motifs, is involved in cell growth regulation. Genes Dev 1993;7:735-48. https://doi.org/10.1101/gad.7.5.735 
  29. Chowdhury TA, Kleene KC. Identification of potential regulatory elements in the 5' and 3' UTRs of 12 translationally regulated mRNAs in mammalian spermatids by comparative genomics. J Androl 2012;33:244-56. https://doi.org/10.2164/jandrol.110.012492 
  30. Snyder E, Soundararajan R, Sharma M, Dearth A, Smith B, Braun RE. Compound heterozygosity for Y Box proteins causes sterility due to loss of translational repression. PLoS Genet 2015;11:e1005690. https://doi.org/10.1371/journal.pgen.1005690 
  31. Lu ZH, Books JT, Ley TJ. Cold shock domain family members YB-1 and MSY4 share essential functions during murine embryogenesis. Mol Cell Biol 2006;26:8410-7. https://doi.org/10.1128/mcb.01196-06 
  32. Donner AJ, Ebmeier CC, Taatjes DJ, Espinosa JM. CDK8 is a positive regulator of transcriptional elongation within the serum response network. Nat Struct Mol Biol 2010;17:194-201. https://doi.org/10.1038/nsmb.1752 
  33. Li M, Chen L, Tian S, et al. Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies. Genome Res 2017;27:865-74. https://doi.org/10.1101/gr.207456.116 
  34. Du X, Pan Z, Li Q, Liu H, Li Q. SMAD4 feedback regulates the canonical TGF-β signaling pathway to control granulosa cell apoptosis. Cell Death Dis 2018;9:151. https://doi.org/10.1038/s41419-017-0205-2 
  35. Aragon E, Goerner N, Zaromytidou AI, et al. A Smad action turnover switch operated by WW domain readers of a phosphoserine code. Genes Dev 2011;25:1275-88. https://doi.org/10.1101/gad.2060811 
  36. Albertini DF, Combelles CM, Benecchi E, Carabatsos MJ. Cellular basis for paracrine regulation of ovarian follicle development. Reproduction 2001;121:647-53. https://doi.org/10.1530/rep.0.1210647 
  37. Seino T, Saito H, Kaneko T, Takahashi T, Kawachiya S, Kurachi H. Eight-hydroxy-2'-deoxyguanosine in granulosa cells is correlated with the quality of oocytes and embryos in an in vitro fertilization-embryo transfer program. Fertil Steril 2002;77:1184-90. https://doi.org/10.1016/s0015-0282(02)03103-5