Genome-wide search for copy number variations associated with blood parameters in Large White pigs

Copy number variations (CNVs) are repetitive regions of the genome, ranging from one thousand to several million base pairs in size, that vary between individuals in a population. Due to their greater genome coverage compared to SNPs (single nucleotide polymorphisms), CNVs are an important source of genetic variability and are currently considered an alternative type of DNA marker. To date, there are studies in animal husbandry indicating the effect of CNVs on phenotypic variability. However, few studies have focused on the associations of CNVs with blood parameters, which could help identify subtle mechanisms underlying the physiological regulation of phenotypes associated with health and selection-important traits. The aim of this work was to identify CNVs associated with alanine aminotransferase (ALT), urea (Urea), red blood cell (RBC) and white blood cell (WBC) counts in Large White pigs and to identify candidate genes that may be considered as 

genetic markers in hematopoietic functions, physiological processes and productivity phenotypes. The study was conducted on Large White pigs. Genotyping was performed using the GGP Porcine HD Genomic Profiler v1 biochip containing 80,000 SNPs. Functional annotation was performed according to the Sscrofa11.1 assembly using the Ensembl Genome Browser.  As a result of the study, CNVs (deletions/duplications) associated with ALT, Urea, RBC, and WBC levels were identified in Large White pigs. Genes overlapping CNV regions associated with the studied blood parameters in pigs were identified: ALT (BBS9, TTC14, KCND3, TRPC1, PSMD1, MMP16, KCNJ3, ADAM2); Urea (ESR1, USP8, CAST, CNBD1); RBC (PSMD1, TTC14, FUT8, CSMD3); WBC (BBS9, KCND3, BMPR2). According to the functional annotation, these genes can be considered promising genetic markers for hematopoietic functions, physiological processes, and productivity phenotypes in pigs.

1. Getmantseva L., Kolosova M., Fede K., Korobeinikova A., Kolosov A., Romanets E., et al. Finding Predictors of Leg Defects in Pigs Using CNV-GWAS. Genes (Basel). 2023;14(11):2054. DOI: https://doi.org/10.3390/genes14112054

2. Bovo S., Mazzoni G., Bertolini F., Schiavo G., Galimberti G., Gallo M., et al. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Nature. Scientific Reports. 2019;9:7003. DOI: https://doi.org/10.1038/s41598-019-43297-1

3. Poklukar K., Čandek-Potokar M., Vrecl M., Batorek-Lukač N., Fazarinc G., Kress K., et al. Adipose Tissue Gene Expression of Entire Male, Immunocastrated and Surgically Castrated Pigs. International Journal of Molecular Sciences. 2021;22:1768. DOI: https://doi.org/10.3390/ijms22041768

4. Fontanesi L. Metabolomics and livestock genomics: Insights into a phenotyping frontier and its applications in animal breeding. Animal Frontiers. 2016;6(1):73–79. DOI: https://doi.org/10.2527/af.2016-0011

5. Koshkina O. A., Deniskova T. E., Zinovieva N. A. Copy number variation (CNV) as a promising genetic marker: distribution, validation methods and candidate genes in genomes of livestock species (review). Agrarnaya nauka EvroSevero-Vostoka = Agricultural Science Euro-North-East. 2020;21(4):355-368. (In Russ.). DOI: https://doi.org/10.30766/2072-9081.2020.21.4.355-368

6. Shao X., Lv N., Liao J., Long J., Xue R., Ai N., et al. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC Medical Genetics. 2019;20(1):175. DOI: https://doi.org/10.1186/s12881-019-0909-5

7. Hilger A. C., Dworschak G. C., Reutter H. M. Lessons Learned from CNV Analysis of Major Birth Defects. International Journal of Molecular Sciences. 2020;21(21):8247. DOI: https://doi.org/10.3390/ijms21218247

8. Wright D., Boije H., Meadows J. R., Bed'hom B., Gourichon D., Vieaud A., et al. Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens. PLoS genetics. 2009;5(6):e1000512. DOI: https://doi.org/10.1371/journal.pgen.1000512

9. Sundström E., Imsland F., Mikko S., Wade C., Sigurdsson S., Pielberg G. R., et al. Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses. BMC Genomics. 2012;13:365. DOI: https://doi.org/10.1186/1471-2164-13-365

10. Hillbertz S., Isaksson N. H., Karlsson M., Hellmén E. K., Pielberg E., Savolainen G. R., et al. Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nature genetics. 2007;39:1318–1320. DOI: https://doi.org/10.1038/ng.2007.4

11. Sun G., Liang X., Qin K., Qin Y., Shi X., Cong P., et al. Functional Analysis of KIT Gene Structural Mutations Causing the Porcine Dominant White Phenotype Using Genome Edited Mouse Models. Frontiers in genetics. 2020;11:138. DOI: https://doi.org/10.3389/fgene.2020.00138

12. Zappaterra M., Gioiosa S., Chillemi G., Zambonelli P., Davoli R. Muscle transcriptome analysis identifies genes involved in ciliogenesis and themolecular cascade associatedwith intramuscular fat content in LargeWhite heavy pigs. PLoS One. 2020;15:e0233372. DOI: https://doi.org/10.1371/journal.pone.0233372

13. Dauben C. M., Pröll-Cornelissen M. J., Heuß E. M., Appel A. K., Henne H., Roth K., et al. Genome-wide associations for immune traits in two maternal pig lines. BMC Genomics. 2021;22:717. DOI: https://doi.org/10.1186/s12864-021-07997-1

14. Ghomsi S. O. M., Pechangou S. N., Maafo R. S., Mouafo H. T., Etchu A. K., Bilong F. C. B., Moundipa P. F. Assessment of the digestibility, growth performance, hematological and serum biochemical profile of Bandjock Local Pigs (BLP) and Duroc X Large White pigs (DLW). Journal Veterinary and Animal Science. 2024;25:100370. DOI: https://doi.org/10.1016/j.vas.2024.100370

15. Al-Mat'hammi A. A., Alzahrani S. A., Alsefry F. S., Ghurab S., Alghamdi M. Homozygous Pathogenic Variant in BBS9 Gene: A Detailed Case Study of Bardet-Biedl Syndrome. Cureus. 2024;16(7):e65774. DOI: https://doi.org/10.7759/cureus.65774

16. Liu L., Wang W., Liu W., Li X., Yi G., Adetula A. A., et al. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. International Journal of Molecular Sciences. 2024;25(5):2874. DOI: https://doi.org/10.3390/ijms25052874

17. Hsiao C-T., Tropea T. F., Fu S-J., Bardakjian T. M., Gonzalez-Alegre P., Soong B-W., et al. Rare. Gain- of-Function KCND3 Variant Associated with Cerebellar Ataxia, Parkinsonism, Cognitive Dysfunction, and Brain Iron Accumulation. International Journal of Molecular Sciences. 2021;22(15):8247. DOI: https://doi.org/10.3390/ijms22158247

18. Lam L. K. M., Murphy S., Kokkinaki D., Venosa A., Sherrill-Mix S., Casu C., et al. DNA binding to TLR9 expressed by red blood cells promotes innate immune activation and anemia. Science Translational Medicine. 2021;13(616):eabj1008. DOI: https://doi.org/10.1126/scitranslmed.abj1008

19. Chen X., Liu G., Wu B. Analysis and experimental validation of the innate immune gene PSMD1 in liver hepatocellular carcinoma and pan-cancer. Heliyon. 2023;9(11):e21164. DOI: https://doi.org/10.1016/j.heliyon.2023.e21164

20. Lu Y-Q., Wang Y. Multi-Omic Analysis Reveals Genetic Determinants and Therapeutic Targets of Chronic Kidney Disease and Kidney Function. International Journal of Molecular Sciences. 2024;25(11):6033. DOI: https://doi.org/10.3390/ijms25116033

21. Lee W. W., Lee C. G., Ki C. S. KCNJ3 is a novel candidate gene for autosomal dominant pure hereditary spastic paraplegia identified using whole genome sequencing. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 2024;195(7):e32984. DOI: https://doi.org/10.1002/ajmg.b.32984

22. Bindesbøll C., Aas A., Ogmundsdottir M. H., Pankiv S., Reine T., Zoncu R., Simonsen A. NBEAL1 controls SREBP2 processing and cholesterol metabolism and is a susceptibility locus for coronary artery disease. Scientific reports. 2020;10:4528. DOI: https://doi.org/10.1038/s41598-020-61352-0

23. Kurbanov B. B., Kurbanov D. D., Ibragimov Z. Z. Features of ESR1 gene polymorphism in women with preeclampsy. Vestnik Natsional'nogo mediko-khirurgicheskogo Tsentra im. N. I. Pirogova = Bulletin of Pirogov National Medical & Surgical Center. 2021;16(2):58–60. (In Russ.). DOI: https://doi.org/10.25881/20728255_2021_16_2_58

24. Kitamura H. Ubiquitin-Specific Proteases (USPs) and Metabolic Disorders. Journal of Molecular Sciences. 2023;24(4):3219. DOI: https://doi.org/10.3390/ijms24043219

25. Yuan H., Wei W., Zhang Y., Li C., Zhao S., Chao Z., et al. Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China's Native Pig Breeds via Whole-Genome Resequencing. International Journal of Molecular Sciences. 2024;25(11):5843. DOI: https://doi.org/10.3390/ijms25115843

26. Hodonsky C. J., Baldassari A. R., Bien S. A., Raffield L. M., Highland H. M., Sitlani C. M., et al. Ancestryspecific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics. BMC Genomics. 2020;21:228. DOI: https://doi.org/10.1186/s12864-020-6626-9

27. Qiang Y. X., Deng Y. T., Zhang Y. R., Wang H. F., Zhang W., Dong Q., et al. Associations of blood cell indices and anemia with risk of incident dementia: A prospective cohort study of 313,448 participants. Alzheimer's & Dementia Journal. 2023;19(9):3965–3976. DOI: https://doi.org/10.1002/alz.13088

28. Shi M., Nan X-R., Liu B-Q. The Multifaceted Role of FUT8 in Tumorigenesis: From Pathways to Potential Clinical Applications. International Journal of Molecular Sciences. 2024;25(2):1068. DOI: https://doi.org/10.3390/ijms25021068

29. Xi K., Cai S. Q., Yan H. F., Tian Y., Cai J., Yang X. M., et al. CSMD3 Deficiency Leads to Motor Impairments and Autism-Like Behaviors via Dysfunction of Cerebellar Purkinje Cells in Mice. Journal of Neuroscience. 2023;43(21):3949–3969. DOI: https://doi.org/10.1523/JNEUROSCI.1835-22.2023

30. Tsyklauri O., Niederlova V., Forsythe E., Prasai A., Drobek A., Kasparek P. et al. Bardet-Biedl Syndrome ciliopathy is linked to altered hematopoiesis and dysregulated self-tolerance. EMBO Reports. 2021;22:e50785. DOI: https://doi.org/10.15252/embr.202050785

31. Amandykova M., Akhatayeva Z., Kozhakhmet A., Kapassuly T., Orazymbetova Z., Yergali K., et al. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat–Wool Sheep Breed. Genes. 2023;14(11):1988. DOI: https://doi.org/10.3390/genes14111988