Contribution of All Single Nucleotide Polymorphisms (SNPs) and Minor Allele Frequency Groups to Genetic Variation of Quantitative Traits in Suffolk Sheep

Subject Areas : Camel

A. Taheri Yeganeh ¹ , M.R. Sanjabi ² , J. Fayazi ³ , M. Zandi ⁴ , J. Van der Werf ⁵

1 - Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
2 - Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
3 - Department of Animal Science, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Khuzestan, Iran
4 - Department of Agriculture, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
5 - School of Environmental and Rural Science, University of New England, Armidale, Australia

Received: 2023-05-23 Accepted : 2023-08-11 Published : 2023-12-01

Keywords:

References:

Abdollahi-Arpanahi R., Pakdel A., Nejati-Javaremi A., Moradi Shahrbabak M., Morota G., Valente, B.D., Kranis A., Rosa G.J.M. and Gianola D. (2014). Dissection of additive genetic variability for quantitative traits in chickens using SNP markers. Anim. Breed. Genet. 131, 183-193.

Emrani H., Vaez Torshizi R., Masoudi A. and Ehsani A. (2017). Estimation of genomic heritability for growth traits in an F2 cross of Arian broiler line and Azerbaijan indigenous chicken using 60K SNP Beadchip. Anim. Sci. J. (Pajouhesh and Sazandegi). 114, 273-284.

Gu X.R., Feng C.G., Ma L., Song C., Wang Y.Q., Da Y., Li H., Chen K., Ye S., Ge C., Hu X. and Li N. (2011). Genome-wide association study of body weight in chicken F2 resource population. PLoS One. 6(7), e21872.

Haile-Mariam M., Nieuwhof G., Beard K., Konstatinov K. and Hayes B. (2013). Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations. J. Anim. Breed. Genet. 130, 20-31.

Hayes B.J., Bowman P.J., Chamberlain A.J. and Goddard M.E. (2009). Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92, 433-443.

Jensen J., Su G. and Madsen P. (2012). Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle. BMC Genet. 13, 44-51.

Lee S.H., DeCandia T.R., Ripke S., Yang J., Sullivan P.F., Goddard M.E., Keller M.E., Matthew C., Visscher Peter M. and Wray Naomi R. (2012). Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat. Genet. 44, 247-250.

Lee S.H., Harold D., Nyholt D.R., Goddard M.E., Zondervan K.T., Williams J., Montgomery G.W., Wray N.R. and Visscher P.M. (2013). Estimation and partitioning of polygenic variation captured by common SNPs for Alzheimer's disease, multiple sclerosis, and endometriosis. Hum. Mol. Genet. 22, 832-841.

Meuwissen T.H., Hayes B.J. and Goddard M.E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics. 157, 1819-1829.

Meuwissen T.H., Hayes B.J., MacLeod I. and Goddard M. (2022). Identification of genomic variants causing variation in quantitative traits: A review. Agriculture. 12(10), 1713-1721.

Ogawa S.H., Matsuda1 H., Taniguchi Y., Watanabe T., Sugimoto Y. and Iwaisaki H. (2016). Estimated genetic variance explained by single nucleotide polymorphisms of different minor allele frequencies for carcass traits in japanese black cattle. J. Biosci. Med. 4, 89-97.

Pérez P. and de los Campos G. (2013). BGLR: A statistical package for whole genome regression and prediction. R package version. Genetics. 198(2), 483-495.

Pimentel E.C.G., Erbe M., Konig S. and Simianer H. (2011). Genome partitioning of genetic variation for milk production and composition traits in Holstein cattle. Front. Genet. 2, 19-27.

Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A.R., Bender D., Maller J., Sklar P., de Bakker P.I.W., Daly M.J. and Sham P.C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. American J. Hum. Genet. 81, 559-575.

Rashedi Dehsahraei A., Fayazi J., Abdollahi Arpanahi R., Van Der Werf J. and Roshanfekr H. (2017). Estimation of variance components for the body weight of Merino sheep at birth and weaning using single nucleotide markers and REML and Bayesian approaches. J. Rumin. Res. 5(2), 29-44.

Rashedi Dehsahraei A., Fayazi J., Abdollahi Arpanahi R., Van Der Werf J. and Roshanfekr H. (2018). The effect of Prosopis fractal on the performance, some blood parameters, and immune and antioxidant system of broiler chickens under heat stress conditions. Anim. Sci. J. (Pajouhesh and Sazandegi). 120, 35-46.

Sun Y.F., Liu R.R., Zheng M.Q., Zhao G.P., Zhang L., Wu D., Hu Y.D., Li P. and Wen J. (2013). Genome-wide association study on shank length and shank girth in chicken. Chinese's J. Anim. Vet. Sci. 44, 358-365.

Taheri Yeganeh A., Sanjabi M.R., Fayazi J., Zandi M. and Van der Werf J. (2022). Estimation of variance components and genome partitioning according to minor allele frequency for quantitative traits in sheep. Res. Anim. Prod. 13, 35-42.

Uemoto Y., Sasaki S., Kojima T., Sugimoto Y. and Watanabe T. (2015). Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle. BMC Genet. 16, 134-142.

VanRaden P.M. (2008). Efficient methods to compute genomic predictions. J. Dairy Sci. 91, 4414-4423.

Yang J., Benyamin B., McEvoy B.P., Gordon S., Henders A.K., Nyholt D.R., Madden P.A., Heath A.C., Martin N.G., Montgomery G.W., Goddard M.E. and Visscher P.M. (2010). Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42, 565-569.