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Genome-wide association study of birth weight in sheep

Published online by Cambridge University Press:  08 January 2019

M. Ghasemi ,
P. Zamani Open the ORCID record for P. Zamani [Opens in a new window] ,
M. Vatankhah  and
R. Abdoli
M. Ghasemi
Affiliation:
Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
P. Zamani*
Affiliation:
Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
M. Vatankhah
Affiliation:
Department of Animal Science, Agriculture and Natural Resources Research Center, Shahrekord, Iran
R. Abdoli
Affiliation:
Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
*
†E-mail: pzamani@basu.ac.ir
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Abstract

Birth weight is the earliest available growth trait with considerable impacts on lamb survivability and growth performance traits. This study was conducted to perform a genome-wide association study of birth weight in a meat-type sheep. A total of 132 Lori-Bakhtiari sheep were selected based on estimated of breeding values (EBVs) for BW analyses. The selected animals were genotyped using Illumina Ovine SNP50 Bead Chip. After quality control, a total of 41 323 single-nucleotide polymorphisms (SNPs) and 130 sheep were used for subsequent analyses. Plink 1.90 beta software was used for the analyses. Seven SNPs on chromosomes 1, 16, 19 and 22 were detected based on genome-wide unadjusted P-values (P <10−6), which jointly accounted for 1.2% of total genetic variation. However, based on Bonferroni-adjusted P-values, only three SNPs on chromosome 1 had significant associations with EBVs for birth weight (P <0.05), which jointly explained 0.8% of total genetic variation. A total of seven genes were found in 50 kb intervals from the three significant SNPs on chromosome 1, but only three genes, including RAB6B (a member of RAS oncogene family), Tf serotransferrin and GIGYF2 (a GRB10 interacting GYF protein 2), could be considered as candidate genes for birth weight in future studies. The results of this study may facilitate potential use of the genes involving in growth and production traits for genetic improvement of productivity in sheep.

Keywords

body weightquantitative trait locisingle nucleotide polymorphismcandidate geneLori-Bakhtiari
Type
Research Article
Information
animal , Volume 13 , Issue 9 , September 2019 , pp. 1797 - 1803
Copyright
© The Animal Consortium 2019 

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References

Al-Mamun, HA, Kwan, P, Clark, SA, Ferdosi, MH, Tellam, R and 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.CrossRefGoogle ScholarPubMed
Barrett, JC, Fry, B, Maller, J and Daly, MJ 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265.CrossRefGoogle ScholarPubMed
Buzanskas, ME, Grossi, DA, Baldi, F, Barrozo, D, Silva, LOC, Torres Júnior, RAA, Munari, DP and Alencar, MM 2010. Genetic associations between stayability and reproductive and growth traits in Canchim beef cattle. Livestock Science 132, 107–112.CrossRefGoogle Scholar
Buzanskas, ME, Grossi, DA, Ventura, RV, Schenkel, FS, Sargolzaei, M, Meirelles, SL, Mokry, FB, Higa, RH, Mudadu, MA, da Silva, MV, Niciura, SC, Torres, RA Jr, Alencar, MM, Regitano, LC and Munari, DP 2014. Genome-wide association for growth traits in Canchim beef cattle. PLoS ONE 9, e94802, 1–8. https://doi.org/10.1371/journal.pone.0094802.CrossRefGoogle ScholarPubMed
Cavanagh, CR, Jonas, E, Hobbs, M, Thomson, PC, Tammen, I and Raadsma, HW 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, 1–14.CrossRefGoogle ScholarPubMed
Chang, CC, Chow, CC, Tellier, LCAM, Vattikuti, S, Purcell, SM and Lee, JJ 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, 7, 1–16. https://doi.org/10.1186/s13742-015-0047-8.CrossRefGoogle ScholarPubMed
Dekkers, JCM 2004. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. Journal of Animal Science 82, 313–328.Google ScholarPubMed
Eberlein, A, Takasuga, A, Setoguchi, K, Pfuhl, R, Flisikowski, K, Fries, R, Klopp, N, Fürbass, R, Weikard, R and Kühn, C 2009. Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene. Genetics 183, 951–964.CrossRefGoogle Scholar
Fletcher, J and Huehns, ER 1968. Function of transferrin. Nature 218, 1211–1214.CrossRefGoogle ScholarPubMed
Forrest, RH, Hickford, JGH and Frampton, CM 2007. Polymorphism at the ovine 3-adrenergic receptor locus (ADRB3) and its association with lamb mortality. Journal of Animal Science 85, 2801–2806.CrossRefGoogle Scholar
Gholibeikifard, A, Aminafshar, M and Hosseinpour Mashhadi, M 2013. Polymorphism of IGF-I and ADRB3 genes and their association with growth traits in the Iranian Baluchi sheep. Journal of Agricultural Science and Technology 15, 1153–1162.Google Scholar
Gholizadeh, M, Rahimi-Mianji, G, Nejati-Javaremi, A, de Koning, DJ and Jonas, E 2015. Genome wide association study to detect QTL for body weight in Baluchi sheep. Journal of Genetics 93, 489–493.CrossRefGoogle Scholar
Giovannone, B, Tsiaras, WG, de la Monte, S, Klysik, J, Lautier, C, Karashchuk, G, Goldwurm, S and Smith, RJ 2009. GIGYF2 gene disruption in mice results in neurodegeneration and altered insulin-like growth factor signaling. Human Molecular Genetics 18, 4629–4639.CrossRefGoogle ScholarPubMed
Goddard, ME and Hayes, BJ 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics 10, 381–391.CrossRefGoogle ScholarPubMed
Haldar, A, French, MC, Brauning, R, Edwards, SJ, O’Connell, AR, Farquhar, PA, Davis, GH, Johnstone, PD and Juengel, JL 2014. Single-nucleotide polymorphisms in the LEPR gene are associated with divergent phenotypes for age at onset of puberty in Davisdale ewes. Biology of Reproduction 90, 33, 1–7. https://doi.org/10.1095/biolreprod.113.115923.CrossRefGoogle ScholarPubMed
Ju, ZH, Li, QL, Huang, JM, Hou, MH, Li, RL, Li, JB, Zhong, JF and Wang, CF 2011. Three novel SNPs of the bovine Tf gene in Chinese native cattle and their associations with milk production traits. Genetics and Molecular Research 10, 340–352.CrossRefGoogle ScholarPubMed
Kmieć, M 1999. Transferrin polymorphism versus growth rate in lambs, Polish long-wool sheep. II. Analysis of relation between transferrin polymorphism of lamb blood serum versus growth rate of lambs up to age of 5 months. Archives Tierzucht 42, 469–479.Google Scholar
Li, L and Brown, DJ 2015. Estimation of genetic parameters for lambing ease, birthweight and gestation length in Australian sheep. Animal Production Science 56, 934–940.CrossRefGoogle Scholar
Margawati, ET, Raadsma, HW, Martojo, H and Muladmo, S 2006. Quantitative trait loci (QTL) analysis for production traits of birth weight and weight 360 days in backcross sheep. HAYATI. Journal of Biosciences 13, 31–35.Google Scholar
Matika, O, Riggio, V, Anselme-Moizan, M, Law, AS, Pong-Wong, R, Archibald, AL and Bishop, SC 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, 1–15.CrossRefGoogle ScholarPubMed
McRae, AF, Bishop, SC, Walling, GA, Wilson, AD and Visscher, RM 2005. Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree. Animal Science 80, 135–141.CrossRefGoogle Scholar
Meyer, K 2007. Wombat – A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML). Journal of Zhejiang University Science B 8, 815–821.CrossRefGoogle Scholar
Mudadu, MA, Porto-Neto, LR, Mokry, FB, Tizioto, PC, Oliveira, PS, Tullio, RR, Nassu, RT, Niciura, SC, Tholon, P, Alencar, MM, Higa, RH, Rosa, AN, Feijó, GL, Ferraz, AL, Silva, LO, Medeiros, SR, Lanna, DP, Nascimento, ML, Chaves, AS, Souza, AR, Packer, IU, Torres, RA Jr, Siqueira, F, Mourão, GB, Coutinho, LL, Reverter, A and Regitano, LC 2016. Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle. BMC Genomics 17, 235, 1–16. https://doi.org/10.1186/s12864-016-2535-3.Google ScholarPubMed
National Research Council 2007. Nutrient requirements of small ruminants: sheep, goats, cervids, and new world camelids. The National Academies Press, Washington, DC, USA.Google Scholar
Nicolazzi, EL, Caprera, A, Nazzicari, N, Cozzi, P, Strozzi, F, Lawley, C, Pirani, A, Soans, C, Brew, F, Jorjani, H, Evans, G, Simpson, B, Tosser-Klopp, G, Brauning, R, Williams, JL and Stella, A 2015. SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species. BMC Genomics 16, 283, 1–6. https://doi.org/10.1186/s12864-015-1497-1.CrossRefGoogle ScholarPubMed
Pantopoulos, K, Porwal, SK, Tartakoff, A and Devireddy, L 2012. Mechanisms of mammalian iron homeostasis. Biochemistry 51, 5705–5724.CrossRefGoogle ScholarPubMed
Ptáček, M, Ducháček, J, Stádník, L, Haki, J and Fantová, M 2017. Analysis of multivariate relations among birth weight, survivability traits, growth performance, and some important factors in Suffolk lambs. Archives Animal Breeding 60, 43–50.CrossRefGoogle Scholar
R Development Core Team 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.Google Scholar
Raadsma, HW, Thomson, PC, Zenger, KR, Cavanagh, C, Lam, MK, Jonas, E, Jones, M, Attard, G, Palmer, D and Nicholas, FW 2009. Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight. Genetics Selection Evolution 41, 34, 1–17. https://doi.org/10.1186/1297-9686-41-34.CrossRefGoogle ScholarPubMed
SAS Institute 2013. Users Guide, Version 9.4: Statistics. SAS Institute, Cary, NC, USA.Google Scholar
Senkal, RH, Ahmed, JR, Mahmood, FA and Abdulkareem, TA 2017. Association of transferrin gene polymorphism A14037G and C14081T SNPS with the productive performance of Holstein-Frisian cows. International. Journal of Science and Nature 8, 117–121.Google Scholar
Setoguchi, K, Furuta, M, Hirano, T, Nagao, T, Watanabe, T, Sugimoto, Y and Takasuga, A 2009. Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate. BMC Genetics 10, 43, 1–12. https://doi.org/10.1186/1471-2156-10-43.CrossRefGoogle ScholarPubMed
Setoguchi, K, Watanabe, T, Weikard, R, Albrecht, E, Kühn, C, Kinoshita, A, Sugimoto, Y and Takasuga, A 2011. The SNP c.1326T >G in the non-SMC condensin I complex, subunit G (NCAPG) gene encoding a p.Ile442Met variant is associated with an increase in body frame size at puberty in cattle. Animal Genetics 42, 650–655.CrossRefGoogle Scholar
Turner, SD 2014. qqman: An R package for visualizing GWAS results using Q-Q and manhattan plots. bioRxiv preprint first posted online May 14, 2014. https://doi.org/10.1101/005165.CrossRefGoogle Scholar
Walling, GA, Visscher, PM, Wilson, AD, McTeir, BL, Simm, G and Bishop, SC. 2004. Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations. Journal of Animal Science 82, 2234–2245.CrossRefGoogle ScholarPubMed
Widmann, P, Reverter, A, Fortes, MRS, Weikard, R, Suhre, K, Hammon, H, Albrecht, E and Kuehn, C 2013. A systems biology approach using metabolomics data reveals genes and pathways interacting to modulate divergent growth in cattle. BMC Genomics 14, 798, 1–17. https://doi.org/10.1186/1471-2164-14-798.CrossRefGoogle ScholarPubMed
Yang, J, Lee, SH, Goddard, ME and Visscher, PM 2011a. GCTA: a tool for genome-wide complex trait analysis. American Journal of Human Genetics 88, 76–82.CrossRefGoogle Scholar
Yang, J, Weedon, MN, Purcell, S, Lettre, G, Estrada, K, Willer, CJ, Smith, AV, Ingelsson, E, O’Connell, JR, Mangino, M, Mägi, R, Madden, PA, Heath, AC, Nyholt, DR, Martin, NG, Montgomery, GW, Frayling, TM, Hirschhorn, JN, McCarthy, MI, Goddard, ME and Visscher, PM, GIANT Consortium 2011b. Genomic inflation factors under polygenic inheritance. European Journal of Human Genetics 19, 807–812.CrossRefGoogle Scholar
Zamani, P and Mohammadi, H 2008. Comparison of different models for estimation of genetic parameters of early growth traits in the Mehraban sheep. Journal of Animal Breeding and Genetics 125, 25–34.CrossRefGoogle ScholarPubMed
Zamani, P, Moradi, MR, Alipour, D and Ghafouri-Kesbi, F 2016. Combination of B-Spline and Legendre functions in random regression models to fit growth curve of Moghani sheep. Small Ruminant Research 145, 115–122.CrossRefGoogle Scholar
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, 1–12. https://doi.org/10.1371/journal.pone.0066569.Google Scholar
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