Genome-wide association study and gene ontology for growth and wool characteristics in Zandi sheep

Document Type : Original Research Article (Regular Paper)


1 Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Tabriz, East Azerbaijan, Iran.

2 Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Markazi, Iran.

3 Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran.


Genome-wide association studies (GWAS) is a major procedure for studying the genetics of complex economically important traits in sheep. The objective of this study was to determine the genomic regions affecting some growth traits and wool characteristics in Zandi sheep. This study is GWAS implementing a medium-density single nucleotide polymorphism (SNP) panel to determine the putative chromosome area affecting some growth and wool traits in a fat-tailed sheep breed, simultaneously. We used a selective genomic approach sampling DNA from animals at the extreme ends using the estimated breeding values derived from a total population size of over 5,000 animals. The examined phenotypic data included the birth weight, weaning weight, 6, 9, and 12-months after birth weight, pre- and post-weaning average daily gain, fiber diameter (micron), prickle factor (%), staple length (mm), kemp (%) and medullated fiber. Genome-wide association analyses were performed based on the mixed linear model. Twenty-three regions, in which four were associated with more than one trait, located on 12 chromosomeswere associated with the studied growth and wool traits (p <­5×10−6). These genomic regions overlapping with KCNIP4, PPARGC1A, ASAP1, ANK2, WWOX, SYNE1, FBXO5, AKAP6, FABP3, ANGPTL4, ATP6V1B2, PARK2, and KRTAP11-1 genes, were associated with postnatal growth, regulation of metabolic pathways, skeletal muscle differentiation, and bone growth. Gene ontology term enrichment analysis revealed that genes involved in positive regulation of muscle structure, and muscle tissue development were over-represented in the identified candidate genes.


Main Subjects

  • Abdoli, R., Mirhoseini, S., Hossein-Zadeh, N.G., Zamani, P., Moradi, M.H., Ferdosi, M.H., Gondro, C., 2019. Genome-wide association study of first lambing age and lambing interval in sheep. Small Ruminant Research 178, 43-45.
  • Al-Mamun, H.A., Kwan, P., Clark, S.A., Ferdosi, M.H., Tellam, R., Gondro, C., 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.
  • Bohlouli, M., Mohammadi, H., Alijani, S., 2013. Genetic evaluation and genetic trend of  growth traits of  Zandi sheep in semi-arid Iran using random regression models. Small Ruminant Research 114, 195–201.
  • Bolormaa, S., Hayes, B.J., van der Werf, J.H.J., Pethick, D., Goddard, M.E., Daetwyler, H.D., 2016. Detailed phenotyping identifies genes with pleiotropic effects on body composition. BMC Genomics 17, 224.
  • Cavanagh, C.R., Jonas, E., Hobbs, M., Thomson, P.C., Tammen, I., Raadsma, H.W., 2010. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. Genetics Selection Evolution 42, 36.
  • Chang, C.C., Chow, C.C., Tellier, L.C.A.M., Vattikuti, S., Purcell, S.M., Lee, J.J., 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7.
  • Ebrahimi, F., Gholizadeh, M., Rahimi-Mianji, G., Farhadi, A., 2017. Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip. Tropical Animal Health and Production 8, 1657-1662.
  • Esfandyari, H., Aslaminejad, A.A., Rafat, S.A., 2017. Wool characteristics in the third generation of Arkharmerino × Ghezel and Arkharmerino × Moghani crossbreed sheep. Tropical Animal Health and Production 7, 1337-1343.
  • Esmailizadeh, A.K., 2010. A partial genome scan to identify quantitative trait loci affecting birth weight in Kermani sheep. Small Ruminant Research 94, 73–78.
  • Gholizadeh, M., Rahimi-Mianji, G., Nejati-Javaremi, A., 2015. Genomewide association study of body weight traits in Baluchi sheep. Journal of Genetics 94, 143–146.
  • He, L.C., Li, P.H., Ma, X., Sui S.P., Gao ,S., Kim S.W. Gu Y.Q., Huang Y., Ding N.S., Huang R.H., 2017. Identification of new single nucleotide polymorphisms affecting total number born and candidate genes related to ovulation rate in Chinese Erhualian pigs. Animal Genetics 48, 48–54.
  • Hu, Z.L., Park, C.A., Reecy, J.M., 2016. Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research 44, 827–833.
  • Huang, D.W., Sherman, B.T., Lempicki, R.A., 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44–57.
  • Matika, O., Riggio, V., Anselme-Moizan M., Law A.S., Pong-Wong R., Archibald A.L., Bishop S.C., 2016. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs. Genetics Selection Evolution 48, 11.
  • Mohammadi, H., Rafat, S.A., Moradi Shahrebabak, H., Shodja, J., Moradi, M.H., 2018. An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed. Journal of Animal Science Research 28, 193-204. (In persian).
  • Pasandideh, M, Rahimi-Mianji G, Gholizadeh, M., 2018. A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep. Journal of Genetics 97, 493-503.
  • Pasandideh, M., Gholizadeh, M., Rahimi-Mianji, G., 2020. Identification of two novel SNPs affecting lambing traits in sheep by using a 50K SNP-Chip. Small Ruminant Research 191, 106193.
  • Ponz, R., Moreno, C., Allain, D., Elsen, J.M., Lantier, F., Lantier, I., Brunel, J.C., Pérez-Enciso, M., 2001. Assessment of genetic variation explained by markers for wool traits in sheep via a segment mapping approach. Mammalian Genome 12, 569–572.
  • Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Julian, M., 2007. PLINK:  a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics 81, 559-575.
  • Rogers, M.A., Langbein, L., Winter, H., Ehmann, C., Praetzel, S., Schweizer, J., 2002. Characterization of a first domain of human high glycine-tyrosine and high sulfur keratin-associated protein (KAP) genes on chromosome 21q22. The Journal of Biological Chemistry 277, 48993–49002.
  • Wang, Z., Zhang, H., Yang, H., Wang, S., Rong, E., Pei, W., Li, H., Wang, N., 2014. Genome-wide association study for wool production traits in a Chinese Merino sheep population. PLoS One 9, e107101.
  • Weng, Z., Su, H., Saatchi, M., Lee, J., Thomas, M.G., Dunkelberger, J.R., Garrick, D.J., 2016. Genome-wide association study of growth and body composition traits in Brangus beef cattle. Livestock Science 183, 4–11.
  • Xu, S.S., Ren, X., Yang, GL., Xie, X.L., Zhao, Y.X., Zhang, M., Shen, Z.Q., Ren, Y.L., Gao, L., Shen, M., Kantanen, J., Li, M.H., 2017. Genome-wide association analysis identifies the genetic basis of fat deposition in the tails of sheep (Ovis aries). Animal Genetics 48, 560-569.
  • Zhang, H., Wang, Z., Wang, S., Li, H., 2012. Progress of genome wide association study in domestic animals. Journal of Animal Science and Biotechnology 3, 26.
  • Zhang, L., Liu, J., Zhao, F., Ren, H., Xu, L., Lu, J., Zhang, S., Zhang, X., Wei, C., Lu, G., 2013. Genome-wide association studies for growth and meat production traits in sheep. PLoS One 8, e66569.