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Genome-wide Association Study (GWAS) and Its Application for Improving the Genomic Estimated Breeding Values (GEBV) of the Berkshire Pork Quality Traits 원문보기

Asian-Australasian journal of animal sciences, v.28 no.11, 2015년, pp.1551 - 1557  

Lee, Young-Sup (Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University) ,  Jeong, Hyeonsoo (Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University) ,  Taye, Mengistie (Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University) ,  Kim, Hyeon Jeong (C&K Genomics Inc.) ,  Ka, Sojeong (Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University) ,  Ryu, Youn-Chul (Division of Biotechnology, Sustainable Agriculture Research Institute, Jeju National University) ,  Cho, Seoae (C&K Genomics Inc.)

Abstract ▼ AI-Helper 아이콘AI-Helper

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GW...

주제어

#Best Linear Unbiased Prediction   #Genome Wide Association Study   #Missing Heritability Problem   #Sherman-Morrison-Woodbury Lemma   #Single Nucleotide Polymorphism-Genomic Best Linear Unbiased Prediction   #Berkshire Pigs  

AI 본문요약
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제안 방법

  • , 2012a). This was the basis of our study because GWAS could detect the putative QTL regions and it could improve the BLUP.

대상 데이터

  • We used data from 702 (365 male, 204 female, 133 castrated male) Berkshire pigs. Animals were raised with the same commercial diet from the Dasan experimental farm in Namwon, Korea.

이론/모형

  • Linear regression GWAS: We used the linear regression model in PLINK software (additive option) for the genome-wide association (GWA) analysis with the sex adjusted data. The P-value less than the stringent level of 0.
  • Where G matrix is the genomic relationship matrix. To calculate the Gu matrix, i.e., SNP-SNP relationship matrix, we applied the Sherman-Morrison-Woodbury lemma (Sherman and Morrison, 1950; Woodbury, 1950).
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참고문헌 (24)

  1. Bolormaa S Pryce JE Kemper K Savin K Hayes BJ Barendse W Zhang Y Reich CM Mason BA Bunch RJ 2013 Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in bos taurus, bos indicus, and composite beef cattle J Anim Sci 91 3088 3104 23658330 

    상세보기

  2. Davis CG Lin B-H 2005 Factors affecting us pork consumption US Department of Agriculture, Economic Research Service Washington, DC, USA 

  3. Eichler EE Flint J Gibson G Kong A Leal SM Moore JH Nadeau JH 2010 Missing heritability and strategies for finding the underlying causes of complex disease Nat Rev Genet 11 446 450 20479774 

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  4. Endelman JB 2011 Ridge regression and other kernels for genomic selection with r package rrblup Plant Genome 4 250 255 

  5. Feero WG Guttmacher AE Manolio TA 2010 Genomewide association studies and assessment of the risk of disease N Engl J Med 363 166 176 20647212 

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  6. Fernando RL Dekkers JC Garrick DJ 2014 A class of bayesian methods to combine large numbers of genotyped and non-genotyped animals for whole-genome analyses Genet Sel Evol 46 50 25253441 

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  7. Goddard M Hayes BJ Meuwissen THE 2011 Using the genomic relationship matrix to predict the accuracy of genomic selection J Anim Breed Genet 128 409 421 22059574 

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  8. Henderson CR 1975 Best linear unbiased estimation and prediction under a selection model Biometrics 31 423 447 1174616 

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  9. Hennig C 2010 Fpc: Flexible procedures for clustering R package version 2 0 3 https://cran.r-project.org/web/packages/fpc/ , Accessed August 13, 2015. 

  10. Jiang J 1997 A derivation of blup—best linear unbiased predictor Stat Probabil Lett 32 321 324 

  11. Lee T Shin D-H Cho S Kang HS Kim SH Lee H-K Kim H Seo K-S 2014a Genome-wide association study of integrated meat quality-related traits of the duroc pig breed Asian Australas J Anim 27 303 309 

  12. Lee Y-S Kim H-J Cho S Kim H 2014b The usage of an snp-snp relationship matrix for best linear unbiased prediction (blup) analysis using a community-based cohort study Genome Inform 12 254 260 

  13. Leeds TD 2005 Pork Quality Improvement: Estimates of Genetic Parameters and Evaluation of Novel Selection Criteria PhD Thesis The Ohio State University Columbus, OH, USA 

  14. Legarra A Aguilar I Misztal I 2009 A relationship matrix including full pedigree and genomic information J Dairy Sci 92 4656 4663 19700729 

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  15. Manolio TA Collins FS Cox NJ Goldstein DB Hindorff LA Hunter DJ McCarthy MI Ramos EM Cardon LR Chakravarti A 2009 Finding the missing heritability of complex diseases Nature 461 747 753 19812666 

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  16. Meuwissen TH Hayes BJ Goddard ME 2001 Prediction of total genetic value using genome-wide dense marker maps Genetics 157 1819 1829 11290733 

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  17. Purcell S Neale B Todd-Brown K Thomas L Ferreira MA Bender D Maller J Sklar P De Bakker PI Daly MJ 2007 Plink: A tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 81 559 575 17701901 

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  18. Sellier P 1998 Genetics of meat and carcass traits The Genetics of the Pig Rothschild M Ruvinsky A CAB International Wallingford, Oxon, UK 463 510 

  19. Sherman J Morrison WJ 1950 Adjustment of an inverse matrix corresponding to a change in one element of a given matrix Ann Math Stat 21 124 127 

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  20. Soller M Weigend S Romanov MN Dekkers JCM Lamont SJ 2006 Strategies to assess structural variation in the chicken genome and its associations with biodiversity and biological performance Poult Sci 85 2061 2078 17135660 

  21. Woodbury MA 1950 Inverting modified matrices Memorandum report Princeton University Princeton, NJ USA 42 106 

  22. Yang J Benyamin B McEvoy BP Gordon S Henders AK Nyholt DR Madden PA Heath AC Martin NG Montgomery GW 2010 Common snps explain a large proportion of the heritability for human height Nat Genet 42 565 569 20562875 

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  23. Zhang H Wang Z Wang S Li H 2012a Progress of genome wide association study in domestic animals J Anim Sci Biotech 3 26 

  24. Zhang Z He J Zhang H Gao P Erbe M Simianer H Li J 2014 Results of genome wide association studies improve the accuracy of genomic selection 10th world congress on genetics applied to livestock production The Westin Bayshore, Vancouver, BC, Canada #695 (the poster number) 

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