Genome Wide Association Studies, Next Generation Sequencing and Their Application in Animal Breeding and Genetics: A Review
الموضوعات :ح. خانزاده 1 , ن. قوی حسین-زاده 2 , ش. قوتی 3
1 - Department of Animal Science, Faculty of Agricultural Science, University of Guilan, Rasht, Iran
2 - Department of Animal Science, Faculty of Agricultural Science, University of Guilan, Rasht, Iran
3 - Department of Animal Science, Faculty of Agricultural Science, University of Guilan, Rasht, Iran
الکلمات المفتاحية: Livestock, genome wide association studies, genomics, next generation sequenc-ing,
ملخص المقالة :
Recently genetic studies have been revolutionized by next generation sequencing (NGS) technology, and it is expected that the use of this technology will largely eliminate defects in the methods of association studies. The NGS technology is becoming the premier tool in genetics. However, at the moment the use of this method is limited especially in the livestock due to high cost and computational problems. But it is expected that the development of sequencing and computing technologies and reducing the cost will have significant impacts on the livestock health and production. This study reviews the literature on genetic association studies, NGS technologies and their application in animal breeding.
Abdoli R., Mirhoseini S.Z., Ghavi Hossein-Zadeh N., Zamani P., Ferdosi M.H. and Gondro C. (2019). Genome-wide association study of four composite reproductive traits in Iranian fat-tailed sheep. Reprod. Fertil. Dev. 31, 1127-1133.
Abdoli R., Mirhoseini S., Ghavi Hossein-Zadeh N., Zamani P. and Gondro C. (2018). Genome wide association study to identify genomic regions affecting prolificacy in Lori Bakhtiari sheep. Anim. Genet. 49(5), 488-491.
Ajay S.S., Parker S.C., Abaan H.O., Fajardo K.V.F. and Margulies E.H. (2011). Accurate and comprehensive sequencing of personal genomes. Genome Res. 21(9), 1498-1505.
Andersson L. (2001). Genetic dissection of phenotypic diversity in farm animals. Nat. Rev. Genet. 2(2), 130-138.
Arif I.A., Bakir M.A., Khan H.A., Al Farhan A.H., Al Homaidan A.A., Bahkali A.H., Al Sadoon M. and Shobrak M. (2010). A brief review of molecular techniques to assess plant diversity. Int. J. Mol. Sci. 11(5), 2079-2096.
Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., Hall K.P., Evers D.J., Barnes C.L. and Bignell H.R. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456(7218), 53-59.
Bickhart D.M., Hou Y., Schroeder S.G., Alkan C., Cardone M.F., Matukumalli L.K., Song J., Schnabel R.D., Ventura M. and Taylor J.F. (2012). Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res. 22(4), 778-790.
Bisht S.S. and Panda A.K. (2014). DNA Sequencing: Methods and Applications Pp. 11-23 in Advances in Biotechnology. I.R. Mamta Baunthiya and J. Saxena, Eds. Springer-Verlag Berlin Heidelberg Publisher, Berlin, Germany.
Blaby-Haas C.E. and de Crécy-Lagard V. (2011). Mining high-throughput experimental data to link gene and function. Trends Biotechnol. 29(4),174-182.
Blow N. (2008). DNA sequencing: Generation next-next. Nature Publishing Group, Berlin, Germany.
Chaitankar V., Karakülah G., Ratnapriya R., Giuste F.O., Brooks M.J. and Swaroop A. (2016). Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog. Retin. Eye. Res. 55, 1-31.
Chen W. (2011). Statistical methods and analysis in genome wide association studies and next-generation sequencing. Ph D. Thesis. the University of Michigan, Michigan, United State.
Clarke A.J. and Cooper D.N. (2010). GWAS: Heritability missing in action? European J. Hum. Genet. 18(8), 859-861.
Clop A., Vidal O. and Amills M. (2012). Copy number variation in the genomes of domestic animals. Anim. Genet. 43(5), 503-517.
Conrad D.F., Pinto D., Redon R., Feuk L., Gokcumen O., Zhang Y., Aerts J., Andrews T.D., Barnes C. and Campbell P. (2010). Origins and functional impact of copy number variation in the human genome. Nature. 464(7289), 704-712.
Cosart T., Beja-Pereira A., Chen S., Ng S.B., Shendure J. and Luikart G. (2011). Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genom. 12(1), 347-355.
D’Agostino N. and Tripodi P. (2017). NGS-based genotyping, high-throughput phenotyping and genome-wide association studies laid the foundations for next-generation breeding in horticultural crops. Diversity. 9(3), 38-42.
De Donato M., Peters S.O., Mitchell S.E., Hussain T. and Imumorin I.G. (2013). Genotyping-by-sequencing (GBS): A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing. PLoS One. 8(5), e62137.
Deamer D.W. and Akeson M. (2000). Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 18(4), 147-151.
DePristo M.A., Banks E., Poplin R., Garimella K.V., Maguire J.R., Hartl C., Philippakis A.A., Del Angel G., Rivas M.A. and Hanna M. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43(5), 491-498.
Dong Y., Xie M., Jiang Y., Xiao N., Du X., Zhang W., Tosser-Klopp G., Wang J., Yang S. and Liang J. (2013). Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol. 31(2), 135-142.
Dunisławska A., Łachmańska J., Sławińska A. and Siwek M. (2017). Next generation sequencing in animal science-a review. Anim. Sci. Pap. Rep. 35(3), 205-224.
Eck S.H., Benet-Pagès A., Flisikowski K., Meitinger T., Fries R. and Strom T.M. (2009). Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol. 10(8), 82-90.
Edwards J.S., Atlas S.R., Wilson S.M., Cooper C.F., Luo L. and Stidley C.A. (2014). Integrated statistical and pathway appr-approach to next-generation sequencing analysis: A family-based study of hypertension. BMC Proc. 8(1), 104-111.
Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S. and Mitchell S.E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS One. 6(5), e19379.
Fan B., Du Z., Gorbach D.M. and Rothschild M.F. (2010). Development and Application of high-density SNP Arrays in genomic studies of domestic animals. Asian-Australasian J. Anim. Sci. 23(7), 833-847.
FAO. (2016). Application of Genome Sequencing for Sustainable Agriculture and Food Security. Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
Feng S. (2015). Design and association methods for next-generation sequencing studies for quantitative traits. Ph D. Thesis. the University of Michigan, Michigan, United State.
Feng Y., Zhang Y., Ying C., Wang D. and Du C. (2015). Nanopore-based fourth-generation DNA sequencing technology. Genom. Proteom. Bioinf. 13(1), 4-16.
Feuk L., Carson A.R. and Scherer S.W. (2006). Structural variation in the human genome. Nat. Rev. Genet. 7(2), 85-97.
Fouts D.E., Szpakowski S., Purushe J., Torralba M., Waterman R.C., MacNeil M.D., Alexander L.J. and Nelson K.E. (2012). Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PloS One. 7(11), e48289.
Gabaldón T. and Alioto T.S. (2016). Whole-Genome Sequencing Recommendations Pp. 13-41 in Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. A.M.Aransay, T. Lavín and L. José, Eds. Springer-Verlag Berlin Heidelberg Publisher, Berlin, Germany.
García-Gámez E., Gutiérrez-Gil B., Sahana G., Sánchez J.P., Bayón 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(10), e47782.
Gibson G. (2010). Hints of hidden heritability in GWAS. Nat. Genet. 42(7), 558-560.
Glaubitz J.C., Casstevens T.M., Lu F., Harriman J., Elshire R.J., Sun Q. and Buckler E.S. (2014). TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PloS One. 9(2), e90346.
Goddard M.E., Kemper K.E., MacLeod I.M., Chamberlain A.J. and Hayes, B.J. (2016). Genetics of complex traits: Prediction of phenotype, identification of causal polymorphisms and genetic architecture. Proc. Biol. Sci. 283, 20160569.
Goldstein D.B., Allen A., Keebler J., Margulies E.H., Petrou S., Petrovski S. and Sunyaev S. (2013). Sequencing studies in human genetics: design and interpretation. Nat. Rev. Genet. 14(7), 460-470.
Henrichsen C.N., Chaignat E. and Reymond A. (2009). Copy number variants, diseases and gene expression. Hum. Mol. Gen. 18(1), 1-8.
Hinchcliffe M. and Webster P. (2011). In silico analysis of the exome for gene discovery. Meth. Mol. Biol. 760, 109-128.
Hirschhorn J.N. and Daly M.J. (2005). Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet. 6(2), 95-108.
Hou Y., Liu G.E., Bickhart D.M., Cardone M.F., Wang K., Kim E.S., Matukumalli L.K., Ventura M., Song J. and VanRaden P.M. (2011). Genomic characteristics of cattle copy number variations. BMC Genom. 12, 127-138.
Huang J. (2015). Whole-genome sequencing-based association studies of cardiovascular biomarkers. Ph D. Thesis. University of Cambridge, Cambridge, United Kingdom.
Ibeagha-Awemu E.M., Peters S.O., Akwanji K.A., Imumorin I.G. and Zhao X. (2016). High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits. Sci. Rep. 6, 31109.
Jiang N. (2013). Linkage disequilibrium based eQTL analysis and comparative evolutionary epigenetic regulation of gene transcription. Ph D. Thesis. University of Birmingham, Birmingham, United Kingdom.
Kadarmideen H.N. (2014). Genomics to systems biology in animal and veterinary sciences: Progress, lessons and opportunities. Livest. Sci. 166, 232-248.
Kerstens H.H., Crooijmans R.P., Dibbits B.W., Vereijken A., Okimoto R. and Groenen M.A. (2011). Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries. BMC Genom. 12(1), 94-110.
Korte A. and Farlow A. (2013). The advantages and limitations of trait analysis with GWAS: A review. Plant Methods. 9(29), 29-38.
Kranis A., Gheyas A.A., Boschiero C., Turner F., Yu L., Smith S., Talbot R., Pirani A., Brew F. and Kaiser P. (2013). Development of a high density 600K SNP genotyping array for chicken. BMC Genom. 14(1), 59-72.
Ku C.S. and Roukos D.H. (2013). From next-generation sequencing to nanopore sequencing technology: Paving the way to personalized genomic medicine. Expert. Rev. Med. Devices. 10(1), 1-6.
Lai F.N., Zhai H.L., Cheng M., Ma J.Y., Cheng S.F., Ge W., Zhang G.L., Wang J.J., Zhang R.Q. and Wang X. (2016). Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus). Sci. Rep. 6, 38096-38107.
Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M. and FitzHugh W. (2001). Initial sequencing and analysis of the human genome. Nature. 409(6822), 860-921.
Liu X., Zhang H., Li H., Li N., Zhang Y., Zhang Q., Wang S., Wang Q. and Wang H. (2008). Fine-mapping quantitative trait loci for body weight and abdominal fat traits: Effects of marker density and sample size. Poult. Sci. 87(7), 1314-1319.
Londin E., Yadav P., Surrey S., Kricka L.J. and Fortina P. (2013). Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations. Meth. Mol. Biol. 1015, 127-146.
Luo L., Boerwinkle E. and Xiong M. (2011). Association studies for next-generation sequencing. Genome Res. 21(7), 1099-1108.
Luo L., Zhu Y. and Xiong M. (2012). Quantitative trait locus analysis for next-generation sequencing with the functional linear models. J. Med. Genet. 49(8), 513-524.
Manolio T.A., Collins F.S., Cox N.J., Goldstein D.B., Hindorff L.A., Hunter D.J., McCarthy M.I., Ramos E.M., Cardon L.R. and Chakravarti A. (2009). Finding the missing heritability of complex diseases. Nature. 461(7265), 747-753.
Martin P., Palhière I., Maroteau C., Bardou P., Canale-Tabet K., Sarry J., Woloszyn F., Bertrand-Michel J., Racke I. and Besir H. (2017). A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content. Sci. Rep. 7(1), 1872-1880.
McCarroll S.A. (2008). Extending genome-wide association studies to copy-number variation. Hum. Mol. Gen. 17(2), 35-42.
McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P. and Hirschhorn J.N. (2008). Genome-wide association studies for complex traits: Consensus, uncertainty and challenges. Nat. Rev. Genet. 9(5), 356-369.
Milos P.M. (2010). Helicos single molecule sequencing: Unique capabilities and importance for molecular diagnostics. Genome Biol. 11(1), 14.
Mucha S., Mrode R., Coffey M., Kizilaslan M., Desire S. and Conington J. (2018). Genome-wide association study of conformation and milk yield in mixed-breed dairy goats. J. Dairy Sci. 101(3), 2213-2225.
Nielsen R., Paul J.S., Albrechtsen A. and Song Y.S. (2011). Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12(6), 443-451.
Ozsolak F., Platt A.R., Jones D.R., Reifenberger J.G., Sass L.E., McInerney P., Thompson J.F., Bowers J., Jarosz M. and Milos P.M. (2009). Direct RNA sequencing. Nature. 461, 814-814.
Pareek C.S., Smoczynski R. and Tretyn A. (2011). Sequencing technologies and genome sequencing. J. Appl. Genet. 52, 413-435.
Pértille F., Guerrero-Bosagna C., Da Silva V.H., Boschiero C., da Silva Nunes J.R., Ledur M.C., Jensen P. and Coutinho L.L. (2016). High-throughput and cost-effective chicken genotyping using next-generation sequencing. Sci. Rep. 6, 26929-26941.
Pértille F., Moreira G.C.M., Zanella R., da Silva Nunes J.d.R., Boschiero C., Rovadoscki G.A., Mourão G.B., Ledur M.C. and Coutinho L.L. (2017). Genome-wide association study for performance traits in chickens using genotype by sequencing approach. Sci. Rep. 7, 41748-41758.
Risch N.J. (2000). Searching for genetic determinants in the new millennium. Nature. 405(6788), 847-856.
Rolf M.M., McKay S.D., McClure M.C., Decker J.E., Taxis T.M., Chapple R.H., Vasco D.A., Gregg S.J., Kim J.W. and Schnabel R.D. (2010). How the next generation of genetic technologies will impact beef cattle selection. Pp. In Proc. 42nd Ann. Res. Symp. Ann. Meet., Columbia, United State.
Sanger F. (1977). Nucleotide sequence of bacteriophage (D X174) DNA. Nature. 265(5596), 687-95.
Sartelet A., Li W., Pailhoux E., Richard C., Tamma N., Karim L., Fasquelle C., Druet T., Coppieters W. and Georges M. (2015). Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. BMC Genom. 16(1), 316-324.
Schmid M. and Bennewitz J. (2017). Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs. Arch. Anim. Breed. 60, 335-346.
Schuster S.C. (2007). Next-generation sequencing transforms today's biology. Nat. Methods. 5(1), 16-24.
Sellner E., Kim J., McClure M., Taylor K., Schnabel R. and Taylor J. (2007). Board-invited review: Applications of genomic information in livestock. J. Anim. Sci. 85(12), 3148-3158.
Sharma A., Park J.E., Chai H.H., Jang J.W., Lee S.H. and Lim D. (2017). Next generation sequencing in livestock species: A review. J. Anim. Breed. Genom. 1(1), 23-30.
Shin D.H., Lee H.J., Cho S., Kim H.J., Hwang J.Y., Lee C.K., Jeong J., Yoon D. and Kim H. (2014). Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level. BMC Genom. 15(1), 240-248.
Špehar M., Mrak V., Smatko A., Potočnik K. and Gorjanc G. (2015). Genome-wide association study for dairy traits in Slovenian Brown swiss breed. Slovenian Vet. Res. 52(2), 49-55.
Steinbock L. and Radenovic A. (2015). The emergence of nanopores in next-generation sequencing. Nanotechnology. 26(7), 074003.
Stranger B.E., Forrest M.S., Dunning M., Ingle C.E., Beazley C., Thorne N., Redon R., Bird C.P., de Grassi A. and Lee C. (2007). Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 315(5813), 848-853.
Trapnell C. and Salzberg S.L. (2009). How to map billions of short reads onto genomes. Nat. Biotechnol. 27(5), 455-457.
Wang Q., Li K., Zhang D., Li J., Xu G., Zheng J., Yang N. and Qu L. (2015a). Next-generation sequencing techniques reveal that genomic imprinting is absent in day-old Gallus gallus domesticus brains. PloS One. 10(7), e0132345.
Wang W., Zhang T., Wang J., Zhang G., Wang Y., Zhang Y., Zhang J., Li G., Xue Q. and Han K. (2015b). Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology. Poult. Sci. 95(3), 500-506.
Welderufael B.G., Løvendahl P., De Koning D.J., Janss L. and Fikse F. (2018). Genome-wide association study for susceptibility to-and recoverability from mastitis in Danish Holstein cows. Front. Genet. 9, 141-147.
Wolc A., Arango J., Settar P., Fulton J., Osullivan N., Preisinger R., Habier D., Fernando R., Garrick D. and Hill W. (2012). Genome wide association analysis and genetic architecture of egg weight and egg uniformity in layer chickens. Anim. Genet. 43, 87-96.
Yi G., Qu L., Liu J., Yan Y., Xu G. and Yang N. (2014). Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. BMC Genom. 15(1), 962-971.
Yodklaew P., Koonawootrittriron S., Elzo M.A., Suwanasopee T. and Laodim T. (2017). Genome-wide association study for lactation characteristics, milk yield and age at first calving in a Thai multibreed dairy cattle population. Agric. Nat. Res. 51(3), 223-230.
Yuan J., Wang K., Yi G., Ma M., Dou T., Sun C., Qu L.J., Shen M., Qu L. and Yang N. (2015). Genome-wide association studies for feed intake and efficiency in two laying periods of chickens. Genet. Sel. Evol. 47(1), 82-91.
Zeng P., Zhao Y., Qian C., Zhang L., Zhang R., Gou J., Liu J., Liu L. and Chen F. (2015). Statistical analysis for genome-wide association study. J. Biomed. Res. 29(4), 285-292.
Zhang H., Wang Z., Wang S. and Li H. (2012). Progress of genome wide association study in domestic animals. J. Anim. Sci. Biotechnol. 3(1), 26-32.
Zhang L., Liu J., Zhao F., Ren H., Xu L., Lu J., Zhang S., Zhang X., Wei C. and Lu G. (2013). Genome-wide association studies for growth and meat production traits in sheep. PloS One. 8(6), e66569.
Zhu M., Zhu B., Wang Y., Wu Y., Xu L., Guo L., Yuan Z., Zhang L., Gao X. and Gao H. (2013). Linkage disequilibrium estimation of Chinese beef Simmental cattle using high-density SNP panels. Asian-Australasian J. Anim. Sci. 26(6), 772-779.
Zogopoulos G., Ha K.C., Naqib F., Moore S., Kim H., Montpetit A., Robidoux F., Laflamme P., Cotterchio M. and Greenwood C. (2007). Germ-line DNA copy number variation frequencies in a large North American population. Hum. Genet. 122(3), 345-353.
