Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep

Antonios Kominakis; Aggeliki Saridaki; George Antonakos

doi:doi:10.11648/j.ijgg.20190704.13

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Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep

Antonios Kominakis, Aggeliki Saridaki, George Antonakos

Published in International Journal of Genetics and Genomics (Volume 7, Issue 4)

Received: 18 July 2019 Accepted: 11 September 2019 Published: 21 October 2019

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Abstract

Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were detected by application of a multi-locus mixed model treating markers as fixed additive effects. Positional candidate genes identified within 1Mb flanking distances from significant markers were in silico prioritized based on their functional similarity to a training gene list including 1,120 genes associated with the term ‘immunity’. Association analysis pinpointed 4 chromosome-wide significant SNPs dispersed on four autosomes (OAR2, OAR18, OAR19 and OAR22). A total number of 37 positional candidate genes were identified within the searched genomic distances while 13 candidate genes were highly prioritized. Seven highly prioritized genes (NFIB, GFRA1, PSIP1, ARHGAP5, HECTD1, EMX2, STRN3) along with genes FREM1 and GPR33 had evidenced involvement in immune-related processes. Current results extent previous findings by providing novel candidate genes for the somatic cell count phenotype in dairy sheep.

Published in	International Journal of Genetics and Genomics (Volume 7, Issue 4)
DOI	10.11648/j.ijgg.20190704.13
Page(s)	103-109
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Somatic Cell Count, Mastitis, Dairy Sheep, GWAS, Prioritization Analysis

References

[1]	Bergonier D, de Crémoux R, Rupp R, Lagriffoul G and Berthelot X. 2003. Mastitis of dairy small ruminants. Vet Res 34: 689-716.
[2]	Barillet F, Rupp R, Mignon-Grasteu S, Astruc JM and Jacquin M. 2001. Genetic analysis for mastitis resistance and milk somatic cell score in French Lacaune dairy sheep. Genet Sel Evol 33: 397–415.
[3]	Paape MJ, Poutrel B, Contreras A, Marco JC and Capuco AV. 2001. Milk somatic cells and lactation in small ruminants. J Dairy Sci 84, Supplement, E237-E244.
[4]	Persson-Waller K, Colditz IG and Seow HF. 1997 Accumulation of leucocytes and cytokines in the lactating ovine udder during mastitis due to Staphylococcus aureus and Escherichia coli. Res Vet Sci 62: 63-66.
[5]	Gutiérrez-Gil B, El-Zarei MF, Bayón Y, Alvarez L, de la Fuente LF, San Primitivo F and Arranz JJ 2007. Short communication: detection of quantitative trait loci influencing somatic cell score in Spanish Churra sheep. J Dairy Sci 90: 422-426.
[6]	Barillet F, Arranz JJ, Carta A, Jacquiet P, Stear M and Bishop S 2006. Final consolidated report of the European Union contract of acronym "genesheepsafety" (QTLK5-CT-2000-00656) p. 145.
[7]	Raadsma HW, Jonas E, McGill D, Hobbs M, Lam MK and Thomson PC 2009. Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep. Genet Sel Evol 41: 45.
[8]	Rupp R, Senin P, Sarry J, Allain C, Tasca C, Ligat L, Portes D, Woloszyn F, Bouchez O, Tabouret G, Lebastard M, Caubet C, Foucras G and Tosser-Klopp G 2015. A point mutation in suppressor of cytokine Signalling 2 (Socs2) increases the susceptibility to inflammation of the mammary gland while associated with higher body weight and size and higher milk production in a sheep model. PLoS Genet 11, e1005629.
[9]	Bonnefont CM, Toufeer M, Caubet C, Foulon E, Tasca C, Aurel MR, Bergonier D, Boullier S, Robert-Granié C, Foucras G and Rupp R 2011. Transcriptomic analysis of milk somatic cells in mastitis resistant and susceptible sheep upon challenge with Staphylococcus epidermidis and Staphylococcus aureus. BMC Genomics 12: 208.
[10]	Banos G, Bramis G, Bush SJ, Clark EL, McCulloch MEB, Smith J, Schulze G, Arsenos G, Hume DA and Psifidi A 2017. The genomic architecture of mastitis resistance in dairy sheep. BMC Genomics 18, 624.
[11]	Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M and 2012. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nature Genetics 44: 825-830.
[12]	Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S and Buckler ES 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38: 203-208.
[13]	Sheeter D, Du P, Rought S, Richman D and Corbeil J 2003. Surface CD4 expression modulated by a cellular factor induced by HIV type 1 infection. AIDS Res Hum Retroviruses 19: 117-123.
[14]	Esseghir S, Todd SK, Hunt T, Poulsom R, Plaza-Menacho I, Reis-Filho JS and Isacke CM 2007. A role for glial cell derived neurotrophic factor induced expression by inflammatory cytokines and RET/GFR alpha 1 receptor up-regulation in breast cancer. Cancer Res 67: 11732-11741.
[15]	Passaes CP, Cardoso CC, Caetano DG, Teixeira SL, Guimarães ML, Campos DP, Veloso VG, Babic DZ, Stevenson M, Moraes MO and Morgado MG 2014. Association of single nucleotide polymorphisms in the lens epithelium-derived growth factor (LEDGF/p75) with HIV-1 infection outcomes in Brazilian HIV-1+ individuals. PLoS One 9, e101780.
[16]	Zhou Z, Jiang R, Yang X, Guo H, Fang S, Zhang Y, Cheng Y, Wang J, Yao H and Chao J 2018. circRNA mediates silica-induced macrophage activation via HECTD1/ZC3H12A-dependent ubiquitination. Theranostics 8: 575-592.
[17]	Zhang Y, Cao G, Yuan QG, Li JH and Yang WB 2017. Empty spiracles homeobox 2 (EMX2) inhibits the invasion and tumorigenesis in colorectal cancer cells. Oncol Res 25: 537-544.
[18]	Luo M, Sainsbury J, Tuff J, Lacap PA, Yuan XY, Hirbod T, Kimani J, Wachihi C, Ramdahin S, Bielawny T, Embree J, Broliden K, Ball TB and Plummer FA 2012. A genetic polymorphism of FREM1 is associated with resistance against HIV Infection in the Pumwani sex worker cohort. J Virol 86: 11899–11905.
[19]	Bohnekamp J, Böselt I, Saalbach A, Tönjes A, Kovacs P, Biebermann H, Manvelyan HM, Polte T, Gasperikova D, Lkhagvasuren S, Baier L, Stumvoll M, Römpler H and Schöneberg T 2010. Involvement of the chemokine-like receptor GPR33 in innate immunity. Biochem Biophys Res Commun 396: 272–277.
[20]	Brodie A, Azaria JR and Ofran Y 2016 How far from the SNP may the causative genes be? Nucleic Acids Res 44: 6046-6054.
[21]	Kominakis Α, Hager-Theodorides ΑL, Saridaki Α, Zoidis Ε, Antonakos G and Tsiamis G 2017. Combined GWAS and 'guilt by association' based prioritization analysis identified functional candidate genes for body size in sheep. Genet Sel Evol 49, 41.

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APA Style

Antonios Kominakis, Aggeliki Saridaki, George Antonakos. (2019). Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep. International Journal of Genetics and Genomics, 7(4), 103-109. https://doi.org/10.11648/j.ijgg.20190704.13

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ACS Style

Antonios Kominakis; Aggeliki Saridaki; George Antonakos. Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep. Int. J. Genet. Genomics 2019, 7(4), 103-109. doi: 10.11648/j.ijgg.20190704.13

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AMA Style

Antonios Kominakis, Aggeliki Saridaki, George Antonakos. Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep. Int J Genet Genomics. 2019;7(4):103-109. doi: 10.11648/j.ijgg.20190704.13

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@article{10.11648/j.ijgg.20190704.13,
  author = {Antonios Kominakis and Aggeliki Saridaki and George Antonakos},
  title = {Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep},
  journal = {International Journal of Genetics and Genomics},
  volume = {7},
  number = {4},
  pages = {103-109},
  doi = {10.11648/j.ijgg.20190704.13},
  url = {https://doi.org/10.11648/j.ijgg.20190704.13},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20190704.13},
  abstract = {Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were detected by application of a multi-locus mixed model treating markers as fixed additive effects. Positional candidate genes identified within 1Mb flanking distances from significant markers were in silico prioritized based on their functional similarity to a training gene list including 1,120 genes associated with the term ‘immunity’. Association analysis pinpointed 4 chromosome-wide significant SNPs dispersed on four autosomes (OAR2, OAR18, OAR19 and OAR22). A total number of 37 positional candidate genes were identified within the searched genomic distances while 13 candidate genes were highly prioritized. Seven highly prioritized genes (NFIB, GFRA1, PSIP1, ARHGAP5, HECTD1, EMX2, STRN3) along with genes FREM1 and GPR33 had evidenced involvement in immune-related processes. Current results extent previous findings by providing novel candidate genes for the somatic cell count phenotype in dairy sheep.},
 year = {2019}
}

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TY  - JOUR
T1  - Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep
AU  - Antonios Kominakis
AU  - Aggeliki Saridaki
AU  - George Antonakos
Y1  - 2019/10/21
PY  - 2019
N1  - https://doi.org/10.11648/j.ijgg.20190704.13
DO  - 10.11648/j.ijgg.20190704.13
T2  - International Journal of Genetics and Genomics
JF  - International Journal of Genetics and Genomics
JO  - International Journal of Genetics and Genomics
SP  - 103
EP  - 109
PB  - Science Publishing Group
SN  - 2376-7359
UR  - https://doi.org/10.11648/j.ijgg.20190704.13
AB  - Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were detected by application of a multi-locus mixed model treating markers as fixed additive effects. Positional candidate genes identified within 1Mb flanking distances from significant markers were in silico prioritized based on their functional similarity to a training gene list including 1,120 genes associated with the term ‘immunity’. Association analysis pinpointed 4 chromosome-wide significant SNPs dispersed on four autosomes (OAR2, OAR18, OAR19 and OAR22). A total number of 37 positional candidate genes were identified within the searched genomic distances while 13 candidate genes were highly prioritized. Seven highly prioritized genes (NFIB, GFRA1, PSIP1, ARHGAP5, HECTD1, EMX2, STRN3) along with genes FREM1 and GPR33 had evidenced involvement in immune-related processes. Current results extent previous findings by providing novel candidate genes for the somatic cell count phenotype in dairy sheep.
VL  - 7
IS  - 4
ER  -

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Author Information

Antonios Kominakis

Department of Animal Science, Agricultural University of Athens, Athens, Greece
Aggeliki Saridaki

School of Environmental Engineering, Technical University of Crete, University Campus, Chania, Greece
George Antonakos

Agricultural and Livestock Union of Western Greece, Lepenou, Greece

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Plain Text BibTeX RIS

APA Style

Antonios Kominakis, Aggeliki Saridaki, George Antonakos. (2019). Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep. International Journal of Genetics and Genomics, 7(4), 103-109. https://doi.org/10.11648/j.ijgg.20190704.13

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ACS Style

Antonios Kominakis; Aggeliki Saridaki; George Antonakos. Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep. Int. J. Genet. Genomics 2019, 7(4), 103-109. doi: 10.11648/j.ijgg.20190704.13

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AMA Style

Antonios Kominakis, Aggeliki Saridaki, George Antonakos. Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep. Int J Genet Genomics. 2019;7(4):103-109. doi: 10.11648/j.ijgg.20190704.13

Copy | Download

@article{10.11648/j.ijgg.20190704.13,
  author = {Antonios Kominakis and Aggeliki Saridaki and George Antonakos},
  title = {Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep},
  journal = {International Journal of Genetics and Genomics},
  volume = {7},
  number = {4},
  pages = {103-109},
  doi = {10.11648/j.ijgg.20190704.13},
  url = {https://doi.org/10.11648/j.ijgg.20190704.13},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20190704.13},
  abstract = {Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were detected by application of a multi-locus mixed model treating markers as fixed additive effects. Positional candidate genes identified within 1Mb flanking distances from significant markers were in silico prioritized based on their functional similarity to a training gene list including 1,120 genes associated with the term ‘immunity’. Association analysis pinpointed 4 chromosome-wide significant SNPs dispersed on four autosomes (OAR2, OAR18, OAR19 and OAR22). A total number of 37 positional candidate genes were identified within the searched genomic distances while 13 candidate genes were highly prioritized. Seven highly prioritized genes (NFIB, GFRA1, PSIP1, ARHGAP5, HECTD1, EMX2, STRN3) along with genes FREM1 and GPR33 had evidenced involvement in immune-related processes. Current results extent previous findings by providing novel candidate genes for the somatic cell count phenotype in dairy sheep.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - Novel Candidate Genes for Somatic Cell Count in Frizarta Dairy Sheep
AU  - Antonios Kominakis
AU  - Aggeliki Saridaki
AU  - George Antonakos
Y1  - 2019/10/21
PY  - 2019
N1  - https://doi.org/10.11648/j.ijgg.20190704.13
DO  - 10.11648/j.ijgg.20190704.13
T2  - International Journal of Genetics and Genomics
JF  - International Journal of Genetics and Genomics
JO  - International Journal of Genetics and Genomics
SP  - 103
EP  - 109
PB  - Science Publishing Group
SN  - 2376-7359
UR  - https://doi.org/10.11648/j.ijgg.20190704.13
AB  - Aim of the present study was to identify genomic regions and candidate genes impacting on somatic cell count in the Frizarta dairy sheep. A total number of 482 Frizarta ewes genotyped with the medium density SNP array with available records on milk somatic cell count were used. Associations between genomic markers and the trait under study were detected by application of a multi-locus mixed model treating markers as fixed additive effects. Positional candidate genes identified within 1Mb flanking distances from significant markers were in silico prioritized based on their functional similarity to a training gene list including 1,120 genes associated with the term ‘immunity’. Association analysis pinpointed 4 chromosome-wide significant SNPs dispersed on four autosomes (OAR2, OAR18, OAR19 and OAR22). A total number of 37 positional candidate genes were identified within the searched genomic distances while 13 candidate genes were highly prioritized. Seven highly prioritized genes (NFIB, GFRA1, PSIP1, ARHGAP5, HECTD1, EMX2, STRN3) along with genes FREM1 and GPR33 had evidenced involvement in immune-related processes. Current results extent previous findings by providing novel candidate genes for the somatic cell count phenotype in dairy sheep.
VL  - 7
IS  - 4
ER  -

Copy | Download