Zeraatpisheh, Y., Zerehdaran, S., Javadmanesh, A. (2023). Investigation of metabolic pathways related to the QTLs of parasite resistance trait in sheep genome using gene network and gene ontology. , 36(1), 83-90. doi: 10.22092/vj.2022.357660.1941
Yasaman Zeraatpisheh; Saeed Zerehdaran; Ali Javadmanesh. "Investigation of metabolic pathways related to the QTLs of parasite resistance trait in sheep genome using gene network and gene ontology". , 36, 1, 2023, 83-90. doi: 10.22092/vj.2022.357660.1941
Zeraatpisheh, Y., Zerehdaran, S., Javadmanesh, A. (2023). 'Investigation of metabolic pathways related to the QTLs of parasite resistance trait in sheep genome using gene network and gene ontology', , 36(1), pp. 83-90. doi: 10.22092/vj.2022.357660.1941
Zeraatpisheh, Y., Zerehdaran, S., Javadmanesh, A. Investigation of metabolic pathways related to the QTLs of parasite resistance trait in sheep genome using gene network and gene ontology. , 2023; 36(1): 83-90. doi: 10.22092/vj.2022.357660.1941

Investigation of metabolic pathways related to the QTLs of parasite resistance trait in sheep genome using gene network and gene ontology

تحقیقات دامپزشکی و فرآورده‌های بیولوژیک
Article 12, Volume 36, Issue 1, March 2023, Pages 83-90    PDF (990.76 K)
Document Type: Full Research Paper
DOI: 10.22092/vj.2022.357660.1941
Authors
Yasaman Zeraatpisheh1; Saeed Zerehdaran2; Ali Javadmanesh* 2
1epartment of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad
2Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad
Abstract
In recent decades, advances in DNA-based marker technology and the availability of genomic data such as quantitative trait locus and the study of gene utilization through bioinformatics methods have played an important role in understanding the genetic potential of different traits. In this study, QTLs related to parasite resistance in sheep were prepared through Animal QTL database. The genes for each QTL were then obtained from the sheep reference genome in the NCBI database. Next, in order to understand the relationship between the obtained genes, gene networks for each trait were drawn using Cytoscape v3.8.0 software, and finally Cytoscape software was used to interpret gene networks and study gene ontology. The results of this study showed that there were a total of 71 QTLs for the parasite resistance trait, which included 198 genes. Most of these markers were mapped using methods such as the Genome-Wide Association Study (GWAS), Regional Heritability Mapping (RHM), or Single Nucleotide Polymorphisms (SNPs). Ontological analysis in this study showed 20 biological pathways that four pathways contributed more than others, including: pyruvate metabolic process, antigen processing and presentation of peptide antigen via MHC class I, neural migration and cell adhesion molecule binding. In this study, the ontology of genes was investigated and the metabolic pathways associated with the parasite resistance trait in sheep were obtained through QTLs. Regarding methods and result of the current study, genes and gene ontology associated with other economic traits in sheep a well as other livestock species could be determined.
Keywords
Ontology; QTL; Marker; Parasite
References

1-Al Kalaldeh, M., J. Gibson, S. H. Lee, C. Gondro and J. H. Van Der Werf. 2019. Detection of genomic regions underlying resistance to gastrointestinal parasites in Australian sheep. Genetics Selection Evolution 51: 1-18.
2- Alcaraz, N., H. Kücük, J. Weile, A. Wipat and J. Baumbach. 2011. KeyPathwayMiner: detecting case-specific biological pathways using expression data. Internet Mathematics 7: 299-313.
3-Alipanah, M., Z. Roudbari, A. Javadmanesh, M. Setaei Mokhtari, H. R. Seyedabadi and F. Gharari. 2018. Identification of biological pathways involved in body growth of cattle using gene expression profiles. Animal Sciences Journal 31: 59-70.
4- Bakhshalizadeh, S., S. Zerehdaran and A. Javadmanesh. 2021. Meta-analysis of genome-wide association studies and gene networks analysis for milk production traits in Holstein cows. Livestock Science 250: 104605.
5- Benavides, M. V., T. S. Sonstegard, S. Kemp, J. M. Mugambi, J. P. Gibson, R. L. Baker, O. Hanotte, K. Marshall and C. Van Tassell. 2015. Identification of novel loci associated with gastrointestinal parasite resistance in a Red Maasai x Dorper backcross population. PloS one 10: e0122797.
6- Benavides, M. V., T. S. Sonstegard and C. Van Tassell. 2016. Genomic regions associated with sheep resistance to gastrointestinal nematodes. Trends in parasitology 32: 470-480.
7- Beraldi, D., A. F. McRae, J. Gratten, J. G. Pilkington, J. Slate, P. M. Visscher and J. M. Pemberton. 2007. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries). International Journal for Parasitology 37: 121-129.
8- Brown, D. and N. Fogarty. 2016. Genetic relationships between internal parasite resistance and production traits in Merino sheep. Animal Production Science 57: 209-215.
9- Chikweto, A., K. Tiwari, M. I. Bhaiyat, J. Carloni, K. Pashaian, A. Pashaian, C. De Allie and R. N. Sharma. 2018. Gastrointestinal parasites in small ruminants from Grenada, West Indies: A coprological survey and a review of necropsy cases. Veterinary Parasitology: Regional Studies and Reports 13: 130-134.
10- Chung, H.-J., M. Kim, C. H. Park, J. Kim and J. H. Kim. 2004. ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Research 32: W460-W464.
11- Cockett, N. 2006. The sheep genome. Vertebrate Genomes 2: 79-85.
12- Consortium, C. T. 2003. The nature and identification of quantitative trait loci: a community’s view. Nature Reviews Genetics 4: 911.
13- Consortium, G. O. 2008. The gene ontology project in 2008. Nucleic Acids Research 36: D440-D444.
14- Dessimoz, C. and N. Škunca. 2017. The gene ontology handbook. Springer Nature.
15- Diez-Tascón, C., O. M. Keane, T. Wilson, A. Zadissa, D. L. Hyndman, D. B. Baird, J. C. McEwan and A. M. Crawford. 2005. Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep. Physiological Genomics 21: 59-69.
16- Heino, M. Section. 2014. Quantitative traits.  59-76.  Stock identification methods. Elsevier; 
17- Hu, Z.-L., C. A. Park and J. M. Reecy. 2022. Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services. Nucleic Acids Research 50: D956-D961.
18- Hu, Z.-L., C. A. Park, X.-L. Wu and J. M. Reecy. 2013. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Research 41: D871-D879.
19- Jiang, L., P. Sørensen, B. Thomsen, S. M. Edwards, A. Skarman, C. M. Røntved, M. S. Lund and C. T. Workman. 2012. Gene prioritization for livestock diseases by data integration. Physiological Genomics 44: 305-317.
20- Lopez, B. I., K. G. Santiago, D. Lee, S. Ha and K. Seo. 2020. RNA sequencing (RNA-Seq) based transcriptome analysis in immune response of Holstein cattle to killed vaccine against bovine viral diarrhea virus type I. Animals 10: 344.
21- Marshall, K., J. Maddox, S. H. Lee, Y. Zhang, L. Kahn, H. U. Graser, C. Gondro, S. W. Walkden‐Brown and J. Van Der Werf. 2009. Genetic mapping of quantitative trait loci for resistance to Haemonchus contortus in sheep. Animal Genetics 40: 262-272.
22- Marshall, K., J. Mugambi, S. Nagda, T. Sonstegard, C. Van Tassell, R. Baker and J. P. Gibson. 2013. Quantitative trait loci for resistance to H aemonchus contortus artificial challenge in R ed M aasai and D orper sheep of E ast A frica. Animal Genetics 44: 285-295.
23- Mohammadi, F., M. Tahmoorespur and A. Javadmanesh. 2019. Study of differentially expressed genes, related pathways and gene networks in sheep fetal muscle tissue in thin-and fat-tailed breeds. Animal Science Journal (Pajouhesh and Sazandegi) 32(123): 301-312.
24- Quan, S., X. Nan, K. Wang, L. Jiang, J. Yao and B. Xiong. 2019. Different Diets Change the Expression of Bovine Serum Extracellular Vesicle-miRNAs. Animals 9: 1137.
25- Riggio, V., O. Matika, R. Pong-Wong, M. Stear and S. Bishop. 2013. Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs. Heredity 110: 420-429.
26- Sayre, B. and G. Harris. 2012. Systems genetics approach reveals candidate genes for parasite resistance from quantitative trait loci studies in agricultural species. Animal Genetics 43: 190-198.
27- Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski and T. Ideker. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498-2504.
28- Shin, M.-K., H.-T. Park, S. W. Shin, M. Jung, Y. B. Im, H.-E. Park, Y.-I. Cho and H. S. Yoo. 2015. Whole-blood gene-expression profiles of cows infected with Mycobacterium avium subsp. paratuberculosis reveal changes in immune response and lipid metabolism. Journal of Microbiology and Biotechnology 25: 255-267.
29- Squire, S., I. Robertson, R. Yang, I. Ayi and U. Ryan. 2019. Prevalence and risk factors associated with gastrointestinal parasites in ruminant livestock in the Coastal Savannah zone of Ghana. Acta Tropica 199: 105126.
30- Zhang, L., J. Liu, F. Zhao, H. Ren, L. Xu, J. Lu, S. Zhang, X. Zhang, C. Wei and G. Lu. 2013. Genome-wide association studies for growth and meat production traits in sheep. PloS One 8: e66569.

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