Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip

  • 234 Accesses

  • 2 Citations


Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight. A total of three chromosome-wide significant associations were detected for SNP on chromosomes 17 and 20 affecting greasy fleece weight across the four shearing. One of the significant SNP markers was located within ovine known genes namely FAM101A. Further investigation of these identified regions in validation studies will facilitate the identification of strong candidate genes for wool production in sheep.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2


  1. Abdi, H., 2007. Bonferroni and Šidàk corrections for multiple comparisons. In Encyclopedia of Measurement and Statistics. Thousand Oaks,103-107.

  2. Allain, D., Schibler, L., Mura, L., Barillet, F. and Sechi T,. Rupp, R., Casu, S., Cribiu, E.P. and Carta, A., 2006. QTL detection with DNA markers for wool traits in a sheep backcross SARDA X LACAUNE resource population. 8th World Congress on Genetics Applied to Livestock Production.

  3. Andersson, L. and Georges, M., 2004. Domestic-animal genomics: deciphering the genetics of complex traits. Nature Review Genetics, 5, 202–212.

  4. Barrett, J.C., Fry, B., Maller, J. and Daly, M. J., 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265 .

  5. Beh, K.J., Callaghan, M.J., Leish, Z., Hulme, D.J., Lenane, I. and Maddox, J.F., 2001. A genome scan for QTL affecting fleece and wool traits in Merino sheep. Wool Technology and Sheep Breeding, 49, 88–97.

  6. Bidinost, F., Roldan, D.L., Dodero, A.M., Cano, E.M., Taddeo, H.R., Mueller, J.P. and Poli, M.A., 2008. Wool quantitative trait loci in Merino sheep. Small Ruminant Research, 74, 113–118.

  7. Cano, E.M., Daverio, S., Cáceres, M., Debenedetti, S., Costoya, S., Abad, M., Allain, D., Taddeo, H., Poli, M.A., 2009. Detection of QTL affecting fleece traits on CHI 19 in Angora goats. Trop and Subtropical Agroecosystems. 11, 189–191.

  8. Chen, H.Y., Zeng, X.C., Hui, W.Q., Zhao, Z.S., Jia, B. 2011. Developmental expression patterns and association analysis of sheep KAP8.1 and KAP1.3 genes in Chinese Merino sheep. Indian Journal of Animal Sciences, 81, 391–396.

  9. Debenedetti, S., Cano, E.M., Abad, M., Allain, D., Taddeo, H., Poli, M., 2010. Detection of QTL affecting fleece traits on CHI 5 in a backcross Angora × Creole goats in Argentina–Preliminary results. In: In Proc 9th World Congress on Genetics Applied to Livestock Production, August 1–6, 2010. Germany Communication, Leipzig, p. 0764.

  10. Fogarty, N.M., 2006. Utilization of breed resources for sheep production. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, MG, Brazil (Communication 32–10).

  11. Garcia-Gamez E., Gutierrez Gil, B., Sahana, G., Sanchez, J.P., Bayon, Y. and Arranz, J.J., 2012. GWA analysis for milk production traits in dairy sheep and genetic support for a QTN influencing milk protein percentage in the LALBA gene. PLoS One, 7, e47782.

  12. Goddard, M.E. and Hayes, B.J., 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10: 381–391.

  13. Hu, Z.L., Park, C.A., Wu, X.L. and Reecy, J.M., 2012. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Resesrch, 41, D871–9.

  14. Jiang, L., Liu, J., Sun, D., Ma, P., Ding, X., Yu, Y. and Zhang, Q., 2010. Genome wide association studies for milk production traits in Chinese Holstein population. PLoS One, 5, e13661.

  15. Johnston, S.E., McEwan, J.C., Pickering, N.K., Kijas, J.W., Beraldi, D., Pilkington, J.G., Pemberton AND J.M. and Slate, J., 2011. Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population. Molecular Ecology, 20, 2555–66.

  16. Li, Q. and Yu, K., 2008. Improved correction for population stratification in genome-wide association studies by identifying hidden population structures. Genetic Epidemiology, 32, 215–226.

  17. Ling, Y.H., Xiang, H., Zhang, G., Ding, J.P., Zhang, Z.J., Zhang, Y.H., Han, J.L., Ma, Y.H., Zhang, X.R., 2014. Identification of complete linkage disequilibrium in the DSG4 gene and its association with wool length and crimp in Chinese indigenous sheep. Genetics and Molecular Research 13, 5617–5625.

  18. Li, S., Zhou, H., Gong, H., Zhao, F., Wang, J., Liu, X., Luo, Y., Hickford, J.G.H., 2017. Identification of the Ovine Keratin-Associated Protein 22–1 (KAP22-1) Gene and its effect on wool traits. Genes, 8, 27.

  19. Ma, G-W., Chu, Y-K., Zhang, W-J., Qin, F-Y., Xu, S-S., Yang, H., Rong, E-G., Du, Z-Q., Wang, S-Z, Li, H., Wang, N. 2017. Polymorphisms of FST gene and their association with wool quality traits in Chinese Merino sheep. PLoS ONE, 12(4), e0174868.

  20. Martyniuk, C.J., Perry, G.M.L., Mogahadam, H.K., Ferguson, M.M. and Danzmann, R.G., 2003. The genetic architecture of correlations among growth related traits and male age at maturation in rainbow trout. Journal of Fish Biology, 63, 746–764.

  21. Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., et al., 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One, 4, e5350.

  22. Miller, S.A., Dykes, D.D. and Polesky, H.F., 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research, 16, 1215.

  23. Mucha, S., Bunger, Lutz. and Conington, J., 2015. Genome-wide association study of footrot in Texel sheep. Genetics Selection Evolution, 47, 35

  24. Ponz, R., Moreno, C., Allain, D., Elsen, J.M., Lantier, F., Lantier, I., Brunel, J.C. and Perez-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.

  25. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J. and Sham, P.C. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559–575.

  26. Purvis, I.W. and Franklin, I.R., 2005. Major genes and QTL influencing wool production and quality: a review. Genetic Selection Evolution, 37 (Suppl. 1), S97–S107.

  27. Roldan, D.L., Dodero, A.M., Bidinost, F., Taddeo, H.R., Allain, D., Poli, M.A. and Elsen, J.M., 2010. Merino sheep: a further look at quantitative trait loci for wool production. Animal, 4, 1330–40.

  28. Rong, E.G., Yang, H., Zhang, Z. W., Wang, Z. P., Yan, X. H., Li, H. and Wang, N., 2015. Association of methionine synthase gene polymorphisms with wool production and quality traits in Chinese Merino population. Journal of Animal Science, 93, 4601–4609.

  29. Shen, M., Qu, L., Ma, M., Dou, T., Lu, J., Guo J, Hu, Y., Yi, G., Yuan, J., Sun, C., Wang, K. and Yang, N 2016. Genome-wide association studies for comb traits in chickens. PLoS ONE, 11, e0159081.

  30. Silva VH, Regitano LC, Geistlinger L, Pértille F, Giachetto PF, Brassaloti RA, Morosini, N.S., Zimmer, R. and Coutinho, L.L., 2016. Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle. PLoS ONE, 11, e0157711

  31. Simm, G., 1998. What affects response to selection within breeds? In: Genetic Improvement of Cattle and Sheep. Faming Press, Ipswich, pp. 107–146.

  32. Statistical Analysis System (SAS), 2004. SAS users’ guide, version 9.1. SAS Institute Inc, Cary, North Carolina, USA.

  33. Visser, C., Van Marle-Köster, E., Bovenhuis, H., Crooijmans, R.P.M.A., 2011. QTL for mohair traits in South African Angora goats. Small ruminant research, 100, 8–14.

  34. Wang, D., Sun, Y., Stang, P., JA Berlin, Wilcox, M. A and Li, Q. 2009. Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling. BMC Proceedings, Suppl 7, S109.

  35. Wang, Z., Zhang, H., Yang, H., Wang, S., Rong, E., Pei, W., Li, H. and Wang, N., 2014. Genome-wide association study for wool production traits in a Chinese Merino sheep population. PLoS ONE, 9, e107101.

  36. Yazdi, M.H., Engström, G., Nasholm, A., Johansson, K., Jorjani, H. and Liljedah, L.E., 1997. Genetic parameters for lamb weight at different ages and wool production in Baluchi sheep. Animal Science, 65, 224–255.

  37. Zeng, X.C., Chen, H.Y., Jia, B., Zhao, Z.S., Hui, W.Q., Wang, Z.B. and Du, Y.C., 2011. Identification of SNPs within the sheep PROP1 gene and their effects on wool traits. Molecular Biology Reports, 38, 2723–8.

  38. Zhang, L., Liu, J., Zhao, F., Ren, H., Xu, L., Lu, J., Zhang, S., Zhang, X., Wei, C., Lu, G., Zheng, Y. and Du, L., 2013. Genome-wide association studies for growth and meat production traits in sheep. PLoS One, 8, e66569.

  39. Zhang, C., Bruce, H., Yang, T., Charagu, P., Kemp, R.A., Boddicker, N., Miar Y, Wang, Z. and Plastow, G., 2016. Genome wide association studies (GWAS) identify QTL on SSC2 and SSC17 affecting loin peak shear force in crossbred commercial pigs. PLoS ONE, 11, e0145082.

  40. Zhao, X., Dittmer, K.E., Blair, H.T., Thompson, K.G., Rothschild, M.F. and Garrick, D.J., 2011. A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep. PLoS One, 6, e21739.

  41. Zhou, H., Gong, H., Li, S., Luo, Y., Hickford, J.G.H., 2015. A 57-bp deletion in the ovine KAP6-1 gene affects wool fibre diameter. Journal of Animal Breeding and Genetics, 132, 301–307.

Download references


This study was supported by Iran National Science Foundation (INSF). We also wish to thank Manager of Abbasabad sheep breeding station, Mashhad, Iran, for providing the data and samples.

Author information

Correspondence to Mohsen Gholizadeh.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ebrahimi, F., Gholizadeh, M., Rahimi-Mianji, G. et al. Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip. Trop Anim Health Prod 49, 1657–1662 (2017).

Download citation


  • Genome-wide association
  • Sheep
  • Wool production
  • Quantitative trait loci