Correo Electrónico
DNINFOA - SIA
Bibliotecas
Convocatorias
Identidad U.N.
Published
Genome-wide association study on growth traits in Colombian Hair Sheep
Estudios de asociación en genoma completo para caracteres de crecimiento en Ovinos de Pelo Colombiano
DOI:
https://doi.org/10.15446/rfnam.v77n1.105408Keywords:
Creole sheep, GWAS, Live weight, Microarray, SNPs, Weight gain (en)Ovino criollo, GWAS, Peso vivo, Microarreglo, SNPs, Ganancia de peso (es)
The Colombian hair sheep have characteristics of great interest, among the following: high capacity for adaptation, good fertility, high prolifically, and low presence of diseases, which have been little studied. Currently, genome-wide association studies (GWAS) have been widely used to detect and locate candidate genes. However, in sheep, there is a low number of investigations carried out in GWAS, because the available information is limited, compared to that of other species. This research aimed to conduct a genome wide association study on muscle growth traits using the Illumina OvineSNPs50 BeadChip array. A GWAS using 54.241 single nucleotide polymorphisms (SNPs) was conducted in Ethiopian (44 individuals), Sudan (63), and Pelibuey (60) breeds of Creole hair sheep to evaluate eight growth traits. Quality control was performed using a linear regression model in PLINK. Moreover, a functional analysis was done in the KEGG database using the Ovis aries (sheep) genome v.3.1. In total, 44.396 SNPs that passed quality control were used for the analysis. The 10 most significant SNPs were identified for each trait. The functional analysis allowed the annotating of four candidate genes, namely CEP135, EMCN, PAM, and PIAS2, as the most relevant genes for the traits assessed. Additionally, 27 genes associated with phenotypic traits were considered promising and could also be influencing growth traits. This is the first GWAS on Colombian hair sheep to report genomic traits associated with muscle growth traits. Four candidate genes (CEP135, EMCN, PAM, and PIAS2) associated with eight growth traits were identified by genome-wide association in colombian hair sheep.
Los Ovinos de Pelo Colombiano tienen características de gran interés, entre ellas se resaltan: alta capacidad de adaptación, buena fertilidad, alta prolificidad y baja presencia de enfermedades que han sido poco estudiadas. Actualmente, los estudios de asociación de genoma completo (GWAS) han sido ampliamente usados para detectar y localizar genes candidatos. Sin embargo, en ovinos se cuenta con un bajo número de investigaciones al respecto, debido a que la información disponible se encuentra limitada, en comparación con la de otras especies. El objetivo de esta investigación fue realizar un análisis genómico asociado a caracteres de crecimiento muscular, mediante el uso del microarreglo OvineSNP50 BeadChip de Illumina. Se realizó un GWAS empleando 54,241 polimorfismos de nucleótido simple (SNPs), en ovinos de pelo criollo, en el cual se evaluaron las variedades raciales Etíope (44), Sudán (63) y Pelibuey (60), para ocho caracteres de crecimiento. Se llevó a cabo un control de calidad a través del programa PLINK, por medio de un modelo de regresión lineal. Posteriormente se hizo un análisis funcional, empleando el genoma ovino Ovis aries v.3.1, en la base de datos de KEGG. Después de haber realizado el control de calidad, se analizaron 44,396 SNP. Se identificaron los 10 SNPs más significativos para cada carácter. A través del análisis funcional se logró anotar cuatro posibles genes candidatos (CEP135, EMCN, PAM y PIAS2), como los más importantes en los caracteres evaluados. Adicionalmente, se encontraron 27 genes asociados a los caracteres fenotípicos, los cuales pueden ser prometedores y podrían estar influyendo en los caracteres de crecimiento. Este trabajo es el primer GWAS en ovinos de pelo colombiano en el país, que ha asociado caracteres fenotípicos de crecimiento muscular con caracteres genómicos. El GWAS permitió identificar cuatro posibles genes candidatos (CEP135, EMCN, PAM y PIAS2), asociados a ocho caracteres de crecimiento.
References
AI-Mamun HA, Kwan P, Clark SA, Ferdosi MH et al (2015) Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genetics Selection Evolution 47: 66. https://doi.org/10.1186/s12711-015-0142-4
Romero H, Vanegas R, Riveros E and Arcos D (2002) Ovinos colombianos de pelo: Alternativa productiva para el sur del departamento del Tolima. PE: Corporación Colombiana de Investigación Agropecuaria, Corpoica. Ibagué, Colombia. 78 p. http://hdl.handle.net/20.500.12324/12831
Barrett JC, Fry B, Maller J and Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2): 263-265. https://doi.org/10.1093/bioinformatics/bth457
Burn B, Brown S and Chang C (2011) Regulation of Early Xenopus Development by the PIAS genes. Developmental Dynamics: an official publication of the American Association of Anatomists 240(9): 2120–2126. https://doi.org/10.1002/dvdy.22701
Casas E and White SN (2015) Aplicación de la genómica en características de importancia económica en poblaciones ovinas. pp 35. In: memorias del X seminario internacional de producción de ovinos en el trópico; november 23-26: Villa Hermosa, Tabasco, México.
Corpoica - Corporación Colombiana de Investigación Agropecuaria (2007) Manual para el manejo de las razas criollas ovino de pelo y caprino dentro del plan fomento. PE: Produmedios. Cundinamarca, Colombia. 52 p. http://hdl.handle.net/20.500.12324/13251
Gholizadeh M, Rahimi-Mianji G and Nejati-Javaremi A (2015) Genomewide association study of body weight traits in Baluchi sheep. Journal of Genetics 94(1): 143–146. https://doi.org/10.1007/s12041-015-0469-1
Gogarten SM, Bhangale T, Conomos MP, Laurie CA, McHugh CP et al (2012) GWASTools: an R/Bioconductor package for quality control and analysis of Genome-Wide Association Studies. Bioinformatics 28: 3329–3331. https://doi.org/10.1093/bioinformatics/bts610
Hussain MS, Baig SM, Neumann S, Nürnberg G, Farooq M et al (2012) A truncating mutation of CEP135 causes primary microcephaly and disturbed centrosomal function. American Journal of Human Genetics 90(5): 871–878. https://doi.org/10.1016/j.ajhg.2012.03.016
Kemper KE, Visscher PM and Goddard ME (2012) Genetic architecture of body size in mammals. Genome Biology 13: 244. https://doi.org/10.1186/gb4016
Knapik J, Ropka-Molik K and Pieszka M (2017) Genetic and nutritional factors determining the production and quality of sheep meat – a review. Annals of Animal Science 17(1): 23–40. https://doi.org/10.1515/aoas-2016-0036
Kominakis A, Hager-Theodorides AL, Zoidis E, Saridaki A et al (2017) Combined GWAS and ‘guilt by association’ based prioritization analysis identifies functional candidate genes for body size in sheep. Genetics Selection Evolution 49: 41. https://doi.org/10.1186/s12711-017-0316-3
Kullander K and Klein R (2002) Mechanisms and functions of Eph and ephrin signalling. Nature Reviews Molecular Cell Biology 3(7): 475-486. https://doi.org/10.1038/nrm856
Kumar A, Rajendran V, Sethumadhavan R and Purohit R (2013) CEP proteins: the knights of centrosome dynasty. Protoplasma 250(5): 965-983. https://doi.org/10.1007/s00709-013-0488-9
Li J and Johnson SE (2013) Ephrin-A5 promotes bovine muscle progenitor cell migration before mitotic activation. Journal of Animal Science 91(3): 1086-1093. https://doi.org/10.2527/jas.2012-5728
Matsuura K, Lefebvre PA, Kamiya R and Hirono M (2004) Bld10p, a novel protein essential for basal body assembly in Chlamydomonas: localization to the cartwheel, the first ninefold symmetrical structure appearing during assembly. The Journal of Cell Biology 165(5): 663–671. https://doi.org/10.1083/jcb.200402022
Merkler DJ (1994) C-terminal amidated peptides: production by the in vitro enzymatic amidation of glycine-extended peptides and the importance of the amide to bioactivity. Enzyme and Microbial Technology 16(6): 450–456. https://doi.org/10.1016/0141-0229(94)90014-0
Olfert IM, Baum O, Hellsten Y and Egginton S (2015) Advances and challenges in skeletal muscle angiogenesis. American Journal of Physiology Heart and Circulatory Physiology 310(3): H326–H336. https://doi.org/10.1152/ajpheart.00635.2015
Park-Windhol C, Ng YS, Yang J, Primo V, Saint-Geniez M and D’Amore PA (2017) Endomucin inhibits VEGF-induced endotelial cell migration, growth, and morphogenesis by modulating VEGFR2 signaling. Scientific Reports 7(1): 17138. https://doi.org/10.1038/s41598-017-16852-x
Pasquale EB (2005) Eph receptor signalling casts a wide net on cell behaviour. Nature Reviews Molecular Cell Biology 6: 462-475. https://doi.org/10.1038/nrm1662
Peng WF, Xu SS, Ren X, Lv FH, Xie XL et al (2017) A genome-wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep (Ovis aries). Animal Genetics 48(5): 570-579. https://doi.org/10.1111/age.12575
Prigge ST, Mains RE, Eipper BA and Amzel LM (2000) New insights into copper monooxygenases and peptide amidation: structure, mechanism and function. Cellular and Molecular Life Sciences 57(8): 1236–1259. https://doi.org/10.1007/pl00000763
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA et al (2007) PLINK: a tool set for whole-genome association and populationbased linkage analyses. American Journal of Human Genetics 81(3): 559-575. https://doi.org/10.1086/519795
Roberts PJ and Der CJ (2007) Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer. Oncogene 26(22): 3291-3310. https://doi.org/10.1038/sj.onc.1210422
Traci AC, Ning Y, Hsu M, Peng B et al (2005) Deletion of peptide amidation enzymatic activity leads to edema and embryonic lethality in the mouse. Developmental Biology 287(2): 301-313. https://doi.org/10.1016/j.ydbio.2005.09.001
Vergara GO, Medina H, Sierra RC, Simanca SJ and Bustamante YM (2017) Determinación de la curva de crecimiento en ovinos criollos de pelo, mediante la utilización del modelo Gompertz, en el trópico bajo colombiano. Revista UDCA. Actualidad & Divulgación Científica 20(2): 385-391. https://doi.org/10.31910/rudca.v20.n2.2017.396
Vergara-Garay O, Llorente-Martínez E, Ramos-Caro L, BustamanteYánez M and Simanca-Sotelo JC (2016) Descripción del crecimiento en ovinos criollos utilizando el modelo Brody. Orinoquía 20(2): 34-9. https://doi.org/10.22579/20112629.351
Yu G and He Q (2016) ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular Biosystems 12(2): 477-479. https://doi.org/10.1039/C5MB00663E
Zhang L, Liu J, Zhao F, Ren H, Xu L et al (2013) Genome-Wide Association Studies for Growth and Meat Production Traits in Sheep. PLoS One 8(6): e66569. https://doi.org/10.1371/journal.pone.0066569
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C and Weir BS (2012) A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics. 28: 3326–3328. https://doi.org/10.1093/bioinformatics/bts606
Zuleta SM, Roncallo FB, Ávila ME, Mojica RJE, Castro RE and Rodríguez FG (2009) Manejo de ovinos de pelo en el trópico. PE: Produmedios. Bogotá, Colombia. 59 p.
How to Cite
APA
ACM
ACS
ABNT
Chicago
Harvard
IEEE
MLA
Turabian
Vancouver
Download Citation
CrossRef Cited-by
1. Eymen Demir, Umit Bilginer, Huriye Doğru, Burak Karacaören, Hasan Meydan, Zeynep Çiftçi, Serdar Yağci, Sarp Kaya, Taki Karsli. (2026). Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS. Mammalian Genome, 37(1) https://doi.org/10.1007/s00335-026-10203-w.
2. Menghua Li, Hosein Salehian Dehkordi. (2026). Domestic and Wild Sheep. , p.259. https://doi.org/10.1016/B978-0-443-43994-0.00006-X.
Dimensions
PlumX
Article abstract page views
Downloads
License
Copyright (c) 2024 Revista Facultad Nacional de Agronomía Medellín
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
The journal allows the author(s) to maintain the exploitation rights (copyright) of their articles without restrictions. The author(s) accept the distribution of their articles on the web and in paper support (25 copies per issue) under open access at local, regional, and international levels. The full paper will be included and disseminated through the Portal of Journals and Institutional Repository of the Universidad Nacional de Colombia, and in all the specialized databases that the journal considers pertinent for its indexation, to provide visibility and positioning to the article. All articles must comply with Colombian and international legislation, related to copyright.
Author Commitments
The author(s) undertake to assign the rights of printing and reprinting of the material published to the journal Revista Facultad Nacional de Agronomía Medellín. Any quotation of the articles published in the journal should be made given the respective credits to the journal and its content. In case content duplication of the journal or its partial or total publication in another language, there must be written permission of the Director.
Content Responsibility
The Faculty of Agricultural Sciences and the journal are not necessarily responsible or in solidarity with the concepts issued in the published articles, whose responsibility will be entirely the author or the authors.
