메뉴 건너뛰기




Volumn 47, Issue 1, 2015, Pages

Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle

Author keywords

[No Author keywords available]

Indexed keywords

CATTLE; CHROMOSOME; DATA SET; GENETIC MARKER; GENOME; GENOMICS; HEALTH STATUS; MILK PRODUCTION;

EID: 84937201160     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/s12711-015-0132-6     Document Type: Article
Times cited : (26)

References (44)
  • 1
    • 78649317608 scopus 로고    scopus 로고
    • Predicting genetic predisposition in humans: The promise of whole-genome markers
    • 1:CAS:528:DC%2BC3cXhsVejs7jE 21045869
    • de los Campos G, Gianola D, Allison DB. Predicting genetic predisposition in humans: the promise of whole-genome markers. Nat Rev Genet. 2010; 11:880-6.
    • (2010) Nat Rev Genet , vol.11 , pp. 880-886
    • De Los Campos, G.1    Gianola, D.2    Allison, D.B.3
  • 4
    • 77954140531 scopus 로고    scopus 로고
    • Common SNPs explain a large proportion of the heritability for human height
    • 1:CAS:528:DC%2BC3cXns1GisL8%3D 3232052 20562875
    • Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, et al. Common SNPs explain a large proportion of the heritability for human height. Nat Genet. 2010; 42:565-9.
    • (2010) Nat Genet , vol.42 , pp. 565-569
    • Yang, J.1    Benyamin, B.2    McEvoy, B.P.3    Gordon, S.4    Henders, A.K.5    Nyholt, D.R.6
  • 6
    • 84876171921 scopus 로고    scopus 로고
    • Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study
    • 3542705 23335935
    • Peñagaricano F, Weigel KA, Rosa GJM, Khatib H. Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study. Front Genet. 2012; 3:307.
    • (2012) Front Genet , vol.3 , pp. 307
    • Peñagaricano, F.1    Weigel, K.A.2    Rosa, G.J.M.3    Khatib, H.4
  • 7
    • 78549251736 scopus 로고    scopus 로고
    • Analysing biological pathways in genome-wide association studies
    • 1:CAS:528:DC%2BC3cXhsVejs7nK 21085203
    • Wang K, Li M, Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet. 2010; 11:843-54.
    • (2010) Nat Rev Genet , vol.11 , pp. 843-854
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 8
    • 80051499915 scopus 로고    scopus 로고
    • Rare-variant association testing for sequencing data with the sequence kernel association test
    • 1:CAS:528:DC%2BC3MXovF2mtLc%3D 3135811 21737059
    • Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet. 2011; 89:82-93.
    • (2011) Am J Hum Genet , vol.89 , pp. 82-93
    • Wu, M.C.1    Lee, S.2    Cai, T.3    Li, Y.4    Boehnke, M.5    Lin, X.6
  • 9
    • 84864868742 scopus 로고    scopus 로고
    • Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps
    • Silver M, Montana G. Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Stat Appl Genet Molec Biol. 2012; 11:7.
    • (2012) Stat Appl Genet Molec Biol , vol.11 , pp. 7
    • Silver, M.1    Montana, G.2
  • 10
    • 79960644911 scopus 로고    scopus 로고
    • Gene set analysis of SNP data: Benefits, challenges, and future directions
    • 1:CAS:528:DC%2BC3MXpt1aksLc%3D 3172936 21487444
    • Fridley BL, Biernacka JM. Gene set analysis of SNP data: benefits, challenges, and future directions. Eur J Hum Genet. 2011; 19:837-43.
    • (2011) Eur J Hum Genet , vol.19 , pp. 837-843
    • Fridley, B.L.1    Biernacka, J.M.2
  • 11
    • 84862183331 scopus 로고    scopus 로고
    • Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle
    • 1:CAS:528:DC%2BC38XhslWjt7%2FI 3472176 22694746
    • Jensen J, Su G, Madsen P. Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle. BMC Genet. 2012; 13:44.
    • (2012) BMC Genet , vol.13 , pp. 44
    • Jensen, J.1    Su, G.2    Madsen, P.3
  • 12
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • 1:CAS:528:DC%2BD3cXhvVGqu74%3D 102409 10592173
    • Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 13
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012; 40:109-14. http://www.nordicebv.info.
    • (2012) Nucleic Acids Res , vol.40 , pp. 109-114
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 14
    • 62649155943 scopus 로고    scopus 로고
    • A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals
    • 1:CAS:528:DC%2BD1MXisFCrtL8%3D 2668004 19200528
    • Browning BL, Browning SR. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet. 2009; 84:210-3.
    • (2009) Am J Hum Genet , vol.84 , pp. 210-213
    • Browning, B.L.1    Browning, S.R.2
  • 15
    • 84864072672 scopus 로고    scopus 로고
    • Comparison of genomic predictions using medium-density (∼ 54,000) and high-density (∼777,000) single nucleotide polymorphism marker panels in Nordic Holstein and Red Dairy Cattle populations
    • 1:CAS:528:DC%2BC38XhtVOls7%2FM 22818480
    • Su G, Brøndum RF, Ma P, Guldbrandtsen B, Aamand GP, Lund MS. Comparison of genomic predictions using medium-density (∼ 54,000) and high-density (∼777,000) single nucleotide polymorphism marker panels in Nordic Holstein and Red Dairy Cattle populations. J Dairy Sci. 2012; 95:4657-65.
    • (2012) J Dairy Sci , vol.95 , pp. 4657-4665
    • Su, G.1    Brøndum, R.F.2    Ma, P.3    Guldbrandtsen, B.4    Aamand, G.P.5    Lund, M.S.6
  • 17
    • 84856193183 scopus 로고    scopus 로고
    • A recipe for multiple trait deregression
    • Stranden I, Mantysaari EA. A recipe for multiple trait deregression. Interbull Bull. 2010; 42:21-4.
    • (2010) Interbull Bull , vol.42 , pp. 21-24
    • Stranden, I.1    Mantysaari, E.A.2
  • 21
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5:80.
    • (2004) Genome Biol , vol.5 , pp. 80
    • Gentleman, R.1    Carey, V.2    Bates, D.3    Bolstad, B.4    Dettling, M.5    Dudoit, S.6
  • 22
    • 84937221049 scopus 로고    scopus 로고
    • Org.Bt.eg.db: Genome wide annotation for Bovine
    • Accessed September 1st 2011
    • Carlson M, Falcon S, Pages H, Li N. org.Bt.eg.db: Genome wide annotation for Bovine. R package version 2.5.0. 2011. http://www.bioconductor.org/packages/2.8/data/annotation/html/org.Bt.eg.db.html Accessed September 1st 2011.
    • (2011) R Package Version 2.5.0.
    • Carlson, M.1    Falcon, S.2    Pages, H.3    Li, N.4
  • 23
    • 10744231897 scopus 로고    scopus 로고
    • Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition
    • 1:CAS:528:DC%2BD2cXhvVOisb8%3D 356962 14983021
    • Grisart B, Farnir F, Karim L, Cambisano N, Kim J-J, Kvasz A, et al. Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proc Natl Acad Sci U S A. 2004; 101:2398-403.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 2398-2403
    • Grisart, B.1    Farnir, F.2    Karim, L.3    Cambisano, N.4    Kim, J.-J.5    Kvasz, A.6
  • 24
    • 55849129528 scopus 로고    scopus 로고
    • Genomic measures of relationship and inbreeding
    • VanRaden PM. Genomic measures of relationship and inbreeding. Interbull Bull. 2007; 37:33-6.
    • (2007) Interbull Bull , vol.37 , pp. 33-36
    • Vanraden, P.M.1
  • 26
    • 84877772849 scopus 로고    scopus 로고
    • A powerful and efficient set test for genetic markers that handles confounders
    • 1:CAS:528:DC%2BC3sXptFCmt7Y%3D 3673214 23599503
    • Listgarten J, Lippert C, Kang EY, Xiang J, Kadie CM, Heckerman D. A powerful and efficient set test for genetic markers that handles confounders. Bioinformatics. 2013; 29:1526-33.
    • (2013) Bioinformatics , vol.29 , pp. 1526-1533
    • Listgarten, J.1    Lippert, C.2    Kang, E.Y.3    Xiang, J.4    Kadie, C.M.5    Heckerman, D.6
  • 27
    • 84895801913 scopus 로고    scopus 로고
    • Advantages and pitfalls in the application of mixed-model association methods
    • 3989144 24473328
    • Yang J, Zaitlen NA, Goddard ME, Visscher PM, Price AL. Advantages and pitfalls in the application of mixed-model association methods. Nat Genet. 2014; 46:100-6.
    • (2014) Nat Genet , vol.46 , pp. 100-106
    • Yang, J.1    Zaitlen, N.A.2    Goddard, M.E.3    Visscher, P.M.4    Price, A.L.5
  • 28
    • 84907223324 scopus 로고    scopus 로고
    • MultiBLUP: Improved SNP-based prediction for complex traits
    • 1:CAS:528:DC%2BC2cXhsFaksLnF 4158754 24963154
    • Speed D, Balding DJ. MultiBLUP: improved SNP-based prediction for complex traits. Genome Res. 2014; 24:1550-7.
    • (2014) Genome Res , vol.24 , pp. 1550-1557
    • Speed, D.1    Balding, D.J.2
  • 30
    • 77949354967 scopus 로고
    • Restricted maximum likelihood estimation of variance components for univariate animal models using sparse matrix techniques and average information
    • 1:CAS:528:DyaK2MXjvVCqsbs%3D
    • Johnson DL, Thompson R. Restricted maximum likelihood estimation of variance components for univariate animal models using sparse matrix techniques and average information. J Dairy Sci. 1995; 78:449-56.
    • (1995) J Dairy Sci , vol.78 , pp. 449-456
    • Johnson, D.L.1    Thompson, R.2
  • 32
    • 33750127274 scopus 로고    scopus 로고
    • A note on the asymptotic distribution of likelihood ratio tests to test variance components
    • 16899155
    • Visscher PM. A note on the asymptotic distribution of likelihood ratio tests to test variance components. Twin Res Hum Genet. 2006; 9:490-5.
    • (2006) Twin Res Hum Genet , vol.9 , pp. 490-495
    • Visscher, P.M.1
  • 33
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: Methodological issues
    • 1:CAS:528:DC%2BD2sXmtVKqtLs%3D 17303618
    • Goeman JJ, Bühlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics. 2007; 23:980-7.
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Bühlmann, P.2
  • 34
    • 77049105737 scopus 로고    scopus 로고
    • Accessed October 17th 2012
    • Koenker R. quantreg: Quantile regression. 2012. http://cran.r-project.org/web/packages/quantreg/index.html Accessed October 17th 2012.
    • (2012) Quantreg: Quantile Regression
    • Koenker, R.1
  • 36
  • 37
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Statist Soc Ser B. 1995; 57:289-300.
    • (1995) J Roy Statist Soc ser B. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 39
    • 84858043632 scopus 로고    scopus 로고
    • Old and new stories: Revelations from functional analysis of the bovine mammary transcriptome during the lactation cycle
    • 1:CAS:528:DC%2BC38XksFGlsbo%3D 3299771 22428004
    • Bionaz M, Periasamy K, Rodriguez-Zas SL, Everts RE, Lewin HA, Hurley WL, et al. Old and new stories: Revelations from functional analysis of the bovine mammary transcriptome during the lactation cycle. PLoS ONE. 2012; 7:e33268.
    • (2012) PLoS ONE , vol.7
    • Bionaz, M.1    Periasamy, K.2    Rodriguez-Zas, S.L.3    Everts, R.E.4    Lewin, H.A.5    Hurley, W.L.6
  • 40
    • 84862829863 scopus 로고    scopus 로고
    • Retinoic acid signaling and the initiation of mammary gland development
    • 1:CAS:528:DC%2BC38XksFeisbo%3D 22387209
    • Cho K-W, Kwon H-J, Shin J-O, Lee J-M, Cho S-W, Tickle C, et al. Retinoic acid signaling and the initiation of mammary gland development. Dev Biol. 2012; 365:259-66.
    • (2012) Dev Biol , vol.365 , pp. 259-566
    • Cho, K.-W.1    Kwon, H.-J.2    Shin, J.-O.3    Lee, J.-M.4    Cho, S.-W.5    Tickle, C.6
  • 41
    • 28444470457 scopus 로고    scopus 로고
    • Retinoic acid signaling is required for proper morphogenesis of mammary gland
    • 1:CAS:528:DC%2BD2MXhtlCisrjO 16217742
    • Wang YA, Shen K, Wang Y, Brooks SC. Retinoic acid signaling is required for proper morphogenesis of mammary gland. Dev Dyn. 2005; 234:892-9.
    • (2005) Dev Dyn , vol.234 , pp. 892-899
    • Wang, Y.A.1    Shen, K.2    Wang, Y.3    Brooks, S.C.4
  • 42
    • 84879000583 scopus 로고    scopus 로고
    • Retinol and retinyl esters: Biochemistry and physiology
    • 3679378 23625372
    • O'Byrne SM, Blaner WS. Retinol and retinyl esters: biochemistry and physiology. J Lipid Res. 2013; 54:1731-43.
    • (2013) J Lipid Res , vol.54 , pp. 1731-1743
    • O'Byrne, S.M.1    Blaner, W.S.2
  • 43
    • 63249133298 scopus 로고    scopus 로고
    • Retinol esterification by DGAT1 is essential for retinoid homeostasis in murine skin
    • 1:CAS:528:DC%2BD1MXhsFKqurY%3D 2640966 19028692
    • Shih MYS, Kane MA, Zhou P, Yen CLE, Streeper RS, Napoli JL, et al. Retinol esterification by DGAT1 is essential for retinoid homeostasis in murine skin. J Biol Chem. 2009; 284:4292-9.
    • (2009) J Biol Chem , vol.284 , pp. 4292-4299
    • Shih, M.Y.S.1    Kane, M.A.2    Zhou, P.3    Yen, C.L.E.4    Streeper, R.S.5    Napoli, J.L.6
  • 44
    • 79952049778 scopus 로고    scopus 로고
    • In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis
    • 1:CAS:528:DC%2BC3MXjtVylt7w%3D 3053262 21352611
    • Buitenhuis B, Røntved CM, Edwards SM, Ingvartsen KL, Sørensen P. In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis. BMC Genomics. 2011; 12:130.
    • (2011) BMC Genomics , vol.12 , pp. 130
    • Buitenhuis, B.1    Røntved, C.M.2    Edwards, S.M.3    Ingvartsen, K.L.4    Sørensen, P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.