Characterization of feed conversion by sex chromosomes via full genome association study

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The study of quantitative and qualitative traits from a genetic perspective is impossible without considering diseases or characteristics linked to sex. Currently, genomic selection based on sex chromosomes, conducted through genome-wide association studies (GWAS), has not been a key factor in developing specialized code and functional gene annotation, taking into account GO and KEGG libraries, as well as the analysis of previously identified genes. The aim of this research was to develop a software code for conducting GWAS on pig sex chromosomes and to identify functionally significant genes to explain the "phenotype-sex genetics" relationship. This will further refine the selection process for pigs in the population nucleus and enable the prediction of hereditary diseases in animals. In this article, we performed, for the first time, a GWAS analysis of genomic estimated breeding values for the feed conversion trait, focusing solely on sex chromosomes (sGWAS). Structural annotation identified 21 genes located on the X chromosome and 8 genes on the Y chromosome, including the homologous XY region. Cluster analysis of the identified genes revealed a significant association with the feed conversion ratio in eight of them: STS, DDX3X, PUDP, PNPLA4, DHRSX, GPR143, SHROOM2, and PRKX. Functional annotation of these genes highlighted their significant contribution to biological processes, including hereditary diseases and sex-linked specificity.

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作者简介

A. Belous

Federal Research Center for Animal Husbandry named after Academy Member L.K. Ernst

编辑信件的主要联系方式.
Email: belousa663@gmail.com
俄罗斯联邦, Dubrovitsy, Moscow Region, 142132

P. Otradnov

Federal Research Center for Animal Husbandry named after Academy Member L.K. Ernst

Email: belousa663@gmail.com
俄罗斯联邦, Dubrovitsy, Moscow Region, 142132

A. Sermyagin

Federal Research Center for Animal Husbandry named after Academy Member L.K. Ernst

Email: belousa663@gmail.com
俄罗斯联邦, Dubrovitsy, Moscow Region, 142132

N. Zinovieva

Federal Research Center for Animal Husbandry named after Academy Member L.K. Ernst

Email: belousa663@gmail.com
俄罗斯联邦, Dubrovitsy, Moscow Region, 142132

参考

  1. Указ Президента РФ от 28.02.2024 № 145 «О Стратегии научно-технологического развития Российской Федерации».
  2. Gustavsson I. Standard karyotype of the domestic pig. Committee for the Standardized Karyotype of the Domestic Pig // Hereditas. 1988. V. 109. P. 151–157. https://doi.org/10.1111/j.1601-5223.1988.tb00351.x
  3. Adega F., Chaves R., Guedes-Pinto H. Chromosome restriction enzyme digestion in domestic pig (Sus scrofa) Constitutive heterochromatin arrangement // Genes Genet. Syst. 2005. V. 80. P. 49–56. https://doi.org/10.1266/ggs.80.49
  4. Hansen K.M. Sequential Q- and C-band staining of pig chromosomes, and some comments on C-band polymorphism and C-band technique // Hereditas. 1982. V. 96. P. 183–189. https://doi.org/10.1111/j.1601-5223.1982.tb00848.x
  5. Quilter C.R., Blott S.C., Mileham A.J. et al. A mapping and evolutionary study of porcine sex chromosome gene // Mamm. Genome. 2002. V. 13. P. 588–594. https://doi.org/10.1007/s00335-002-3026-1
  6. Cornefert-Jensen F., Hare W.C., Abt D.A. Identification of the sex chromosomes of the domestic pig // J. Hered. 1968. V. 59. P. 251–255. https://doi.org/10.1093/oxfordjournals.jhered.a107710
  7. Grunwald D., Geffrotin C., Chardon P. et al. Swine chromosomes: flow sorting and spot blot hybridization // Cytometry. 1986. V. 7. P. 582–588. https://doi.org/10.1002/cyto.990070613
  8. Thomsen P.D., Hindkjaer J., Christensen K. Assignment of a porcine male-specific DNA repeat to Y-chromosomal heterochromatin // Cytogenet. Cell Genet. 1992. V. 61. P. 152–154. https://doi.org/10.1159/000133395
  9. Alfoldi J., Skaletsky H., Graves T. et al. Sequence of the mouse Y Chromosome. Seattle: USA, 2004.
  10. Alföldi J.E. Sequence of the mouse Y chromosome: PhD Thesis. Massachusetts: Massachusetts Inst. Technol., Department of Biol., 2008.
  11. Hamilton C.K., Revay T., Domander R. et al. A large expansion of the HSFY gene family in cattle shows dispersion across Yq and Testis-Specific Expression // PLoS One. 2011. V. 6 (3). https://doi.org/10.1371/journal.pone.0017790
  12. Horng Y.-M., Huang M.-C. Male-specific DNA sequences in pigs // Theriogenology. 2003. V. 59. P. 841–848. https://doi.org/10.1016/S0093-691X(02)01150-0
  13. Pérez-Pérez J., Barragán C. Isolation of four pig male-specific DNA fragments by RDA // Anim. Genet. 1998. V. 29. P. 157–158.
  14. Skinner B.M., Lachani K., Sargent C.A., Affara N.A. Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region // BMC Genet. 2013. V. 14 (3). https://doi.org/10.1186/1471-2156-14-3
  15. Park J., Cho Y.G., Kim J.K., Kim H.H. STS and PUDP deletion identified by targeted panel sequencing with CNV analysis in X-linked ichthyosis // Genes (Basel). 2023. V. 14. (10). https://doi.org/10.3390/genes14101925
  16. Moghaddam S., Houshangi A.F., Eshratkhah B., Allahvirdizadeh R. Clinical report of a Holstein's calf with ichthyosis // Vet. Res. Forum. 2021. V. 12. № 1. P. 133–135. https://doi.org/10.30466/vrf.2020.117113.2783
  17. Câmara A.C.L., Borges P.A.C., Paiva S.A., Pierezan F. Ichthyosis fetalis in a cross-bred lamb // Vet. Dermatol. 2017. V. 28. P. 516–525. https://doi.org/10.1111/vde.12459
  18. Belknap E.B., Dunstan R.W. Congenital ichthyosis in a llama // J. Am. Vet. Med. Assoc. 1990. V. 197(6). P. 764–767.
  19. Holmes R.S. Vertebrate patatin-like phospholipase domain-containing protein 4 (PNPLA4) genes and proteins: A gene with a role in retinol metabolism // 3 Biotech. 2012. V. 2. P. 277–286. https://doi.org/10.1007/s13205-012-0063-7
  20. Gray K.A., Yates B., Seal R.L. et al. Genenames.org: the HGNC resources in 2015 // Nucl. Acids Res. 2015. V. 43(D1). P. D1079–D1085. https://doi.org/10.1093/nar/gku1071
  21. Dodé C., Hardelin J.P. Kallmann syndrome // Eur. J. Hum. Genet. 2009. V. 17(2). P. 139–146. https://doi.org/10.1038/ejhg.2008.206
  22. MacColl G., Bouloux P., Quinton R. Kallmann syndrome: adhesion, afferents, and anosmia // Neuron. 2002. V. 34. № 5. P. 675–678. https://doi.org/10.1016/s0896-6273(02)00720-1
  23. Prakash S.K., Paylor R., Jenna S. et al. Functional analysis of ARHGAP6, a novel GTPase-activating protein for RhoA // Hum. Mol. Genet. 2000. V. 9(4). P. 477–488. https://doi.org/10.1093/hmg/9.4.477
  24. Brunet T., McWalter K., Mayerhanser K. et al. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder // Genet. Med. 2021. V. 23(2). P. 384–395. https://doi.org/10.1038/s41436-020-00993-y
  25. Deciphering Developmental Disorders Study. Prevalence and architecture of de novo mutations in developmental disorders // Nature. 2017. V. 542. P. 433–438. https://doi.org/10.1038/nature21062
  26. Lucas C.G., Spate A.M., Samuel M.S. et al. A novel swine sex-linked marker and its application across different mammalian species // Transgenic Res. 2020. V. 29. P. 395–407. https://doi.org/10.1007/s11248-020-00204-z
  27. O'Connor E., Eisenhaber B., Dalley J. et al. Species specific membrane anchoring of nyctalopin, a small leucine-rich repeat protein // Human Mol. Genet. 2005. V. 14(13). P. 1877–1887. https://doi.org/10.1093/hmg/ddi194
  28. Huang T.N., Hsueh Y.P. CASK point mutation regulates protein-protein interactions and NR2b promoter activity // Biochem. Biophys. Res Commun. 2009. V. 382(1). P. 219–222. https://doi.org/10.1016/j.bbrc.2009.03.015
  29. Najm J., Horn D., Wimplinger I. et al. Mutations of CASK cause an X-linked brain malformation phenotype with microcephaly and hypoplasia of the brainstem and cerebellum // Nat. Genet. 2008. V. 40. P. 1065–1067. https://doi.org/10.1038/ng.194
  30. Atasoy D., Schoch S., Ho A. et al. Deletion of CASK in mice is lethal and impairs synaptic function // Proc. Natl Acad. Sci. USA. 2007. V. 104(7). P. 2525–2530. https://doi.org/10.1073/pnas.0611003104
  31. Engemaier E., Römpler H., Schöneberg T., Schulz A. Genomic and supragenomic structure of the nucleotide-like G-protein-coupled receptor GPR34 // Genomics. 2006. V. 87(2). P. 254–264. https://doi.org/10.1016/j.ygeno.2005.10.001
  32. Engel K.M., Schröck K., Teupser D. et al. Reduced food intake and body weight in mice deficient for the G protein-coupled receptor GPR82 // PLoS One. 2011. V. 6(12). https://doi.org/10.1371/journal.pone.0029400
  33. Sallmann G.B., Bray P.J., Rogers S. et al. Scanning the ocular albinism 1 (OA1) gene for polymorphisms in congenital nystagmus by DHPLC // Ophthalmic Genet. 2006. V. 27. P. 43–49. https://doi.org/10.1080/13816810600677834
  34. Jia X., Yuan J., Jia X. et al. GPR143 mutations in Chinese patients with ocular albinism type 1 // Mol. Med. Rep. 2017. V. 15(5). P. 3069–3075. https://doi.org/10.3892/mmr.2017.6366
  35. Clapier C.R., Iwasa J., Cairns B.R., Peterson C.L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes // Nat. Rev. Mol. Cell. Biol. 2017. V. 18(7). P. 407–422. https://doi.org/10.1038/nrm.2017.26
  36. Picketts D., Mirzaa G., Yan K. et al. Pathogenic variants in SMARCA1 cause an X-linked neurodevelopmental disorder modulated by NURF complex composition // Res. Sq. [Preprint]. 2023. https://doi.org/10.21203/rs.3.rs-3317938/v1
  37. Festa B.P., Berquez M., Gassama A. et al. OCRL deficiency impairs endolysosomal function in a humanized mouse model for Lowe syndrome and Dent disease // Hum. Mol. Genet. 2019. V. 28(12). P. 1931–1946. https://doi.org/10.1093/hmg/ddy449
  38. Gianesello L., Arroyo J., Del Prete D. et al. Genotype phenotype correlation in dent disease 2 and review of the literature: OCRL gene pleiotropism or extreme phenotypic variability of Lowe syndrome? // Genes (Basel). 2021. V. 12(10). https://doi.org/10.3390/genes12101597
  39. Tatemoto K., Hosoya M., Habata Y. et al. Isolation and characterization of a novel endogenous peptide ligand for the human APJ receptor // Biochem. Biophys. Res. Commun. 1998. V. 251 (2). P. 471–476. https://doi.org/10.1006/bbrc.1998.9489
  40. Tatemoto K., Takayama K., Zou M.X. et al. The novel peptide apelin lowers blood pressure via a nitric oxide-dependent mechanism // Regul. Pept. 2001. V. 99(2–3). P. 87–92. https://doi.org/10.1016/s0167-0115(01)00236-1
  41. Hu G., Wang Z., Zhang R. et al. The role of apelin/apelin receptor in energy metabolism and water homeostasis: A comprehensive narrative review // Front. in Physiology. 2021. V. 12. https://doi.org/10.3389/fphys.2021.632886
  42. Sörhede Winzell M., Magnusson C., Ahrén B. The apj receptor is expressed in pancreatic islets and its ligand, apelin, inhibits insulin secretion in mice // Regul. Pept. 2005. V. 131(1–3). P. 12–17. https://doi.org/10.1016/j.regpep.2005.05.004
  43. Dray C., Knauf C., Daviaud D. et al. Apelin stimulates glucose utilization in normal and obese insulin-resistant mice // Cell. Metab. 2008. V. 8(5). P. 437–445. https://doi.org/10.1016/j.cmet.2008.10.003
  44. Kawamata Y., Habata Y., Fukusumi S. et al. Molecular properties of apelin: tissue distribution and receptor binding // Biochim. Biophys. Acta. 2001. V. 1538(2–3). P. 162–171. https://doi.org/10.1016/s0167-4889(00)00143-9
  45. Mercati F., Scocco P., Maranesi M. et al. Apelin system detection in the reproductive apparatus of ewes grazing on semi-natural pasture // Theriogenology. 2019. V. 139. P. 156–166. https://doi.org/10.1016/j.theriogenology.2019.08.012
  46. Rak A., Drwal E., Rame C. et al. Expression of apelin and apelin receptor (APJ) in porcine ovarian follicles and in vitro effect of apelin on steroidogenesis and proliferation through APJ activation and different signaling pathways // Theriogenology. 2017. V. 96. P. 126–135. https://doi.org/10.1016/j.theriogenology.2017.04.014
  47. Wang X., Liu X., Song Z. et al. Emerging roles of APLN and APELA in the physiology and pathology of the female reproductive system // PeerJ. 2020. V. 8. e10245. https://doi.org/10.7717/peerj.10245
  48. Dobrzyn K., Kiezun M., Kopij G. et al. Apelin-13 modulates the endometrial transcriptome of the domestic pig during implantation // BMC Genomics. 2024. V. 25(501). https://doi.org/10.1186/s12864-024-10417-9
  49. Duan Q.L., Nikpoor B., Dube M.P. et al. A variant in XPNPEP2 is associated with angioedema induced by angiotensin I-converting enzyme inhibitors // Am. J. Hum. Genet. 2005. V. 77(4). P. 617–626. https://doi.org/10.1086/496899
  50. Delmonte O.M., Bergerson J.R.E., Kawai T. et al. SASH3 variants cause a novel form of X-linked combined immunodeficiency with immune dysregulation // Blood. 2021. V. 138(12). P. 1019–1033. https://doi.org/10.1182/blood.2020008629
  51. Maak S., Boettcher D., Tetens J. et al. Expression of microRNAs is not related to increased expression of ZDHHC9 in hind leg muscles of splay leg piglets // Mol. Cell. Probes. 2010. V. 24(1). P. 32–37. https://doi.org/ 10.1016/j.mcp.2009.09.001
  52. Paganini L., Hadi L.A., Chetta M. et al. A HS6ST2 gene variant associated with X-linked intellectual disability and severe myopia in two male twins // Clin. Genet. 2019. V. 95(3). P. 368–374. https://doi.org/10.1111/cge.13485
  53. Li Q.Y., Zhang Y.C., Wei C. et al. The association between mutations in ubiquitin-specific protease 26 (USP26) and male infertility: A systematic review and meta-analysis // Asian. J. Androl. 2022. V. 24(4). P. 422–429. https://doi.org/10.4103/aja2021109
  54. Skinner B.M., Lachani K., Sargent C.A., Affara N.A. Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region // BMC Genet. 2013. V. 14. https://doi.org/10.1186/1471-2156-14-3
  55. Zhang G., Luo Y., Li G. et al. DHRSX, a novel non-classical secretory protein associated with starvation induced autophagy // Int. J. Med. Sci. 2014. V. 11(9). P. 962–970. https://doi.org/10.7150/ijms.9529

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1. JATS XML
2. Fig. 1. Genome-wide association study of sex chromosomes. 1 – chromosome X, 2 – chromosome Y, 3 – homologous region of chromosomes X and Y.

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3. Fig. 2. Cluster relationships between genes obtained using the STRING program (string-db.org).

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