دورية أكاديمية
أعرض في EDS

A Mixed Model Approach to Genome-Wide Association Studies for Selection Signatures, with Application to Mice Bred for Voluntary Exercise Behavior.

التفاصيل البيبلوغرافية
العنوان: A Mixed Model Approach to Genome-Wide Association Studies for Selection Signatures, with Application to Mice Bred for Voluntary Exercise Behavior.
المؤلفون: Xu S; Department of Botany and Plant Sciences, University of California, Riverside, California 92521., Garland T; Department of Biology, University of California, Riverside, California 92521 tgarland@ucr.edu.
المصدر: Genetics [Genetics] 2017 Oct; Vol. 207 (2), pp. 785-799. Date of Electronic Publication: 2017 Aug 03.
نوع المنشور: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: United States NLM ID: 0374636 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1943-2631 (Electronic) Linking ISSN: 00166731 NLM ISO Abbreviation: Genetics Subsets: MEDLINE
أسماء مطبوعة: Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Austin, Tex. [etc.]
مواضيع طبية MeSH: Physical Conditioning, Animal* , Selective Breeding*, Mice, Inbred Strains/*genetics , Motor Activity/*genetics, Animals ; Chromosomes/genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Genome-Wide Association Study/methods ; Male ; Mice ; Polymorphism, Single Nucleotide ; Selection, Genetic
مستخلص: Selection experiments and experimental evolution provide unique opportunities to study the genetics of adaptation because the target and intensity of selection are known relatively precisely. In contrast to natural selection, where populations are never strictly "replicated," experimental evolution routinely includes replicate lines so that selection signatures-genomic regions showing excessive differentiation between treatments-can be separated from possible founder effects, genetic drift, and multiple adaptive solutions. We developed a mouse model with four lines within a high running (HR) selection treatment and four nonselected controls (C). At generation 61, we sampled 10 mice of each line and used the Mega Mouse Universal Genotyping Array to obtain single nucleotide polymorphism (SNP) data for 25,318 SNPs for each individual. Using an advanced mixed model procedure developed in this study, we identified 152 markers that were significantly different in frequency between the two selection treatments. They occurred on all chromosomes except 1, 2, 8, 13, and 19, and showed a variety of patterns in terms of fixation (or the lack thereof) in the four HR and four C lines. Importantly, none were fixed for alternative alleles between the two selection treatments. The current state-of-the-art regularized F test applied after pooling DNA samples for each line failed to detect any markers. We conclude that when SNP or sequence data are available from individuals, the mixed model methodology is recommended for selection signature detection. As sequencing at the individual level becomes increasingly feasible, the new methodology may be routinely applied for detection of selection.
(Copyright © 2017 by the Genetics Society of America.)
References: Genetics. 2003 Dec;165(4):2259-68. (PMID: 14704201)
Nat Rev Genet. 2005 Feb;6(2):95-108. (PMID: 15716906)
PLoS Genet. 2016 Aug 04;12 (8):e1006178. (PMID: 27490364)
Theor Appl Genet. 2012 Jul;125(2):201-10. (PMID: 22614179)
Genet Epidemiol. 2010 Jan;34(1):100-5. (PMID: 19434714)
J Exp Biol. 2011 Jan 15;214(Pt 2):206-29. (PMID: 21177942)
Evolution. 2013 Nov;67(11):3102-19. (PMID: 24151996)
Mol Ecol. 2005 Feb;14(2):351-61. (PMID: 15660930)
Mol Biol Evol. 2014 Apr;31(4):1040-55. (PMID: 24441104)
Nature. 1950 Aug 12;166(4215):247-9. (PMID: 15439261)
Behav Genet. 1998 May;28(3):227-37. (PMID: 9670598)
Genetics. 1989 Jan;121(1):185-99. (PMID: 2563713)
Evolution. 1969 Mar;23 (1):72-84. (PMID: 28562963)
Biometrics. 1986 Jun;42(2):381-91. (PMID: 3741976)
Ann Eugen. 1951 Mar;15(4):323-54. (PMID: 24540312)
Proc Biol Sci. 2011 Feb 22;278(1705):574-81. (PMID: 20810439)
Heredity (Edinb). 2005 Mar;94(3):347-55. (PMID: 15536483)
PLoS Genet. 2011 Mar;7(3):e1001336. (PMID: 21437274)
Comp Biochem Physiol A Mol Integr Physiol. 1999 Jun;123(2):155-62. (PMID: 10425735)
Curr Biol. 2012 May 8;22(9):794-800. (PMID: 22445301)
Heredity (Edinb). 2015 May;114(5):431-40. (PMID: 25269380)
Curr Biol. 2001 May 15;11(10):R388-90. (PMID: 11378402)
Nature. 2012 Apr 04;484(7392):55-61. (PMID: 22481358)
Heredity (Edinb). 2017 Jan;118(1):42-51. (PMID: 27848948)
Heredity (Edinb). 2003 Jun;90(6):459-67. (PMID: 12764421)
Heredity (Edinb). 2015 Dec;115(6):538-46. (PMID: 26126541)
Genetics. 2000 Jul;155(3):1439-47. (PMID: 10880501)
Genetica. 1995;96(1-2):3-12. (PMID: 7607457)
Mol Biol Evol. 2016 Sep;33(9):2429-40. (PMID: 27401229)
Mol Biol Evol. 2016 Jun;33(6):1381-95. (PMID: 26882987)
Nat Genet. 2006 Feb;38(2):203-8. (PMID: 16380716)
Genetics. 1994 Nov;138(3):963-71. (PMID: 7851788)
Evolution. 1998 Aug;52(4):950-956. (PMID: 28565205)
Evol Anthropol. 2016 May 6;25(3):98-104. (PMID: 27312181)
G3 (Bethesda). 2015 Dec 18;6(2):263-79. (PMID: 26684931)
Evolution. 1984 Nov;38(6):1358-1370. (PMID: 28563791)
PLoS One. 2013 Oct 11;8(10):e77588. (PMID: 24147032)
فهرسة مساهمة: Keywords: F statistics; behavior; exercise; experimental evolution; population differentiation
تواريخ الأحداث: Date Created: 20170805 Date Completed: 20180205 Latest Revision: 20181113
رمز التحديث: 20240513
مُعرف محوري في PubMed: PMC5629339
DOI: 10.1534/genetics.117.300102
PMID: 28774881
قاعدة البيانات: MEDLINE
الوصف
تدمد:1943-2631
DOI:10.1534/genetics.117.300102