Study of haplotype blocks structure and haplotype based genome scan in autosomal chromosomes to body weight gain trait in Zandi sheep breed

Document Type : Research Paper

Authors


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 Evaluation 47:66.
Arias JA, Keehan M, Fisher P, Coppieters W and Spelman R, 2009. A high density linkage map of the bovine genome. BMC Genetics 10: 18-30.
Barrett JC, Fry B, Maller J and Daly MJ, 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
Bolormaa S, Pryce JE, Reverter A, Zhang Y, Barendse W, Kemper K, Tier B, Savin K, Hayes BJ and Goddard ME, 2014. A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genetics 10(3): e1004198.
Bolormaa S, Hayes BJ, van der Werf JH, Pethick D, Goddard ME and Daetwyler HD, 2016. Detailed phenotyping identifies genes with pleiotropic effects on body composition. BMC Genomics 17:224.
Bohlouli M, Mohammadi H and 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.
Espigolan R, Baldi F, Boligon AA, Souza FRP, Gordo DGM, Tonussi RL, Cardoso DF, Oliveira HN, Tonhati H, Sargolzaei M, Schenkel FS, Carvalheiro R, Ferro JA and Albuquerque LG, 2013. Study of whole genome linkage disequilibrium in Nellore cattle. BMC Genomics 14:305.
Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J and Blumenstiel B, 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
Garcia-Gamez E, Sahana G, Gutierrez-Gil B and Arranz J, 2012. Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genetics 13:43.
Gilmour A, Gogel B, Cullis and Thompson R, 1999. ASReml User Guide Release 2.0. VSN International Ltd, Hempstead, UK.
Gholizadeh M, Rahimi Mianji G and Nejati Javaremi A, 2014. Linkage disequilibrium estimation and haplotype based genome-wide association to detect QTLs affecting twinning rate in Baluchi sheep. Research on Animal Production 10: 166-178.
Johnston SE, McEwan JC, Pickering NK, Kijas JW, Beraldi D, Pilkington JG, Pemberton JM 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(12):  2555–2566.
Kijas JW, Johannes A, Ben Hayes L, Boitard S, PortoNeto LR, Cristobal MS, Servin B, McCulloch R, Whan V, Gietzen K, Paiva S, Barendse W, Ciani E, Raadsma H, McEwan J and Dalrymple B, 2012. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology 10: 1-14.
Liu S, He S, Chen L, Li W, Di J and Liu M, 2017. Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genome 17: 1-13.
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 Evaluation 48:11.
Meadows JR, Chan EK and Kijas JW, 2008. Linkage disequilibrium compared between five populations of domestic sheep. BMC Genetics 30; 9:61.
Mohammadi H, Moradi Shahrebabak M and Sadeghi M, 2013. Association between single nucleotide polymorphism in the ovine DGAT1 gene and carcass traits in two Iranian sheep breeds. Animal Biotechnology 24: 159–167.
Mohammadi H, Rafat SA, Moradi shahrebabak H, Shodja J and Moradi MH, 2018. An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed. Journal of Animal Science Researches (Agricultural science) 28(2); 193-204.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ and Sham PC, 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. The American Journal of Human Genetics 81: 559-575.
Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR and Simianer H, 2010. The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics 41: 346–356.
Riggio V, Matika O, Pong-Wong R, Stear MJ and Bishop SC, 2013. Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs. Heredity 110:4 20–9.
Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF and Ackerman HC, 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419(6909): 832-837.
Scheet P and Stephens M, 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. American Journal Human Genetics 78(4): 629–644.
Teo YY, Fry AE, Clark TG, Tai ES and Seielstad M, 2007. On the usage of HWE for identifying genotyping errors. Annals of Human Genetics 71: 701-703.
Wall JD, Pritchard JK, 2003. Haplotype blocks and linkage disequilibrium in the human genome. Nature Reviews Genetics 4: 587–597.
Wang S., Dvorkin D and Da Y, 2012. SNPEVG: a graphical tool for GWAS graphing with mouse clicks. BMC Bioinformatics 13: 319-326.
William GH, 1974. Estimation of linkage disequilibrium in randomly mating populations. Heredity 33: 229–239.
Zhao FP, Wang GK, Zeng T, Wei CH, Zhang L, Wang HH, Zhang SZ, Liu RZ, Liu Z and Du LX, 2014. Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations. Livestock Science 170: 22–29.